HEADER SIGNALING PROTEIN 08-OCT-16 5H1D TITLE CRYSTAL STRUCTURE OF C-TERMINAL OF RHOGDI2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHO GDP-DISSOCIATION INHIBITOR 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 61-201; COMPND 5 SYNONYM: RHO GDI 2,LY-GDI,RHO-GDI BETA; COMPND 6 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: ARHGDIB, GDIA2, GDID4, RAP1GN1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21-GOLD(DE3)PLYSS AG; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.LIU REVDAT 3 08-NOV-23 5H1D 1 REMARK REVDAT 2 22-FEB-17 5H1D 1 JRNL REVDAT 1 26-OCT-16 5H1D 0 JRNL AUTH J.LIU,J.GAO,F.LI,R.MA,Q.WEI,A.WANG,J.WU,K.RUAN JRNL TITL NMR CHARACTERIZATION OF WEAK INTERACTIONS BETWEEN RHOGDI2 JRNL TITL 2 AND FRAGMENT SCREENING HITS. JRNL REF BIOCHIM. BIOPHYS. ACTA V.1861 3061 2017 JRNL REFN ISSN 0006-3002 JRNL PMID 27721047 JRNL DOI 10.1016/J.BBAGEN.2016.10.003 REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 24783 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1260 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 36.3510 - 3.1071 0.98 2778 135 0.1604 0.1960 REMARK 3 2 3.1071 - 2.4663 1.00 2667 150 0.1791 0.2111 REMARK 3 3 2.4663 - 2.1546 1.00 2620 153 0.1580 0.2191 REMARK 3 4 2.1546 - 1.9576 1.00 2588 135 0.1387 0.2060 REMARK 3 5 1.9576 - 1.8173 1.00 2613 139 0.1371 0.2101 REMARK 3 6 1.8173 - 1.7102 1.00 2563 133 0.1245 0.1710 REMARK 3 7 1.7102 - 1.6245 1.00 2574 140 0.1289 0.1815 REMARK 3 8 1.6245 - 1.5538 1.00 2572 136 0.1303 0.2235 REMARK 3 9 1.5538 - 1.4940 1.00 2548 139 0.1420 0.2057 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.80 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 : 0.004 1119 REMARK 3 ANGLE : 0.709 1514 REMARK 3 CHIRALITY : 0.076 166 REMARK 3 PLANARITY : 0.005 190 REMARK 3 DIHEDRAL : 18.179 418 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5H1D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1300001825. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24846 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.494 REMARK 200 RESOLUTION RANGE LOW (A) : 47.833 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09000 REMARK 200 FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.80 REMARK 200 R MERGE FOR SHELL (I) : 0.50200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: 1RHO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 1500, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 48.40000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.51000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.51000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 72.60000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.51000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.51000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.20000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.51000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.51000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 72.60000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.51000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.51000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 24.20000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 48.40000 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 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 A 432 LIES ON A SPECIAL POSITION. 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 HIS A 59 REMARK 465 MET A 60 REMARK 465 ASP A 61 REMARK 465 PRO A 62 REMARK 465 LYS A 63 REMARK 465 ALA A 64 REMARK 465 THR A 200 REMARK 465 GLU A 201 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 ARG A 117 -36.75 -134.76 REMARK 500 THR A 179 -159.48 -147.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 499 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A 500 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH A 501 DISTANCE = 6.94 ANGSTROMS DBREF 5H1D A 61 201 UNP P52566 GDIR2_HUMAN 61 201 SEQADV 5H1D HIS A 59 UNP P52566 EXPRESSION TAG SEQADV 5H1D MET A 60 UNP P52566 EXPRESSION TAG SEQRES 1 A 143 HIS MET ASP PRO LYS ALA PRO ASN VAL VAL VAL THR ARG SEQRES 2 A 143 LEU THR LEU VAL CYS GLU SER ALA PRO GLY PRO ILE THR SEQRES 3 A 143 MET ASP LEU THR GLY ASP LEU GLU ALA LEU LYS LYS GLU SEQRES 4 A 143 THR ILE VAL LEU LYS GLU GLY SER GLU TYR ARG VAL LYS SEQRES 5 A 143 ILE HIS PHE LYS VAL ASN ARG ASP ILE VAL SER GLY LEU SEQRES 6 A 143 LYS TYR VAL GLN HIS THR TYR ARG THR GLY VAL LYS VAL SEQRES 7 A 143 ASP LYS ALA THR PHE MET VAL GLY SER TYR GLY PRO ARG SEQRES 8 A 143 PRO GLU GLU TYR GLU PHE LEU THR PRO VAL GLU GLU ALA SEQRES 9 A 143 PRO LYS GLY MET LEU ALA ARG GLY THR TYR HIS ASN LYS SEQRES 10 A 143 SER PHE PHE THR ASP ASP ASP LYS GLN ASP HIS LEU SER SEQRES 11 A 143 TRP GLU TRP ASN LEU SER ILE LYS LYS GLU TRP THR GLU FORMUL 2 HOH *201(H2 O) HELIX 1 AA1 ASP A 90 LYS A 95 1 6 HELIX 2 AA2 GLY A 165 ARG A 169 5 5 SHEET 1 AA1 4 THR A 84 ASP A 86 0 SHEET 2 AA1 4 VAL A 67 VAL A 75 -1 N LEU A 72 O MET A 85 SHEET 3 AA1 4 GLU A 106 VAL A 115 -1 O LYS A 110 N THR A 73 SHEET 4 AA1 4 TYR A 153 LEU A 156 -1 O TYR A 153 N PHE A 113 SHEET 1 AA2 4 THR A 84 ASP A 86 0 SHEET 2 AA2 4 VAL A 67 VAL A 75 -1 N LEU A 72 O MET A 85 SHEET 3 AA2 4 GLU A 106 VAL A 115 -1 O LYS A 110 N THR A 73 SHEET 4 AA2 4 GLU A 160 GLU A 161 -1 O GLU A 160 N TYR A 107 SHEET 1 AA3 5 ILE A 99 LYS A 102 0 SHEET 2 AA3 5 LEU A 187 LYS A 196 1 O SER A 194 N ILE A 99 SHEET 3 AA3 5 GLY A 170 ASP A 180 -1 N SER A 176 O TRP A 189 SHEET 4 AA3 5 VAL A 120 ARG A 131 -1 N TYR A 130 O HIS A 173 SHEET 5 AA3 5 VAL A 134 TYR A 146 -1 O PHE A 141 N TYR A 125 CRYST1 55.020 55.020 96.800 90.00 90.00 90.00 P 43 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 0.018175 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018175 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010331 0.00000