PDB Short entry for 1F2V HEADER ISOMERASE 29-MAY-00 1F2V TITLE CRYSTAL STRUCTURE ANALYSIS OF PRECORRIN-8X METHYLMUTASE OF AEROBIC TITLE 2 VITAMIN B12 SYNTHESIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRECORRIN-8X METHYLMUTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: COBH; COMPND 5 EC: 5.4.1.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS DENITRIFICANS; SOURCE 3 ORGANISM_TAXID: 43306; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PLM1 KEYWDS ALPHA-BETA WIND, DOUBLY WOUND SHEET, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.W.SHIPMAN,D.LI,C.A.ROESSNER,A.I.SCOTT,J.C.SACCHETTINI REVDAT 4 07-FEB-24 1F2V 1 SEQADV REVDAT 3 13-JUL-11 1F2V 1 VERSN REVDAT 2 24-FEB-09 1F2V 1 VERSN REVDAT 1 18-JUL-01 1F2V 0 JRNL AUTH L.W.SHIPMAN,D.LI,C.A.ROESSNER,A.I.SCOTT,J.C.SACCHETTINI JRNL TITL CRYSTAL STRUCTURE OF PRECORRIN-8X METHYL MUTASE. JRNL REF STRUCTURE V. 9 587 2001 JRNL REFN ISSN 0969-2126 JRNL PMID 11470433 JRNL DOI 10.1016/S0969-2126(01)00618-9 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 8066 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 598 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1541 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.50 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.334 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1F2V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-00. REMARK 100 THE DEPOSITION ID IS D_1000011176. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-99 REMARK 200 TEMPERATURE (KELVIN) : 120.0 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 3 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MACSCIENCE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8066 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 20.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.27800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 37.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, MAGNESIUM CHLORIDE, TRIS REMARK 280 -HCL, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 45.00045 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.99986 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.00045 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.99986 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DIMER CONSTRUCTED FROM CHAIN A REMARK 300 AND SYMMETRY PARTNER GENERATED BY THE TWO-FOLD. 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 90.00090 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 -8 REMARK 465 ARG A -7 REMARK 465 GLY A -6 REMARK 465 SER A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 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 OD1 ASP A 174 NH2 ARG A 189 2.15 REMARK 500 O ASP A 59 OG SER A 63 2.17 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 125 -77.57 -9.14 REMARK 500 ASN A 137 -53.34 -133.82 REMARK 500 REMARK 500 REMARK: NULL DBREF 1F2V A 2 210 UNP P21638 COBH_PSEDE 2 210 SEQADV 1F2V MET A -8 UNP P21638 EXPRESSION TAG SEQADV 1F2V ARG A -7 UNP P21638 EXPRESSION TAG SEQADV 1F2V GLY A -6 UNP P21638 EXPRESSION TAG SEQADV 1F2V SER A -5 UNP P21638 EXPRESSION TAG SEQADV 1F2V HIS A -4 UNP P21638 EXPRESSION TAG SEQADV 1F2V HIS A -3 UNP P21638 EXPRESSION TAG SEQADV 1F2V HIS A -2 UNP P21638 EXPRESSION TAG SEQADV 1F2V HIS A -1 UNP P21638 EXPRESSION TAG SEQADV 1F2V HIS A 0 UNP P21638 EXPRESSION TAG SEQADV 1F2V HIS A 1 UNP P21638 EXPRESSION TAG SEQRES 1 A 219 MET ARG GLY SER HIS HIS HIS HIS HIS HIS PRO GLU TYR SEQRES 2 A 219 ASP TYR ILE ARG ASP GLY ASN ALA ILE TYR GLU ARG SER SEQRES 3 A 219 PHE ALA ILE ILE ARG ALA GLU ALA ASP LEU SER ARG PHE SEQRES 4 A 219 SER GLU GLU GLU ALA ASP LEU ALA VAL ARG MET VAL HIS SEQRES 5 A 219 ALA CYS GLY SER VAL GLU ALA THR ARG GLN PHE VAL PHE SEQRES 6 A 219 SER PRO ASP PHE VAL SER SER ALA ARG ALA ALA LEU LYS SEQRES 7 A 219 ALA GLY ALA PRO ILE LEU CYS ASP ALA GLU MET VAL ALA SEQRES 8 A 219 HIS GLY VAL THR ARG ALA ARG LEU PRO ALA GLY ASN GLU SEQRES 9 A 219 VAL ILE CYS THR LEU ARG ASP PRO ARG THR PRO ALA LEU SEQRES 10 A 219 ALA ALA GLU ILE GLY ASN THR ARG SER ALA ALA ALA LEU SEQRES 11 A 219 LYS LEU TRP SER GLU ARG LEU ALA GLY SER VAL VAL ALA SEQRES 12 A 219 ILE GLY ASN ALA PRO THR ALA LEU PHE PHE LEU LEU GLU SEQRES 13 A 219 MET LEU ARG ASP GLY ALA PRO LYS PRO ALA ALA ILE LEU SEQRES 14 A 219 GLY MET PRO VAL GLY PHE VAL GLY ALA ALA GLU SER LYS SEQRES 15 A 219 ASP ALA LEU ALA GLU ASN SER TYR GLY VAL PRO PHE ALA SEQRES 16 A 219 ILE VAL ARG GLY ARG LEU GLY GLY SER ALA MET THR ALA SEQRES 17 A 219 ALA ALA LEU ASN SER LEU ALA ARG PRO GLY LEU FORMUL 2 HOH *220(H2 O) HELIX 1 1 ASP A 9 ALA A 25 1 17 HELIX 2 2 SER A 31 GLY A 46 1 16 HELIX 3 3 SER A 47 ARG A 52 5 6 HELIX 4 4 ASP A 59 ALA A 70 1 12 HELIX 5 5 ALA A 78 VAL A 85 1 8 HELIX 6 6 THR A 86 LEU A 90 5 5 HELIX 7 7 PRO A 103 GLY A 113 1 11 HELIX 8 8 THR A 115 ALA A 120 1 6 HELIX 9 9 LEU A 121 LEU A 123 5 3 HELIX 10 10 TRP A 124 ALA A 129 1 6 HELIX 11 11 ALA A 138 ASP A 151 1 14 HELIX 12 12 GLY A 168 ASN A 179 1 12 HELIX 13 13 GLY A 194 ARG A 207 1 14 SHEET 1 A 6 PHE A 54 PHE A 56 0 SHEET 2 A 6 PHE A 185 VAL A 188 -1 N ILE A 187 O VAL A 55 SHEET 3 A 6 ALA A 158 GLY A 161 1 O ILE A 159 N ALA A 186 SHEET 4 A 6 VAL A 132 ILE A 135 1 O VAL A 133 N LEU A 160 SHEET 5 A 6 ILE A 74 CYS A 76 1 O LEU A 75 N ALA A 134 SHEET 6 A 6 VAL A 96 CYS A 98 1 O ILE A 97 N CYS A 76 CRYST1 90.100 36.600 60.300 90.00 113.80 90.00 C 1 2 1 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 0.011111 0.000000 0.004900 0.00000 SCALE2 0.000000 0.027778 -0.000001 0.00000 SCALE3 0.000000 0.000000 0.018215 0.00000