CCP4 Version 4.0 ...

Alexei Vagin’s automated program for molecular replacement.

Right: Surface complementarity between influzena virus tern N9 neuraminidase (right) and the NC10 single-chain antibody variable domain (left), based on the coordinates of the PDB entry 1A14. The interface is shown opened out in book-like fashion, with Sc values coloured from white (Sc = 0.0) to blue (Sc=1.0). Regions shown in red have Sc<0.0, or lie outside of the buried area considered for the calculation of Sc.

The picture was generated using the program SC , and displayed using GRASP (Nichols, A.J., (1993) Biophys. J. 64, A116.)

Program using direct methods to break the intrinsic phase ambiguity in OAS and SIR problems (Q. Hao, Y.X. Gu, C.D. Zheng & H.F. Fan).

Mike Lawrence’s program for determining the shape complementarity statistic Sc of two interacting molecular surfaces.

CCP4i provides a simple graphical user interface for running the CCP4

programs, plus a set of utilities for easy viewing of standard CCP4-format files, a database facility to assist with project

management, and an integrated help system.

CCP4i version 1.1.1 is now officially part of the main suite and is no longer

distributed separately.

Data harvesting

The most recent version of the CCP4 suite is 4.0, which was released in January 2000, with a minor patch release shortly after. Below are some of the highlights in this latest version of the Suite.

molrep

sc

oasis

The program utilises new approaches in data processing and rotational and translation searching to give improved molecular replacement solutions.

Left: The enzyme D-alanine-D-lactate ligase (VanA) from Enterococcus faecium BM4147 is directly responsible for the biosynthesis of alternate cell wall precursors in clinically prevalent Enterococcal species which are resistant to the glycopeptide antiobiotic Vancomycin.

Updated programs•DM 2.0.5 - density modification package.•SCALA 2.7.2 - scale together multiple observations of reflections.•TOPP 6.5 - automatic topological and atomic comparison program.•AMORE - a major new version of Jorge Navaza’s molecular replacement package.•RASMOL 2.7.1 - updated version of the molecular visualisation program.•SFCHECK 5.3.4 - program for assessing agreement between atomic model and X-ray data.•ARP_WARP 5.0 - popular automated refinement program.

ccp4i: CCP4 graphical interface

Direct Methods on their own require high resolution - OASIS however has been successful at moderate resolution (1.4 - 2.5Å).

Left: Rusticyanin is a type-1 blue copper protein (17kDa) and is thought to be a principal component in the iron respiratory electron transport chain of Thiobacillus ferrooxidans.

The structure of rusticyanin was solved with the aid of the OASIS program using one

Data harvesting means that the software used in structure solution outputs details of the method used and the results obtained (for example,

the heavy atom sites used in phasing).

The information is stored in deposition files (also called harvest files) - by the time the user is ready to deposit the model coordinates there should be a collection of such files holding details of how the model was obtained. These can be sent directly to the deposition centre - thereby by-passing

much of the manual processing required by AutoDep.

Within CCP4 4.0 the programs SCALA, TRUNCATE, MLPHARE, REFMAC and RESTRAIN have been upgraded to produce harvest files.

For more information on Data Harvesting see CCP4 Newsletters 37 (October 1999) and 35 (July 1998).

Reference: Lawrence, M.C. & Coleman, P.M. (1993) “Shape complementarity at protein/protein interfaces” J. Mol. Biol. 234, 946-950.

The structure of VanA was determined from data extending to 2.5Å with the aid of MOLREP. The structure of the active site was found to differ significantly from the model previously assumed (from the functionally related D-Alanyl-D-Alanine ligase from E. coli), leading to a revised understanding of the mechanism for Vancomycin resistance.

Reference: Roper, D.I., Huyton T., Veguine A., & Dodson G. (2000) “The Molecular Basis of Vancomycin Resistance in Clinically Relevant Enterococci. Crystal Structure of D-alanyl-D-lactate ligase (VanA)” PNAS (in press)

Future developmentsCCP4NT : a preliminary version is now available which allows

the CCP4 suite to run under Microsoft NT

wavelength anomalous scattering data at 2.1Å resolution collected near the copper absorption edge.

Reference: Harvey, I., Hao, Q., Duke, E.M.H., Ingledew, W.J. & Hasnain, S.S. (1998) Acta. Cryst. D54 629-635 “Structure Determination of a 16.8 kDa Copper Protein at 2.1Å Resolution Using Anomalous Scattering Data with Direct Methods.”

REFMAC : the current β-release of Refmac includes: refinement of TLS parameters; bulk solvent correction; new dictionary. It

also dispences with the need to run PROTIN.

CCP4 4.1 : the next release will include D*TREK2MTZ, CAVENV, ROTGEN, FFFEAR, MOSFLM and others

MAPSLICE : viewing contoured sections through maps (replacement for NPO)

Plus: updated versions of AREAIMOL, DETWIN, SCALEIT, TRUNCATE and others