HEADER BIOSYNTHETIC PROTEIN 19-JAN-07 2E8B TITLE CRYSTAL STRUCTURE OF THE PUTATIVE PROTEIN (AQ1419) FROM AQUIFEX TITLE 2 AEOLICUS VF5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE MOLYBDOPTERIN-GUANINE DINUCLEOTIDE BIOSYNTHESIS COMPND 3 PROTEIN A; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 224324; SOURCE 4 STRAIN: VF5; SOURCE 5 GENE: MOBA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) CODONPLUS-RIL-X; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-21A KEYWDS PUTATIVE PROTEIN, AQ_1419, MOLYBDENUM COFACTOR, STRUCTURAL GENOMICS, KEYWDS 2 NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL KEYWDS 3 ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, KEYWDS 4 BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.S.KUMAREVEL,S.M.MALATHY SONY,M.N.PONNUSWAMY,S.KURAMITSU,S.YOKOYAMA, AUTHOR 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 13-MAR-24 2E8B 1 REMARK REVDAT 3 13-JUL-11 2E8B 1 VERSN REVDAT 2 24-FEB-09 2E8B 1 VERSN REVDAT 1 22-JAN-08 2E8B 0 JRNL AUTH T.S.KUMAREVEL,S.M.MALATHY SONY,M.N.PONNUSWAMY,S.KURAMITSU, JRNL AUTH 2 S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF THE PUTATIVE PROTEIN (AQ1419) FROM JRNL TITL 2 AQUIFEX AEOLICUS VF5 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 925066.140 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 24212 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1217 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.61 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.71 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3786 REMARK 3 BIN R VALUE (WORKING SET) : 0.2650 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 193 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.021 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1493 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 192 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.51000 REMARK 3 B22 (A**2) : 2.94000 REMARK 3 B33 (A**2) : -1.43000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.120 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.560 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.490 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.280 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.350 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 46.64 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : DNA-RNA_REP.PARAM REMARK 3 TOPOLOGY FILE 4 : ION.PARAM REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2E8B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000026351. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97891, 0.97944, 0.9 REMARK 200 MONOCHROMATOR : SI DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24264 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 REMARK 200 RESOLUTION RANGE LOW (A) : 42.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.820 REMARK 200 R MERGE (I) : 0.05800 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) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.23 REMARK 200 R MERGE FOR SHELL (I) : 0.34100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM IODIDE, 20% PEG3350, PH REMARK 280 6.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 25.55300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.35800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.39750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.35800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.55300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.39750 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 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 ARG A 2 REMARK 465 THR A 3 REMARK 465 GLU A 189 REMARK 465 ASP A 190 REMARK 465 LEU A 191 REMARK 465 LYS A 192 REMARK 465 ARG A 193 REMARK 465 ILE A 194 REMARK 465 LEU A 195 REMARK 465 ALA A 196 REMARK 465 ILE A 197 REMARK 465 GLU A 198 REMARK 465 ASN A 199 REMARK 465 HIS A 200 REMARK 465 TYR A 201 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 TRP A 6 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 6 CZ3 CH2 REMARK 470 ARG A 7 CG CD NE CZ NH1 NH2 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 TRP A 6 N - CA - CB ANGL. DEV. = -11.2 DEGREES REMARK 500 THR A 187 N - CA - C ANGL. DEV. = 34.4 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 SER A 10 -72.00 -86.93 REMARK 500 ALA A 95 131.63 -38.55 REMARK 500 THR A 131 -129.35 -115.92 REMARK 500 ASN A 186 -143.26 -160.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: AAE001001419.1 RELATED DB: TARGETDB DBREF 2E8B A 1 201 UNP O67413 MOBA_AQUAE 1 201 SEQRES 1 A 201 MET ARG THR PHE THR TRP ARG LYS GLY SER LEU SER LYS SEQRES 2 A 201 VAL ASN THR CYS TYR VAL LEU ALA GLY GLY LYS SER LYS SEQRES 3 A 201 ARG PHE GLY GLU ASP LYS LEU LEU TYR GLU ILE LYS GLY SEQRES 4 A 201 LYS LYS VAL ILE GLU ARG VAL TYR GLU THR ALA LYS SER SEQRES 5 A 201 VAL PHE LYS GLU VAL TYR ILE VAL ALA LYS ASP ARG GLU SEQRES 6 A 201 LYS PHE SER PHE LEU ASN ALA PRO VAL VAL LEU ASP GLU SEQRES 7 A 201 PHE GLU GLU SER ALA SER ILE ILE GLY LEU TYR THR ALA SEQRES 8 A 201 LEU LYS HIS ALA LYS GLU GLU ASN VAL PHE VAL LEU SER SEQRES 9 A 201 GLY ASP LEU PRO LEU MET LYS LYS GLU THR VAL LEU TYR SEQRES 10 A 201 VAL LEU GLU ASN PHE LYS GLU PRO VAL SER VAL ALA LYS SEQRES 11 A 201 THR GLU LYS LEU HIS THR LEU VAL GLY VAL TYR SER LYS SEQRES 12 A 201 LYS LEU LEU GLU LYS ILE GLU GLU ARG ILE LYS LYS GLY SEQRES 13 A 201 ASP TYR ARG ILE TRP ALA LEU LEU LYS ASP VAL GLY TYR SEQRES 14 A 201 ASN GLU VAL GLU ILE PRO GLU GLU LEU ARG TYR THR LEU SEQRES 15 A 201 LEU ASN MET ASN THR LYS GLU ASP LEU LYS ARG ILE LEU SEQRES 16 A 201 ALA ILE GLU ASN HIS TYR FORMUL 2 HOH *192(H2 O) HELIX 1 1 ASP A 31 SER A 52 1 22 HELIX 2 2 ARG A 64 ASN A 71 5 8 HELIX 3 3 ALA A 83 ALA A 95 1 13 HELIX 4 4 LYS A 111 ASN A 121 1 11 HELIX 5 5 LEU A 145 LYS A 155 1 11 HELIX 6 6 ARG A 159 GLY A 168 1 10 HELIX 7 7 PRO A 175 LEU A 183 5 9 SHEET 1 A 7 VAL A 74 LEU A 76 0 SHEET 2 A 7 GLU A 56 ALA A 61 1 N ILE A 59 O VAL A 75 SHEET 3 A 7 THR A 16 GLY A 22 1 N VAL A 19 O TYR A 58 SHEET 4 A 7 ASN A 99 SER A 104 1 O LEU A 103 N TYR A 18 SHEET 5 A 7 LEU A 134 SER A 142 -1 O GLY A 139 N VAL A 102 SHEET 6 A 7 VAL A 126 LYS A 130 -1 N ALA A 129 O VAL A 138 SHEET 7 A 7 ASN A 170 GLU A 173 1 O ASN A 170 N VAL A 126 CISPEP 1 GLU A 124 PRO A 125 0 -0.08 CRYST1 51.106 56.795 62.716 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 0.019567 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017607 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015945 0.00000