HEADER SIGNALING PROTEIN 18-JUN-13 4L9U TITLE STRUCTURE OF C-TERMINAL COILED COIL OF RASGRP1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS GUANYL-RELEASING PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 739-793; COMPND 5 SYNONYM: CALCIUM AND DAG-REGULATED GUANINE NUCLEOTIDE EXCHANGE FACTOR COMPND 6 II, CALDAG-GEFII, RAS GUANYL-RELEASING PROTEIN; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RASGRP1, RASGRP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.S.IWIG,Y.VERCOULEN,R.DAS,T.BARROS,A.LIMNANDER,Y.CHE,J.G.PELTON, AUTHOR 2 D.E.WEMMER,J.P.ROOSE,J.KURIYAN REVDAT 2 28-FEB-24 4L9U 1 REMARK SEQADV REVDAT 1 21-AUG-13 4L9U 0 JRNL AUTH J.S.IWIG,Y.VERCOULEN,R.DAS,T.BARROS,A.LIMNANDER,Y.CHE, JRNL AUTH 2 J.G.PELTON,D.E.WEMMER,J.P.ROOSE,J.KURIYAN JRNL TITL STRUCTURAL ANALYSIS OF AUTOINHIBITION IN THE RAS-SPECIFIC JRNL TITL 2 EXCHANGE FACTOR RASGRP1. JRNL REF ELIFE V. 2 00813 2013 JRNL REFN ESSN 2050-084X JRNL PMID 23908768 JRNL DOI 10.7554/ELIFE.00813 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.830 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.6 REMARK 3 NUMBER OF REFLECTIONS : 27209 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1352 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 27.9156 - 3.4481 0.93 2657 109 0.1989 0.2210 REMARK 3 2 3.4481 - 2.7376 0.94 2633 147 0.1839 0.2058 REMARK 3 3 2.7376 - 2.3918 0.94 2631 158 0.1720 0.2170 REMARK 3 4 2.3918 - 2.1732 0.93 2627 127 0.1772 0.2189 REMARK 3 5 2.1732 - 2.0175 0.90 2543 127 0.1835 0.2098 REMARK 3 6 2.0175 - 1.8986 0.91 2556 103 0.2042 0.2502 REMARK 3 7 1.8986 - 1.8035 0.91 2595 127 0.2474 0.3200 REMARK 3 8 1.8035 - 1.7250 0.90 2529 150 0.2782 0.3462 REMARK 3 9 1.7250 - 1.6586 0.91 2528 159 0.2858 0.3319 REMARK 3 10 1.6586 - 1.6014 0.89 2558 145 0.2941 0.2945 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 819 REMARK 3 ANGLE : 1.146 1109 REMARK 3 CHIRALITY : 0.067 127 REMARK 3 PLANARITY : 0.004 142 REMARK 3 DIHEDRAL : 15.116 341 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'B' REMARK 3 ORIGIN FOR THE GROUP (A): -9.2367 30.5929 -3.7696 REMARK 3 T TENSOR REMARK 3 T11: 0.1125 T22: 0.1600 REMARK 3 T33: 0.1145 T12: -0.0021 REMARK 3 T13: -0.0325 T23: 0.0264 REMARK 3 L TENSOR REMARK 3 L11: 3.8979 L22: 5.6345 REMARK 3 L33: 2.3862 L12: 0.2730 REMARK 3 L13: -0.1290 L23: 0.2980 REMARK 3 S TENSOR REMARK 3 S11: 0.0926 S12: -0.0010 S13: -0.5628 REMARK 3 S21: 0.3329 S22: 0.1217 S23: -0.5316 REMARK 3 S31: 0.2906 S32: 0.0453 S33: 0.2138 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND ((RESSEQ 784:793)) REMARK 3 ORIGIN FOR THE GROUP (A): -8.2099 51.9610 -21.6716 REMARK 3 T TENSOR REMARK 3 T11: 0.3853 T22: 0.2966 REMARK 3 T33: 0.1798 T12: -0.0014 REMARK 3 T13: -0.0065 T23: 0.0221 REMARK 3 L TENSOR REMARK 3 L11: 2.2027 L22: 1.7151 REMARK 3 L33: 2.3435 L12: -0.5310 REMARK 3 L13: 0.1199 L23: 1.7286 REMARK 3 S TENSOR REMARK 3 S11: 0.1497 S12: 0.1262 S13: 0.1628 REMARK 3 S21: -0.0599 S22: 0.0248 S23: -0.0437 REMARK 3 S31: -0.0565 S32: 0.1811 S33: 0.0180 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND ((RESSEQ 745:783)) REMARK 3 ORIGIN FOR THE GROUP (A): -13.3286 27.9121 -9.4570 REMARK 3 T TENSOR REMARK 3 T11: 0.1532 T22: 0.1689 REMARK 3 T33: 0.1473 T12: 0.0041 REMARK 3 T13: -0.0291 T23: -0.0177 REMARK 3 L TENSOR REMARK 3 L11: 2.9323 L22: 7.9917 REMARK 3 L33: 1.8632 L12: 0.3784 REMARK 3 L13: -0.1156 L23: -1.0945 REMARK 3 S TENSOR REMARK 3 S11: -0.0158 S12: 0.2111 S13: -0.6022 REMARK 3 S21: -0.1311 S22: 0.2272 S23: 0.2491 REMARK 3 S31: 0.2949 S32: -0.0583 S33: -0.0282 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4L9U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000080362. