HEADER OXIDOREDUCTASE 09-JAN-13 4IP6 TITLE C-TERMINAL DOMAIN OF THE THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD, TITLE 2 Q488A MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN (UNP RESIDUES 444-565); COMPND 5 SYNONYM: THIOL:DISULFIDE EXCHANGE PROTEIN DSBD, C-TYPE CYTOCHROME COMPND 6 BIOGENESIS PROTEIN CYCZ, INNER MEMBRANE COPPER TOLERANCE PROTEIN, COMPND 7 PROTEIN-DISULFIDE REDUCTASE, DISULFIDE REDUCTASE; COMPND 8 EC: 1.8.1.8; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: DSBD, CUTA2, CYCZ, DIPZ, B4136, JW5734; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS THIOREDOXIN, THIOL:DISULFIDE OXIDOREDUCTASE, BACTERIAL PERIPLASM, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR E.SARIDAKIS,D.A.I.MAVRIDOU,C.REDFIELD REVDAT 5 20-SEP-23 4IP6 1 REMARK SEQADV REVDAT 4 15-NOV-17 4IP6 1 REMARK REVDAT 3 09-APR-14 4IP6 1 JRNL REVDAT 2 12-FEB-14 4IP6 1 JRNL REVDAT 1 25-DEC-13 4IP6 0 JRNL AUTH D.A.MAVRIDOU,E.SARIDAKIS,P.KRITSILIGKOU,E.C.MOZLEY, JRNL AUTH 2 S.J.FERGUSON,C.REDFIELD JRNL TITL AN EXTENDED ACTIVE-SITE MOTIF CONTROLS THE REACTIVITY OF THE JRNL TITL 2 THIOREDOXIN FOLD. JRNL REF J.BIOL.CHEM. V. 289 8681 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 24469455 JRNL DOI 10.1074/JBC.M113.513457 REMARK 2 REMARK 2 RESOLUTION. 2.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.060 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.2 REMARK 3 NUMBER OF REFLECTIONS : 6832 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.610 REMARK 3 FREE R VALUE TEST SET COUNT : 315 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 32.6231 - 2.8098 0.93 3563 176 0.1820 0.2440 REMARK 3 2 2.8098 - 2.2300 0.81 2954 139 0.1821 0.2706 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 38.30 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 1.820 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.37940 REMARK 3 B22 (A**2) : 1.56960 REMARK 3 B33 (A**2) : 1.80980 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 964 REMARK 3 ANGLE : 0.938 1311 REMARK 3 CHIRALITY : 0.057 152 REMARK 3 PLANARITY : 0.004 173 REMARK 3 DIHEDRAL : 14.632 346 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4IP6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000077033. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7224 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.230 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.15500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : 0.38200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.960 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: PDB ENTRY 2FWF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21 MG/ML PROTEIN, 25% PEG4000, 0.1 M REMARK 280 SODIUM CACODYLATE, PH 5.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K 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 17.44550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.14950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.75350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.14950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.44550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.75350 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 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 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 423 REMARK 465 ASP A 424 REMARK 465 THR A 425 REMARK 465 GLN A 426 REMARK 465 THR A 427 REMARK 465 VAL A 549 REMARK 465 PRO A 550 REMARK 465 ARG A 551 REMARK 465 GLY A 552 REMARK 465 SER A 553 REMARK 465 GLY A 554 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 HIS A 428 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 503 CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 442 CD OE1 REMARK 480 LYS A 465 CE REMARK 480 ASP A 483 CG 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 THR A 471 -56.96 -123.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4IP1 RELATED DB: PDB REMARK 900 C-TERMINAL DOMAIN OF THE THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD, REMARK 900 Q488K MUTANT DBREF 4IP6 A 425 546 UNP P36655 DSBD_ECOLI 444 565 SEQADV 4IP6 MET A 423 UNP P36655 EXPRESSION TAG SEQADV 4IP6 ASP A 424 UNP P36655 EXPRESSION TAG SEQADV 4IP6 ALA A 488 UNP P36655 GLN 507 ENGINEERED MUTATION SEQADV 4IP6 GLY A 547 UNP P36655 EXPRESSION TAG SEQADV 4IP6 LEU A 548 UNP P36655 EXPRESSION TAG SEQADV 4IP6 VAL A 549 UNP P36655 EXPRESSION TAG SEQADV 4IP6 PRO A 550 UNP P36655 EXPRESSION TAG SEQADV 4IP6 ARG A 551 UNP P36655 EXPRESSION TAG SEQADV 4IP6 GLY A 552 UNP P36655 EXPRESSION TAG SEQADV 4IP6 SER A 553 UNP P36655 EXPRESSION TAG SEQADV 4IP6 GLY A 554 UNP P36655 EXPRESSION TAG SEQRES 1 A 132 MET ASP THR GLN THR HIS LEU ASN PHE THR GLN ILE LYS SEQRES 2 A 132 THR VAL ASP GLU LEU ASN GLN ALA LEU VAL GLU ALA LYS SEQRES 3 A 132 GLY LYS PRO VAL MET LEU ASP LEU TYR ALA ASP TRP CYS SEQRES 4 A 132 VAL ALA CYS LYS GLU PHE GLU LYS TYR THR PHE SER ASP SEQRES 5 A 132 PRO GLN VAL GLN LYS ALA LEU ALA ASP THR VAL LEU LEU SEQRES 6 A 132 ALA ALA ASN VAL THR ALA ASN ASP ALA GLN ASP VAL ALA SEQRES 7 A 132 LEU LEU LYS HIS LEU ASN VAL LEU GLY LEU PRO THR ILE SEQRES 8 A 132 LEU PHE PHE ASP GLY GLN GLY GLN GLU HIS PRO GLN ALA SEQRES 9 A 132 ARG VAL THR GLY PHE MET ASP ALA GLU THR PHE SER ALA SEQRES 10 A 132 HIS LEU ARG ASP ARG GLN PRO GLY LEU VAL PRO ARG GLY SEQRES 11 A 132 SER GLY FORMUL 2 HOH *136(H2 O) HELIX 1 1 THR A 436 ALA A 447 1 12 HELIX 2 2 CYS A 461 THR A 471 1 11 HELIX 3 3 ASP A 474 LEU A 481 1 8 HELIX 4 4 ASP A 495 ASN A 506 1 12 HELIX 5 5 HIS A 523 ARG A 527 5 5 HELIX 6 6 ASP A 533 GLN A 545 1 13 SHEET 1 A 4 THR A 432 GLN A 433 0 SHEET 2 A 4 VAL A 485 ASN A 490 1 O LEU A 486 N THR A 432 SHEET 3 A 4 VAL A 452 TYR A 457 1 N MET A 453 O LEU A 487 SHEET 4 A 4 THR A 512 PHE A 516 -1 O PHE A 516 N VAL A 452 SSBOND 1 CYS A 461 CYS A 464 1555 1555 2.05 CISPEP 1 LEU A 510 PRO A 511 0 -0.54 CRYST1 34.891 51.507 84.299 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 0.028661 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019415 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011863 0.00000