HEADER OXIDOREDUCTASE 02-FEB-06 2FWG TITLE HIGH RESOLUTION CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE TITLE 2 ELECTRON TRANSFER CATALYST DSBD (PHOTOREDUCED FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, RESIDUES 419-546; COMPND 5 SYNONYM: PROTEIN-DISULFIDE REDUCTASE, DISULFIDE REDUCTASE, C-TYPE COMPND 6 CYTOCHROME BIOGENESIS PROTEIN CYCZ, INNER MEMBRANE COPPER TOLERANCE COMPND 7 PROTEIN; COMPND 8 EC: 1.8.1.8; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: DSBD, DIPZ, CYCZ, CUTA2, B4136; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 ROSETTA; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PDSBA3 KEYWDS DSBD, THIOREDOXIN-LIKE, C-TERMINAL DOMAIN, PHOTOREDUCED FORM, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR C.U.STIRNIMANN,A.ROZHKOVA,U.GRAUSCHOPF,R.A.BOECKMANN,R.GLOCKSHUBER, AUTHOR 2 G.CAPITANI,M.G.GRUETTER REVDAT 3 25-OCT-23 2FWG 1 SEQADV REVDAT 2 24-FEB-09 2FWG 1 VERSN REVDAT 1 13-JUN-06 2FWG 0 JRNL AUTH C.U.STIRNIMANN,A.ROZHKOVA,U.GRAUSCHOPF,R.A.BOECKMANN, JRNL AUTH 2 R.GLOCKSHUBER,G.CAPITANI,M.G.GRUETTER JRNL TITL HIGH-RESOLUTION STRUCTURES OF ESCHERICHIA COLI CDSBD IN JRNL TITL 2 DIFFERENT REDOX STATES: A COMBINED CRYSTALLOGRAPHIC, JRNL TITL 3 BIOCHEMICAL AND COMPUTATIONAL STUDY JRNL REF J.MOL.BIOL. V. 358 829 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16545842 JRNL DOI 10.1016/J.JMB.2006.02.030 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.149 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 953 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 41402 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.135 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 774 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 32280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 967 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 176 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1118.2 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 893.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 17 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 10677 REMARK 3 NUMBER OF RESTRAINTS : 13304 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.020 REMARK 3 ANGLE DISTANCES (A) : 0.030 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.027 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.069 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.068 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.114 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.049 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.082 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2FWG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-FEB-06. REMARK 100 THE DEPOSITION ID IS D_1000036393. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAY-03 REMARK 200 TEMPERATURE (KELVIN) : 90.9 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8600 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : DYNAMICALLY BENDABLE MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42360 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 16.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12400 REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.42900 REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: MODIFIED VERSION OF 2TRX (SEE PUBLICATION) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M AMMONIUM ACETATE, 0.2M SODIUM REMARK 280 ACETATE, 0.1M SODIUM IODIDE, 40% PEG 4000, PH 4.6, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277.15K 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 15.08400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.91150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.98300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.91150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.08400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.98300 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 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 ALA A 419 REMARK 465 THR A 420 REMARK 465 HIS A 421 REMARK 465 THR A 422 REMARK 465 ALA A 423 REMARK 465 GLN A 424 REMARK 465 THR A 425 REMARK 465 GLN A 426 REMARK 465 ARG A 544 REMARK 465 GLN A 545 REMARK 465 PRO A 546 REMARK 465 HIS A 552 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 HIS A 428 CG ND1 CD2 CE1 NE2 REMARK 480 GLN A 521 CD OE1 NE2 REMARK 480 HIS A 548 CG ND1 CD2 CE1 NE2 REMARK 480 HIS A 549 CB CG ND1 CD2 CE1 NE2 REMARK 480 HIS A 550 CG ND1 CD2 CE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 542 NE - CZ - NH1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 542 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FWE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE ELECTRON TRANSFER REMARK 900 CATALYST DSBD (OXIDIZED FORM) REMARK 900 RELATED ID: 2FWF RELATED DB: PDB REMARK 900 HIGH RESOLUTION CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE REMARK 900 ELECTRON TRANSFER CATALYST DSBD (REDUCED FORM) REMARK 900 RELATED ID: 2FWH RELATED DB: PDB REMARK 900 ATOMIC RESOLUTION CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE REMARK 900 ELECTRON TRANSFER CATALYST DSBD (REDUCED FORM AT PH7) REMARK 900 RELATED ID: 1VRS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DISULFIDE-LINKED COMPLEX BETWEEN THE N- REMARK 900 TERMINAL AND C-TERMINAL DOMAIN OF THE ELECTRON TRANSFER CATALYST REMARK 900 DSBD DBREF 2FWG A 419 546 UNP P36655 DSBD_ECOLI 438 565 SEQADV 2FWG HIS A 547 UNP P36655 EXPRESSION TAG SEQADV 2FWG HIS A 548 UNP P36655 EXPRESSION TAG SEQADV 2FWG HIS A 549 UNP P36655 EXPRESSION TAG SEQADV 2FWG HIS A 550 UNP P36655 EXPRESSION TAG SEQADV 2FWG HIS A 551 UNP P36655 EXPRESSION TAG SEQADV 2FWG HIS A 552 UNP P36655 EXPRESSION TAG SEQRES 1 A 134 ALA THR HIS THR ALA GLN THR GLN THR HIS LEU ASN PHE SEQRES 2 A 134 THR GLN ILE LYS THR VAL ASP GLU LEU ASN GLN ALA LEU SEQRES 3 A 134 VAL GLU ALA LYS GLY LYS PRO VAL MET LEU ASP LEU TYR SEQRES 4 A 134 ALA ASP TRP CYS VAL ALA CYS LYS GLU PHE GLU LYS TYR SEQRES 5 A 134 THR PHE SER ASP PRO GLN VAL GLN LYS ALA LEU ALA ASP SEQRES 6 A 134 THR VAL LEU LEU GLN ALA ASN VAL THR ALA ASN ASP ALA SEQRES 7 A 134 GLN ASP VAL ALA LEU LEU LYS HIS LEU ASN VAL LEU GLY SEQRES 8 A 134 LEU PRO THR ILE LEU PHE PHE ASP GLY GLN GLY GLN GLU SEQRES 9 A 134 HIS PRO GLN ALA ARG VAL THR GLY PHE MET ASP ALA GLU SEQRES 10 A 134 THR PHE SER ALA HIS LEU ARG ASP ARG GLN PRO HIS HIS SEQRES 11 A 134 HIS HIS HIS HIS FORMUL 2 HOH *176(H2 O) HELIX 1 1 THR A 436 LYS A 448 1 13 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 LEU A 505 1 11 HELIX 5 5 HIS A 523 ARG A 527 5 5 HELIX 6 6 ASP A 533 ASP A 543 1 11 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 LEU A 514 N LEU A 454 SSBOND 1 CYS A 461 CYS A 464 1555 1555 2.54 CISPEP 1 LEU A 510 PRO A 511 0 -0.75 CISPEP 2 LEU A 510 PRO A 511 0 0.55 CRYST1 30.168 45.966 73.823 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 0.033148 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021755 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013546 0.00000