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16098 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 27.911 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 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) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM SODIUM ACETATE, 22% PEG 3350, REMARK 280 100 MM LITHIUM SULFATE, 0.4% FORMAMIDE, PH 3.6, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 296K 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 12.43900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 82.52350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.43900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 82.52350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 738 REMARK 465 GLU A 739 REMARK 465 LEU A 740 REMARK 465 ARG A 741 REMARK 465 HIS A 742 REMARK 465 LEU A 743 REMARK 465 ARG A 744 REMARK 465 SER B 738 REMARK 465 GLU B 739 REMARK 465 LEU B 740 REMARK 465 ARG B 741 REMARK 465 HIS B 742 REMARK 465 LEU B 743 REMARK 465 ARG B 744 REMARK 465 VAL B 787 REMARK 465 LEU B 788 REMARK 465 ALA B 789 REMARK 465 GLN B 790 REMARK 465 MET B 791 REMARK 465 GLU B 792 REMARK 465 GLN B 793 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OG1 THR B 747 O2 GOL A 801 2455 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 803 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4L9M RELATED DB: PDB DBREF 4L9U A 739 793 UNP O95267 GRP1_HUMAN 739 793 DBREF 4L9U B 739 793 UNP O95267 GRP1_HUMAN 739 793 SEQADV 4L9U SER A 738 UNP O95267 EXPRESSION TAG SEQADV 4L9U SER B 738 UNP O95267 EXPRESSION TAG SEQRES 1 A 56 SER GLU LEU ARG HIS LEU ARG LEU PRO THR TYR GLN GLU SEQRES 2 A 56 LEU GLU GLN GLU ILE ASN THR LEU LYS ALA ASP ASN ASP SEQRES 3 A 56 ALA LEU LYS ILE GLN LEU LYS TYR ALA GLN LYS LYS ILE SEQRES 4 A 56 GLU SER LEU GLN LEU GLU LYS SER ASN HIS VAL LEU ALA SEQRES 5 A 56 GLN MET GLU GLN SEQRES 1 B 56 SER GLU LEU ARG HIS LEU ARG LEU PRO THR TYR GLN GLU SEQRES 2 B 56 LEU GLU GLN GLU ILE ASN THR LEU LYS ALA ASP ASN ASP SEQRES 3 B 56 ALA LEU LYS ILE GLN LEU LYS TYR ALA GLN LYS LYS ILE SEQRES 4 B 56 GLU SER LEU GLN LEU GLU LYS SER ASN HIS VAL LEU ALA SEQRES 5 B 56 GLN MET GLU GLN HET GOL A 801 6 HET SO4 B 801 5 HET GOL B 802 6 HET GOL B 803 6 HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 3(C3 H8 O3) FORMUL 4 SO4 O4 S 2- FORMUL 7 HOH *74(H2 O) HELIX 1 1 THR A 747 LYS A 783 1 37 HELIX 2 2 VAL A 787 GLU A 792 5 6 HELIX 3 3 THR B 747 HIS B 786 1 40 SITE 1 AC1 4 THR A 747 TYR A 748 THR B 747 TYR B 748 SITE 1 AC2 5 LYS A 770 LYS A 775 GLN B 780 LYS B 783 SITE 2 AC2 5 HOH B 918 SITE 1 AC3 6 GLU A 792 GLN A 793 LYS B 775 SER B 778 SITE 2 AC3 6 GLU B 782 GOL B 803 SITE 1 AC4 5 GLN A 790 HOH A 901 GLU B 782 ASN B 785 SITE 2 AC4 5 GOL B 802 CRYST1 24.878 165.047 28.319 90.00 90.00 90.00 P 21 21 2 8 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 0.040196 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006059 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035312 0.00000