HEADER PROTEIN TRANSPORT 22-MAR-17 5XC3 TITLE CRYSTAL STRUCTURE OF ACANTHAMOEBA POLYPHAGA MIMIVIRUS RAB GTPASE IN TITLE 2 COMPLEX WITH GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE RAB-RELATED GTPASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 9-184; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACANTHAMOEBA POLYPHAGA MIMIVIRUS; SOURCE 3 ORGANISM_COMMON: APMV; SOURCE 4 ORGANISM_TAXID: 212035; SOURCE 5 GENE: MIMI_R214; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RAB GTPASE, ACANTHAMOEBA POLYPHAGA MIMIVIRUS, VESICLE TRAFFICKING, KEYWDS 2 PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR B.KU,J.A.YOU,S.J.KIM REVDAT 2 22-NOV-23 5XC3 1 LINK REVDAT 1 25-OCT-17 5XC3 0 JRNL AUTH B.KU,J.A.YOU,K.J.OH,H.Y.YUN,H.S.LEE,H.C.SHIN,J.JUNG, JRNL AUTH 2 Y.B.SHIN,S.J.KIM JRNL TITL CRYSTAL STRUCTURES OF TWO FORMS OF THE ACANTHAMOEBA JRNL TITL 2 POLYPHAGA MIMIVIRUS RAB GTPASE JRNL REF ARCH. VIROL. V. 162 3407 2017 JRNL REFN ISSN 1432-8798 JRNL PMID 28779233 JRNL DOI 10.1007/S00705-017-3510-2 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.520 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 27374 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.350 REMARK 3 FREE R VALUE TEST SET COUNT : 2011 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 31.6985 - 3.6061 1.00 1954 156 0.1683 0.1767 REMARK 3 2 3.6061 - 2.8629 1.00 1873 148 0.1781 0.1911 REMARK 3 3 2.8629 - 2.5012 1.00 1826 144 0.1942 0.1951 REMARK 3 4 2.5012 - 2.2726 1.00 1839 145 0.1807 0.2374 REMARK 3 5 2.2726 - 2.1097 1.00 1795 146 0.1876 0.2012 REMARK 3 6 2.1097 - 1.9853 1.00 1812 136 0.1850 0.2064 REMARK 3 7 1.9853 - 1.8859 1.00 1801 149 0.1829 0.2173 REMARK 3 8 1.8859 - 1.8038 1.00 1806 139 0.1771 0.2284 REMARK 3 9 1.8038 - 1.7344 1.00 1804 139 0.1790 0.1940 REMARK 3 10 1.7344 - 1.6746 1.00 1776 150 0.1724 0.2060 REMARK 3 11 1.6746 - 1.6222 0.99 1764 142 0.1752 0.1886 REMARK 3 12 1.6222 - 1.5758 1.00 1797 141 0.1772 0.2112 REMARK 3 13 1.5758 - 1.5343 0.99 1753 140 0.1829 0.2371 REMARK 3 14 1.5343 - 1.4969 0.97 1763 136 0.1889 0.2090 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.930 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 : 0.005 1424 REMARK 3 ANGLE : 0.938 1925 REMARK 3 CHIRALITY : 0.085 211 REMARK 3 PLANARITY : 0.004 236 REMARK 3 DIHEDRAL : 18.597 521 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 5XC3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1300003267. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27374 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.497 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 51.9000 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 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: 1TU4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM IODIDE AND 20% (W/V) REMARK 280 POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.78750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.87700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.36300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.87700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.78750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.36300 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL 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 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 ASN A 3 REMARK 465 