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 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) : 1.33 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 RCSB ID CODE IS RCSB011176. 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 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 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 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 350 DISTANCE = 5.05 ANGSTROMS REMARK 525 HOH A 401 DISTANCE = 5.65 ANGSTROMS 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