PDB Short entry for 2AFR HEADER ISOMERASE 26-JUL-05 2AFR TITLE THE CRYSTAL STRUCTURE OF PUTATIVE PRECORRIN ISOMERASE CBIC IN TITLE 2 COBALAMIN BIOSYNTHESIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: COBALAMIN BIOSYNTHESIS PRECORRIN ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 5.4.1.2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEPTOSPIRA INTERROGANS; SOURCE 3 ORGANISM_TAXID: 173; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.XUE,Z.WEI,X.LI REVDAT 4 13-MAR-24 2AFR 1 SEQADV REVDAT 3 13-JUL-11 2AFR 1 VERSN REVDAT 2 24-FEB-09 2AFR 1 VERSN REVDAT 1 04-APR-06 2AFR 0 JRNL AUTH Y.XUE,Z.WEI,X.LI,W.GONG JRNL TITL THE CRYSTAL STRUCTURE OF PUTATIVE PRECORRIN ISOMERASE CBIC JRNL TITL 2 IN COBALAMIN BIOSYNTHESIS JRNL REF J.STRUCT.BIOL. V. 153 307 2006 JRNL REFN ISSN 1047-8477 JRNL PMID 16427313 JRNL DOI 10.1016/J.JSB.2005.11.011 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 302183.140 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.9 REMARK 3 NUMBER OF REFLECTIONS : 10732 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) : 0.224 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1100 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1717 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE : 0.2680 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 187 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1654 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 75 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.27000 REMARK 3 B22 (A**2) : 1.27000 REMARK 3 B33 (A**2) : -2.55000 REMARK 3 B12 (A**2) : 2.25000 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) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.09 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) : 0.42 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.800 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) : 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 : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 34.18 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 2AFR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1000033838. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10964 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 45.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 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 <I/SIGMA(I)> 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ETHANOL, TRIS, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.51700 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 95.03400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 95.03400 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 47.51700 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 96.79566 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 95.03400 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 ASN A 2 REMARK 465 ASP A 3 REMARK 465 MET A 4 REMARK 465 ARG A 5 REMARK 465 GLU A 222 REMARK 465 ARG A 223 REMARK 465 LEU A 224 REMARK 465 GLU A 225 REMARK 465 HIS A 226 REMARK 465 HIS A 227 REMARK 465 HIS A 228 REMARK 465 HIS A 229 REMARK 465 HIS A 230 REMARK 465 HIS A 231 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 GLN A 67 CG CD OE1 NE2 REMARK 470 GLU A 89 CG CD OE1 OE2 REMARK 470 LYS A 112 CG CD CE NZ REMARK 470 ARG A 113 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 219 CG CD CE NZ 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 84 -2.95 -56.30 REMARK 500 SER A 116 -154.15 -137.68 REMARK 500 ASN A 141 -58.04 -137.57 REMARK 500 VAL A 171 -61.53 -97.55 REMARK 500 ARG A 220 3.47 -66.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AFV RELATED DB: PDB REMARK 900 THE SAME PROTEIN OF DIFFERENT CRYSTAL FORM DBREF 2AFR A 1 223 UNP Q8EXP7 Q8EXP7_LEPIN 1 223 SEQADV 2AFR LEU A 224 UNP Q8EXP7 EXPRESSION TAG SEQADV 2AFR GLU A 225 UNP Q8EXP7 EXPRESSION TAG SEQADV 2AFR HIS A 226 UNP Q8EXP7 EXPRESSION TAG SEQADV 2AFR HIS A 227 UNP Q8EXP7 EXPRESSION TAG SEQADV 2AFR HIS A 228 UNP Q8EXP7 EXPRESSION TAG SEQADV 2AFR HIS A 229 UNP Q8EXP7 EXPRESSION TAG SEQADV 2AFR HIS A 230 UNP Q8EXP7 EXPRESSION TAG SEQADV 2AFR HIS A 231 UNP Q8EXP7 EXPRESSION TAG SEQRES 1 A 231 MET ASN ASP MET ARG GLN ILE THR ASN LEU GLY ARG ASN SEQRES 2 A 231 ILE GLU ASN LYS SER PHE SER ILE ILE ASP GLU GLU ALA SEQRES 3 A 231 GLY PRO HIS SER PHE ALA GLN GLU GLU TRP GLU VAL VAL SEQRES 4 A 231 ARG ARG ILE ILE HIS ALA THR ALA ASP PHE ASP TYR LYS SEQRES 5 A 231 ASN ILE THR LYS ILE HIS PRO GLN ALA ILE ASP SER GLY SEQRES 6 A 231 ILE GLN ALA LEU LYS LYS GLY CYS PRO ILE VAL CYS ASP SEQRES 7 A 231 VAL GLN MET ILE LEU SER GLY LEU ASN PRO GLU ARG LEU SEQRES 8 A 231 LYS VAL TYR GLY CYS LYS THR TYR CYS PHE ILE SER ASP SEQRES 9 A 231 GLU ASP VAL ILE GLU ASN ALA LYS ARG LYS ASN SER THR SEQRES 10 A 231 ARG ALA ILE GLU SER ILE GLN LYS ALA ASN SER PHE ASN SEQRES 11 A 231 LEU LEU ASN GLU SER ILE ILE VAL ILE GLY ASN ALA PRO SEQRES 12 A 231 THR ALA LEU LEU GLU ILE GLU LYS LEU ILE ARG GLN GLU SEQRES 13 A 231 GLY ILE LYS PRO ALA LEU ILE VAL GLY VAL PRO VAL GLY SEQRES 14 A 231 PHE VAL SER ALA LYS GLU SER LYS GLU SER ILE LEU LYS SEQRES 15 A 231 LEU GLU TYR TYR ASN VAL THR SER ILE PRO TYR ILE LEU SEQRES 16 A 231 THR MET GLY ARG LYS GLY GLY SER THR ILE ALA VAL ALA SEQRES 17 A 231 ILE LEU HIS ALA LEU LEU LEU LEU SER SER LYS ARG GLY SEQRES 18 A 231 GLU ARG LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *75(H2 O) HELIX 1 1 THR A 8 GLY A 27 1 20 HELIX 2 2 ALA A 32 ALA A 47 1 16 HELIX 3 3 ASP A 50 ILE A 54 1 5 HELIX 4 4 GLN A 60 LYS A 71 1 12 HELIX 5 5 VAL A 79 SER A 84 1 6 HELIX 6 6 ASN A 87 VAL A 93 1 7 HELIX 7 7 ASP A 104 LYS A 114 1 11 HELIX 8 8 THR A 117 PHE A 129 1 13 HELIX 9 9 ALA A 142 GLY A 157 1 16 HELIX 10 10 SER A 172 TYR A 186 1 15 HELIX 11 11 GLY A 202 ARG A 220 1 19 SHEET 1 A 6 THR A 55 ILE A 57 0 SHEET 2 A 6 TYR A 193 THR A 196 -1 O LEU A 195 N LYS A 56 SHEET 3 A 6 LEU A 162 GLY A 165 1 N ILE A 163 O ILE A 194 SHEET 4 A 6 ILE A 136 ILE A 139 1 N ILE A 137 O VAL A 164 SHEET 5 A 6 PRO A 74 CYS A 77 1 N VAL A 76 O VAL A 138 SHEET 6 A 6 LYS A 97 TYR A 99 1 O LYS A 97 N ILE A 75 CRYST1 55.885 55.885 142.551 90.00 90.00 120.00 P 31 2 1 6 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 0.017894 0.010331 0.000000 0.00000 SCALE2 0.000000 0.020662 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007015 0.00000