ASN A 4 REMARK 465 ILE A 173 REMARK 465 ASN A 174 REMARK 465 PRO A 175 REMARK 465 ASP A 176 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU A 170 O HOH A 1301 2.11 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 LYS A 120 32.73 78.07 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 A1398 DISTANCE = 6.13 ANGSTROMS 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 A1201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 19 OG REMARK 620 2 GDP A1200 O2B 91.4 REMARK 620 3 HOH A1309 O 86.8 94.5 REMARK 620 4 HOH A1312 O 177.1 90.7 91.0 REMARK 620 5 HOH A1318 O 91.4 88.3 176.7 90.7 REMARK 620 6 HOH A1339 O 87.5 175.5 89.8 90.6 87.3 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 GDP A 1200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5XC5 RELATED DB: PDB DBREF 5XC3 A 1 176 UNP Q5UQ27 RABL_MIMIV 9 184 SEQRES 1 A 176 MET GLU ASN ASN GLY TYR LYS ILE ILE LEU ILE GLY SER SEQRES 2 A 176 SER GLY VAL GLY LYS SER SER ILE VAL HIS GLN PHE LEU SEQRES 3 A 176 PHE ASN ARG LYS ILE SER ASN VAL SER PRO THR ILE GLY SEQRES 4 A 176 ALA ALA PHE ALA SER LYS GLN VAL ILE ALA LYS ASN GLY SEQRES 5 A 176 LYS THR LEU LYS LEU ASN ILE TRP ASP THR ALA GLY GLN SEQRES 6 A 176 GLU ARG PHE ARG SER ILE THR LYS MET TYR TYR THR ASN SEQRES 7 A 176 SER LEU GLY CYS LEU VAL VAL PHE ASP VAL THR ASP ARG SEQRES 8 A 176 GLU SER PHE ASP ASP VAL TYR TYR TRP ILE ASN ASP LEU SEQRES 9 A 176 ARG ILE ASN CYS HIS THR THR TYR TYR ILE LEU VAL VAL SEQRES 10 A 176 ALA ASN LYS ILE ASP ILE ASP LYS ASN ASN TRP ARG VAL SEQRES 11 A 176 SER GLU ASN GLU ILE LYS LYS PHE CYS ARG ASP ASN ASP SEQRES 12 A 176 CYS ASP TYR VAL PHE ALA SER SER PHE GLU SER ASP THR SEQRES 13 A 176 VAL ASN ASN LEU PHE GLY LYS MET ILE ASP LYS MET SER SEQRES 14 A 176 GLU ILE LYS ILE ASN PRO ASP HET GDP A1200 28 HET MG A1201 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 MG MG 2+ FORMUL 4 HOH *98(H2 O) HELIX 1 AA1 GLY A 17 ASN A 28 1 12 HELIX 2 AA2 GLY A 64 ARG A 69 5 6 HELIX 3 AA3 THR A 72 THR A 77 1 6 HELIX 4 AA4 ASP A 90 CYS A 108 1 19 HELIX 5 AA5 ASP A 124 TRP A 128 5 5 HELIX 6 AA6 SER A 131 ASN A 142 1 12 HELIX 7 AA7 GLU A 153 SER A 169 1 17 SHEET 1 AA1 6 ALA A 43 ILE A 48 0 SHEET 2 AA1 6 THR A 54 TRP A 60 -1 O LEU A 57 N LYS A 45 SHEET 3 AA1 6 TYR A 6 ILE A 11 1 N TYR A 6 O ASN A 58 SHEET 4 AA1 6 GLY A 81 ASP A 87 1 O VAL A 85 N ILE A 11 SHEET 5 AA1 6 TYR A 113 ASN A 119 1 O VAL A 117 N VAL A 84 SHEET 6 AA1 6 ASP A 145 PHE A 148 1 O VAL A 147 N ALA A 118 LINK OG SER A 19 MG MG A1201 1555 1555 2.11 LINK O2B GDP A1200 MG MG A1201 1555 1555 2.00 LINK MG MG A1201 O HOH A1309 1555 1555 2.04 LINK MG MG A1201 O HOH A1312 1555 1555 2.11 LINK MG MG A1201 O HOH A1318 1555 1555 2.07 LINK MG MG A1201 O HOH A1339 1555 1555 2.04 SITE 1 AC1 23 GLY A 15 VAL A 16 GLY A 17 LYS A 18 SITE 2 AC1 23 SER A 19 SER A 20 ASN A 51 GLY A 52 SITE 3 AC1 23 ASN A 119 LYS A 120 ASP A 122 SER A 150 SITE 4 AC1 23 SER A 151 PHE A 152 MG A1201 HOH A1309 SITE 5 AC1 23 HOH A1310 HOH A1312 HOH A1318 HOH A1327 SITE 6 AC1 23 HOH A1363 HOH A1366 HOH A1378 SITE 1 AC2 6 SER A 19 GDP A1200 HOH A1309 HOH A1312 SITE 2 AC2 6 HOH A1318 HOH A1339 CRYST1 35.575 66.726 69.754 90.00 90.00 90.00 P 21 21 21 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 0.028110 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014987 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014336 0.00000