HEADER G PROTEIN 06-MAY-98 2RAP TITLE THE SMALL G PROTEIN RAP2A IN COMPLEX WITH GTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAP2A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1 - 166; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI K12; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: K12; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PTAC32 (RAP2) AND PEMR602 KEYWDS G PROTEIN, GTP HYDROLYSIS, RAS, RAP2A EXPDTA X-RAY DIFFRACTION AUTHOR J.CHERFILS,J.MENETREY,G.LEBRAS REVDAT 6 21-FEB-24 2RAP 1 REMARK LINK REVDAT 5 24-FEB-09 2RAP 1 VERSN REVDAT 4 01-APR-03 2RAP 1 JRNL REVDAT 3 01-DEC-99 2RAP 1 KEYWDS REVDAT 2 29-NOV-99 2RAP 1 TITLE REVDAT 1 17-JUN-98 2RAP 0 JRNL AUTH J.CHERFILS,J.MENETREY,G.LE BRAS,I.JANOUEIX-LEROSEY, JRNL AUTH 2 J.DE GUNZBURG,J.R.GAREL,I.AUZAT JRNL TITL CRYSTAL STRUCTURES OF THE SMALL G PROTEIN RAP2A IN COMPLEX JRNL TITL 2 WITH ITS SUBSTRATE GTP, WITH GDP AND WITH GTPGAMMAS. JRNL REF EMBO J. V. 16 5582 1997 JRNL REFN ISSN 0261-4189 JRNL PMID 9312017 JRNL DOI 10.1093/EMBOJ/16.18.5582 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 6014 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1329 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 13 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 2.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 2.300 REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RAP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178547. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 278 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LURE REMARK 200 BEAMLINE : DW21B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE 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 : 8828 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIFFERENCE FOURIER MAPS REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 8000, 100MM LISO4, 100MM TRIS REMARK 280 PH 8., PH 8.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.06667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 56.13333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 42.10000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 70.16667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 14.03333 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: A 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 2 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 TYR A 71 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 105 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 TRP A 137 CD1 - CG - CD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 TRP A 137 CE2 - CD2 - CG ANGL. DEV. = -5.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR A 32 108.16 -58.18 REMARK 500 ILE A 36 -66.81 -91.02 REMARK 500 GLU A 62 -41.06 -24.60 REMARK 500 ASN A 86 97.90 -161.02 REMARK 500 LYS A 117 38.48 76.99 REMARK 500 LEU A 120 53.54 -100.36 REMARK 500 TYR A 165 52.51 -113.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 181 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 17 OG REMARK 620 2 THR A 35 OG1 125.1 REMARK 620 3 GTP A 180 O3G 149.0 85.6 REMARK 620 4 GTP A 180 O2B 69.1 164.5 80.0 REMARK 620 5 HOH A 223 O 93.3 107.4 80.0 75.8 REMARK 620 6 HOH A 224 O 95.0 89.3 79.2 82.6 152.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 181 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP A 180 DBREF 2RAP A 1 166 UNP P10114 RAP2A_HUMAN 1 167 SEQRES 1 A 167 MET ARG GLU TYR LYS VAL VAL VAL LEU GLY SER GLY GLY SEQRES 2 A 167 VAL GLY LYS SER ALA LEU THR VAL GLN PHE VAL THR GLY SEQRES 3 A 167 THR PHE ILE GLU LYS TYR ASP PRO THR ILE GLU ASP PHE SEQRES 4 A 167 TYR ARG LYS GLU ILE GLU VAL ASP SER SER PRO SER VAL SEQRES 5 A 167 LEU GLU ILE LEU ASP THR ALA GLY THR GLU GLN PHE ALA SEQRES 6 A 167 SER MET ARG ASP LEU TYR ILE LYS ASN GLY GLN GLY PHE SEQRES 7 A 167 ILE LEU VAL TYR SER LEU VAL ASN GLN GLN SER PHE GLN SEQRES 8 A 167 ASP ILE LYS PRO MET ARG ASP GLN ILE ILE ARG VAL LYS SEQRES 9 A 167 ARG TYR GLU LYS VAL PRO VAL ILE LEU VAL GLY ASN LYS SEQRES 10 A 167 VAL ASP LEU GLU SER GLU ARG GLU VAL SER SER SER GLU SEQRES 11 A 167 GLY ARG ALA LEU ALA GLU GLU TRP GLY CYS PRO PHE MET SEQRES 12 A 167 GLU THR SER ALA LYS SER LYS THR MET VAL ASP GLU LEU SEQRES 13 A 167 PHE ALA GLU ILE VAL ARG GLN MET ASN TYR ALA HET MG A 181 1 HET GTP A 180 32 HETNAM MG MAGNESIUM ION HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 GTP C10 H16 N5 O14 P3 FORMUL 4 HOH *13(H2 O) HELIX 1 1 LYS A 16 THR A 25 1 10 HELIX 2 2 GLU A 62 LYS A 73 5 12 HELIX 3 3 GLN A 87 LYS A 104 1 18 HELIX 4 4 GLU A 121 GLU A 222 5 3 HELIX 5 5 SER A 127 GLU A 136 1 10 HELIX 6 6 LYS A 149 ASN A 164 1 16 SHEET 1 A 6 PRO A 140 THR A 144 0 SHEET 2 A 6 PRO A 110 ASN A 116 1 N LEU A 113 O PRO A 140 SHEET 3 A 6 GLY A 77 SER A 83 1 N PHE A 78 O PRO A 110 SHEET 4 A 6 ARG A 2 GLY A 10 1 N VAL A 7 O GLY A 77 SHEET 5 A 6 SER A 49 THR A 58 1 N VAL A 52 O ARG A 2 SHEET 6 A 6 GLU A 37 VAL A 46 -1 N VAL A 46 O SER A 49 LINK OG SER A 17 MG MG A 181 1555 1555 1.72 LINK OG1 THR A 35 MG MG A 181 1555 1555 1.89 LINK O3G GTP A 180 MG MG A 181 1555 1555 2.26 LINK O2B GTP A 180 MG MG A 181 1555 1555 2.61 LINK MG MG A 181 O HOH A 223 1555 1555 1.76 LINK MG MG A 181 O HOH A 224 1555 1555 1.72 SITE 1 AC1 5 SER A 17 THR A 35 GTP A 180 HOH A 223 SITE 2 AC1 5 HOH A 224 SITE 1 AC2 21 GLY A 13 VAL A 14 GLY A 15 LYS A 16 SITE 2 AC2 21 SER A 17 ALA A 18 PHE A 28 ILE A 29 SITE 3 AC2 21 GLU A 30 TYR A 32 THR A 35 GLY A 60 SITE 4 AC2 21 ASN A 116 LYS A 117 ASP A 119 LEU A 120 SITE 5 AC2 21 SER A 145 ALA A 146 MG A 181 HOH A 223 SITE 6 AC2 21 HOH A 224 CRYST1 64.500 64.500 84.200 90.00 90.00 120.00 P 61 6 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 0.015504 0.008951 0.000000 0.00000 SCALE2 0.000000 0.017902 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011876 0.00000