HEADER HYDROLASE 29-NOV-10 3PR1 TITLE CRYSTAL STRUCTURE OF APO THERMOTOGA MARITIMA RIBOSOME BIOGENESIS GTP- TITLE 2 BINDING PROTEIN ENGB COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE GTP-BINDING PROTEIN ENGB; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: ENGB, TM_1466; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRSETA KEYWDS ROSSMANN FOLD, HYDROLASE, GTP BINDING, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR K.H.CHAN,K.B.WONG REVDAT 3 01-NOV-23 3PR1 1 REMARK REVDAT 2 23-NOV-11 3PR1 1 JRNL VERSN REVDAT 1 08-JUN-11 3PR1 0 JRNL AUTH K.H.CHAN,K.B.WONG JRNL TITL STRUCTURE OF AN ESSENTIAL GTPASE, YSXC, FROM THERMOTOGA JRNL TITL 2 MARITIMA JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 67 640 2011 JRNL REFN ESSN 1744-3091 JRNL PMID 21636901 JRNL DOI 10.1107/S1744309111011651 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 8124 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 390 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 28.4054 - 3.3160 0.87 2468 130 0.2207 0.2422 REMARK 3 2 3.3160 - 2.6326 0.98 2689 117 0.1979 0.2563 REMARK 3 3 2.6326 - 2.3000 0.96 2577 143 0.2113 0.3005 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 53.50 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.850 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.59120 REMARK 3 B22 (A**2) : 16.44400 REMARK 3 B33 (A**2) : -15.85280 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 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 : 0.006 1437 REMARK 3 ANGLE : 0.951 1937 REMARK 3 CHIRALITY : 0.060 217 REMARK 3 PLANARITY : 0.004 238 REMARK 3 DIHEDRAL : 16.694 542 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 3PR1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000062715. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54180 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : VARIMAX HR OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8326 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 48.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.4000 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 3PQC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH 5.5, 2.0M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 27.42350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.42350 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 34.85850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.99400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.85850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.99400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 27.42350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.85850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.99400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 27.42350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.85850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.99400 REMARK 290 SMTRY3 8 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 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 262 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 MET A 1 REMARK 465 LYS A 47 REMARK 465 ILE A 48 REMARK 465 ALA A 49 REMARK 465 PHE A 50 REMARK 465 VAL A 51 REMARK 465 SER A 52 REMARK 465 LYS A 53 REMARK 465 THR A 54 REMARK 465 PRO A 55 REMARK 465 GLY A 56 REMARK 465 LYS A 57 REMARK 465 THR A 58 REMARK 465 ARG A 59 REMARK 465 GLY A 79 REMARK 465 TYR A 80 REMARK 465 ALA A 81 REMARK 465 LYS A 82 REMARK 465 VAL A 83 REMARK 465 SER A 84 REMARK 465 LYS A 85 REMARK 465 GLU A 194 REMARK 465 ASN A 195 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 OE2 GLU A 156 OE2 GLU A 156 3555 2.14 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 LEU A 22 -117.14 -116.42 REMARK 500 LYS A 69 -10.04 -143.69 REMARK 500 ARG A 102 75.38 -100.16 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 PO4 A 196 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PQC RELATED DB: PDB DBREF 3PR1 A 1 195 UNP Q9X1H7 ENGB_THEMA 1 195 SEQRES 1 A 195 MET ILE ILE ARG ASP VAL GLU LEU VAL LYS VAL ALA ARG SEQRES 2 A 195 THR PRO GLY ASP TYR PRO PRO PRO LEU LYS GLY GLU VAL SEQRES 3 A 195 ALA PHE VAL GLY ARG SER ASN VAL GLY LYS SER SER LEU SEQRES 4 A 195 LEU ASN ALA LEU PHE ASN ARG LYS ILE ALA PHE VAL SER SEQRES 5 A 195 LYS THR PRO GLY LYS THR ARG SER ILE ASN PHE TYR LEU SEQRES 6 A 195 VAL ASN SER LYS TYR TYR PHE VAL ASP LEU PRO GLY TYR SEQRES 7 A 195 GLY TYR ALA LYS VAL SER LYS LYS GLU ARG MET LEU TRP SEQRES 8 A 195 LYS ARG LEU VAL GLU ASP TYR PHE LYS ASN ARG TRP SER SEQRES 9 A 195 LEU GLN MET VAL PHE LEU LEU VAL ASP GLY ARG ILE PRO SEQRES 10 A 195 PRO GLN ASP SER ASP LEU MET MET VAL GLU TRP MET LYS SEQRES 11 A 195 SER LEU ASN ILE PRO PHE THR ILE VAL LEU THR LYS MET SEQRES 12 A 195 ASP LYS VAL LYS MET SER GLU ARG ALA LYS LYS LEU GLU SEQRES 13 A 195 GLU HIS ARG LYS VAL PHE SER LYS TYR GLY GLU TYR THR SEQRES 14 A 195 ILE ILE PRO THR SER SER VAL THR GLY GLU GLY ILE SER SEQRES 15 A 195 GLU LEU LEU ASP LEU ILE SER THR LEU LEU LYS GLU ASN HET PO4 A 196 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *71(H2 O) HELIX 1 1 THR A 14 TYR A 18 5 5 HELIX 2 2 GLY A 35 ASN A 45 1 11 HELIX 3 3 LYS A 86 ARG A 102 1 17 HELIX 4 4 GLN A 119 LEU A 132 1 14 HELIX 5 5 LYS A 142 VAL A 146 5 5 HELIX 6 6 LYS A 147 SER A 149 5 3 HELIX 7 7 GLU A 150 SER A 163 1 14 HELIX 8 8 GLY A 180 LYS A 193 1 14 SHEET 1 A 7 VAL A 6 ALA A 12 0 SHEET 2 A 7 ILE A 61 VAL A 66 -1 O PHE A 63 N LYS A 10 SHEET 3 A 7 TYR A 70 ASP A 74 -1 O TYR A 70 N VAL A 66 SHEET 4 A 7 GLU A 25 GLY A 30 1 N VAL A 26 O VAL A 73 SHEET 5 A 7 MET A 107 ASP A 113 1 O PHE A 109 N ALA A 27 SHEET 6 A 7 PHE A 136 THR A 141 1 O VAL A 139 N LEU A 110 SHEET 7 A 7 ILE A 170 PRO A 172 1 O ILE A 171 N ILE A 138 SITE 1 AC1 8 ASN A 33 VAL A 34 GLY A 35 LYS A 36 SITE 2 AC1 8 SER A 37 HOH A 203 HOH A 210 HOH A 218 CRYST1 69.717 97.988 54.847 90.00 90.00 90.00 C 2 2 21 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 0.014344 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010205 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018233 0.00000