HEADER SIGNALING PROTEIN 24-FEB-06 2G6F TITLE CRYSTAL STRUCTURE OF THE SH3 DOMAIN OF BETAPIX IN COMPLEX WITH A HIGH TITLE 2 AFFINITY PEPTIDE FROM PAK2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 7; COMPND 3 CHAIN: X; COMPND 4 FRAGMENT: SH3 DOMAIN(RESIDUES 10-63); COMPND 5 SYNONYM: PAK-INTERACTING EXCHANGE FACTOR BETA, BETA-PIX; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: ARHGEF7, PAK3BP, PIXB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P1 KEYWDS SH3 DOMAIN, PEPTIDE INTERACTION, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.HOELZ REVDAT 4 13-MAR-24 2G6F 1 REMARK SEQADV REVDAT 3 24-FEB-09 2G6F 1 VERSN REVDAT 2 09-MAY-06 2G6F 1 JRNL REVDAT 1 11-APR-06 2G6F 0 JRNL AUTH A.HOELZ,J.M.JANZ,S.D.LAWRIE,B.CORWIN,A.LEE,T.P.SAKMAR JRNL TITL CRYSTAL STRUCTURE OF THE SH3 DOMAIN OF BETAPIX IN COMPLEX JRNL TITL 2 WITH A HIGH AFFINITY PEPTIDE FROM PAK2 JRNL REF J.MOL.BIOL. V. 358 509 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16527308 JRNL DOI 10.1016/J.JMB.2006.02.027 REMARK 2 REMARK 2 RESOLUTION. 0.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 40642 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2160 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 0.92 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 0.94 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2757 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.08 REMARK 3 BIN R VALUE (WORKING SET) : 0.3840 REMARK 3 BIN FREE R VALUE SET COUNT : 154 REMARK 3 BIN FREE R VALUE : 0.3670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 478 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 103 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.09000 REMARK 3 B22 (A**2) : -0.25000 REMARK 3 B33 (A**2) : 0.16000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.023 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.023 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.015 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.547 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 498 ; 0.006 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 422 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 682 ; 1.054 ; 1.914 REMARK 3 BOND ANGLES OTHERS (DEGREES): 975 ; 0.662 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 58 ; 5.655 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 28 ;33.906 ;23.571 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 74 ; 9.603 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;12.320 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 65 ; 0.063 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 566 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 115 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 76 ; 0.169 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 421 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 232 ; 0.181 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 281 ; 0.081 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 86 ; 0.100 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 7 ; 0.137 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 51 ; 0.233 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 26 ; 0.120 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 379 ; 1.191 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 126 ; 0.488 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 464 ; 1.441 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 298 ; 1.789 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 215 ; 1.939 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 1271 ; 1.443 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 103 ; 2.454 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 907 ; 3.413 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2G6F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1000036746. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979191 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46091 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.920 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 93.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 53% MPD, 200MM REMARK 280 [CO(NH3)]CL3, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 36.68850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.71350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.68850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 15.71350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: X REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH X 213 LIES ON A SPECIAL POSITION. REMARK 375 HOH X 266 LIES ON A SPECIAL POSITION. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO X 200 DBREF 2G6F X 10 63 UNP O55043 ARHG7_RAT 10 63 SEQADV 2G6F GLY X 5 UNP O55043 CLONING ARTIFACT SEQADV 2G6F PRO X 6 UNP O55043 CLONING ARTIFACT SEQADV 2G6F LEU X 7 UNP O55043 CLONING ARTIFACT SEQADV 2G6F GLY X 8 UNP O55043 CLONING ARTIFACT SEQADV 2G6F SER X 9 UNP O55043 CLONING ARTIFACT SEQRES 1 X 59 GLY PRO LEU GLY SER VAL VAL ARG ALA LYS PHE ASN PHE SEQRES 2 X 59 GLN GLN THR ASN GLU ASP GLU LEU SER PHE SER LYS GLY SEQRES 3 X 59 ASP VAL ILE HIS VAL THR ARG VAL GLU GLU GLY GLY TRP SEQRES 4 X 59 TRP GLU GLY THR HIS ASN GLY ARG THR GLY TRP PHE PRO SEQRES 5 X 59 SER ASN TYR VAL ARG GLU ILE HET NCO X 200 25 HETNAM NCO COBALT HEXAMMINE(III) FORMUL 2 NCO CO H18 N6 3+ FORMUL 3 HOH *103(H2 O) SHEET 1 A 5 ARG X 51 PRO X 56 0 SHEET 2 A 5 TRP X 43 HIS X 48 -1 N HIS X 48 O ARG X 51 SHEET 3 A 5 VAL X 32 VAL X 38 -1 N ARG X 37 O GLU X 45 SHEET 4 A 5 VAL X 10 ALA X 13 -1 N VAL X 11 O ILE X 33 SHEET 5 A 5 VAL X 60 GLU X 62 -1 O ARG X 61 N ARG X 12 CISPEP 1 GLY X 5 PRO X 6 0 0.49 SITE 1 AC1 5 GLU X 22 SER X 28 LYS X 29 GLY X 30 SITE 2 AC1 5 ASP X 31 CRYST1 73.377 31.427 28.171 90.00 90.00 90.00 P 21 21 2 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013628 0.000000 0.000000 0.00000 SCALE2 0.000000 0.031820 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035497 0.00000