HEADER OXIDOREDUCTASE 15-NOV-09 3KP8 TITLE THE THIOREDOXIN-LIKE DOMAIN OF A VKOR HOMOLOG FROM TITLE 2 SYNECHOCOCCUS SP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: VKORC1/THIOREDOXIN DOMAIN PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 186-283; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCOCCUS SP.; SOURCE 3 ORGANISM_TAXID: 321332; SOURCE 4 STRAIN: JA-2-3B'A(2-13); SOURCE 5 GENE: CYB_2278; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BLOOD COAGULATION, DISULFIDE FORMATION, REDOX PARTNER, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR W.LI,S.SCHULMAN,R.J.DUTTON,D.BOYD,J.BECKWITH,T.A.RAPOPORT REVDAT 1 02-MAR-10 3KP8 0 JRNL AUTH W.LI,S.SCHULMAN,R.J.DUTTON,D.BOYD,J.BECKWITH, JRNL AUTH 2 T.A.RAPOPORT JRNL TITL STRUCTURE OF A BACTERIAL HOMOLOGUE OF VITAMIN K JRNL TITL 2 EPOXIDE REDUCTASE. JRNL REF NATURE V. 463 507 2010 JRNL REFN ISSN 0028-0836 JRNL PMID 20110994 JRNL DOI 10.1038/NATURE08720 REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0070 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 11208 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 + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 565 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.66 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 REFLECTION IN BIN (WORKING SET) : 807 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE SET COUNT : 42 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 704 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 53 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.52000 REMARK 3 B22 (A**2) : 0.52000 REMARK 3 B33 (A**2) : -1.03000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.136 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.093 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.060 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.862 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 726 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 995 ; 1.136 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 93 ; 4.943 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 30 ;37.684 ;24.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 97 ;11.942 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ;21.850 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 106 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 573 ; 0.005 ; 0.022 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 466 ; 0.767 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 745 ; 1.389 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 260 ; 1.909 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 250 ; 2.997 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 726 ; 1.071 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 53 ; 3.720 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 704 ; 2.252 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 3KP8 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-09. REMARK 100 THE RCSB ID CODE IS RCSB056274. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11819 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 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: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.6M SODIUM POTASSIUM TARTRATE, 10% REMARK 280 PEG MME 5000, PH 7.8, EVAPORATION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 28.54400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.54400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.91500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.54400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.54400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.91500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.54400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.54400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.91500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.54400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.54400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.91500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 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 19 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 50 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 GLU A 280 REMARK 465 GLU A 281 REMARK 465 GLY A 282 REMARK 465 ARG A 283 REMARK 465 LEU A 284 REMARK 465 GLU A 285 REMARK 465 HIS A 286 REMARK 465 HIS A 287 REMARK 465 HIS A 288 REMARK 465 HIS A 289 REMARK 465 HIS A 290 REMARK 465 HIS A 291 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KP9 RELATED DB: PDB REMARK 900 STRUCTURE OF A BACTERIAL HOMOLOG OF VITAMIN K EPOXIDE REMARK 900 REDUCTASE DBREF 3KP8 A 186 283 UNP Q2JJF6 Q2JJF6_SYNJB 186 283 SEQADV 3KP8 LEU A 284 UNP Q2JJF6 EXPRESSION TAG SEQADV 3KP8 GLU A 285 UNP Q2JJF6 EXPRESSION TAG SEQADV 3KP8 HIS A 286 UNP Q2JJF6 EXPRESSION TAG SEQADV 3KP8 HIS A 287 UNP Q2JJF6 EXPRESSION TAG SEQADV 3KP8 HIS A 288 UNP Q2JJF6 EXPRESSION TAG SEQADV 3KP8 HIS A 289 UNP Q2JJF6 EXPRESSION TAG SEQADV 3KP8 HIS A 290 UNP Q2JJF6 EXPRESSION TAG SEQADV 3KP8 HIS A 291 UNP Q2JJF6 EXPRESSION TAG SEQRES 1 A 106 SER PRO LEU ALA VAL GLY LEU ALA ALA HIS LEU ARG GLN SEQRES 2 A 106 ILE GLY GLY THR MET TYR GLY ALA TYR TRP CYS PRO HIS SEQRES 3 A 106 CYS GLN ASP GLN LYS GLU LEU PHE GLY ALA ALA PHE ASP SEQRES 4 A 106 GLN VAL PRO TYR VAL GLU CYS SER PRO ASN GLY PRO GLY SEQRES 5 A 106 THR PRO GLN ALA GLN GLU CYS THR GLU ALA GLY ILE THR SEQRES 6 A 106 SER TYR PRO THR TRP ILE ILE ASN GLY ARG THR TYR THR SEQRES 7 A 106 GLY VAL ARG SER LEU GLU ALA LEU ALA VAL ALA SER GLY SEQRES 8 A 106 TYR PRO LEU GLU GLU GLY ARG LEU GLU HIS HIS HIS HIS SEQRES 9 A 106 HIS HIS FORMUL 2 HOH *53(H2 O) HELIX 1 1 SER A 186 GLY A 200 1 15 HELIX 2 2 CYS A 209 GLY A 220 1 12 HELIX 3 3 ALA A 221 VAL A 226 5 6 HELIX 4 4 ALA A 241 ALA A 247 1 7 HELIX 5 5 SER A 267 GLY A 276 1 10 SHEET 1 A 4 TYR A 228 GLU A 230 0 SHEET 2 A 4 THR A 202 GLY A 205 1 N MET A 203 O VAL A 229 SHEET 3 A 4 THR A 254 ILE A 257 -1 O THR A 254 N TYR A 204 SHEET 4 A 4 ARG A 260 THR A 263 -1 O TYR A 262 N TRP A 255 SSBOND 1 CYS A 231 CYS A 244 1555 1555 2.06 CISPEP 1 TYR A 252 PRO A 253 0 -7.66 CRYST1 57.088 57.088 57.830 90.00 90.00 90.00 P 42 21 2 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 0.017517 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017517 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017292 0.00000