HEADER ELECTRON TRANSPORT 20-MAR-99 1DCD TITLE DESULFOREDOXIN COMPLEXED WITH CD2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (DESULFOREDOXIN); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO GIGAS; SOURCE 3 ORGANISM_TAXID: 879; SOURCE 4 CELLULAR_LOCATION: CYTOPLASM; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 8 EXPRESSION_SYSTEM_GENE: DSR KEYWDS RUBREDOXIN TYPE PROTEIN, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.ARCHER,A.L.CARVALHO,S.TEIXEIRA,M.J.ROMAO REVDAT 7 09-AUG-23 1DCD 1 REMARK LINK REVDAT 6 13-NOV-19 1DCD 1 JRNL REVDAT 5 04-OCT-17 1DCD 1 REMARK REVDAT 4 13-JUL-11 1DCD 1 VERSN REVDAT 3 24-FEB-09 1DCD 1 VERSN REVDAT 2 01-APR-03 1DCD 1 JRNL REVDAT 1 09-JUL-99 1DCD 0 JRNL AUTH M.ARCHER,A.L.CARVALHO,S.TEIXEIRA,I.MOURA,J.J.MOURA,F.RUSNAK, JRNL AUTH 2 M.J.ROMAO JRNL TITL STRUCTURAL STUDIES BY X-RAY DIFFRACTION ON METAL SUBSTITUTED JRNL TITL 2 DESULFOREDOXIN, A RUBREDOXIN-TYPE PROTEIN. JRNL REF PROTEIN SCI. V. 8 1536 1999 JRNL REFN ISSN 0961-8368 JRNL PMID 10422844 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.ARCHER,R.HUBER,P.TAVARES,I.MOURA,J.J.MOURA,M.A.CARRONDO, REMARK 1 AUTH 2 L.C.SIEKER,J.LEGALL,M.J.ROMAO REMARK 1 TITL CRYSTAL STRUCTURE OF DESULFOREDOXIN FROM DESULFOVIBRIO GIGAS REMARK 1 TITL 2 DETERMINED AT 1.8 A RESOLUTION: A NOVEL NON-HEME IRON REMARK 1 TITL 3 PROTEIN STRUCTURE. REMARK 1 REF J.MOL.BIOL. V. 251 690 1995 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 7666420 REMARK 1 DOI 10.1006/JMBI.1995.0465 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.189 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 4342 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.175 REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 3148 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 522 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 53 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 576.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 2 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2325 REMARK 3 NUMBER OF RESTRAINTS : 2656 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 ANGLE DISTANCES (A) : 0.018 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: GEOMETRIC RESTRAINTS WERE APPLIED TO REMARK 3 THE METAL CENTER (DFIX CD S 2.55 A) REMARK 4 REMARK 4 1DCD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAR-99. REMARK 100 THE DEPOSITION ID IS D_1000000691. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 5.0 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER 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 : 4403 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 14.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.43200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 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: PDB ENTRY 1DXG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% ETHANOL, 0.1 M SODIUM ACETATE PH REMARK 280 5, 0.2 M CACL2, PH 5.0 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 43.64667 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 87.29333 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 87.29333 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 43.64667 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 1630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 118 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 126 LIES ON A SPECIAL POSITION. REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 37 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 9 SG REMARK 620 2 CYS A 12 SG 106.7 REMARK 620 3 CYS A 28 SG 110.1 107.0 REMARK 620 4 CYS A 29 SG 101.3 106.3 124.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B 37 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 9 SG REMARK 620 2 CYS B 12 SG 109.7 REMARK 620 3 CYS B 28 SG 109.7 110.6 REMARK 620 4 CYS B 29 SG 100.6 105.1 120.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CDA REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: CDS(CYS)4 CLUSTER (TETRAHEDRAL COORDINATION) REMARK 800 REMARK 800 SITE_IDENTIFIER: CDB REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: CDS(CYS)4 CLUSTER (TETRAHEDRAL COORDINATION) REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 37 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 37 DBREF 1DCD A 1 36 UNP P00273 DESR_DESGI 2 37 DBREF 1DCD B 1 36 UNP P00273 DESR_DESGI 2 37 SEQRES 1 A 36 ALA ASN GLU GLY ASP VAL TYR LYS CYS GLU LEU CYS GLY SEQRES 2 A 36 GLN VAL VAL LYS VAL LEU GLU GLU GLY GLY GLY THR LEU SEQRES 3 A 36 VAL CYS CYS GLY GLU ASP MET VAL LYS GLN SEQRES 1 B 36 ALA ASN GLU GLY ASP VAL TYR LYS CYS GLU LEU CYS GLY SEQRES 2 B 36 GLN VAL VAL LYS VAL LEU GLU GLU GLY GLY GLY THR LEU SEQRES 3 B 36 VAL CYS CYS GLY GLU ASP MET VAL LYS GLN HET CD A 37 1 HET CD B 37 1 HETNAM CD CADMIUM ION FORMUL 3 CD 2(CD 2+) FORMUL 5 HOH *53(H2 O) SHEET 1 A 2 VAL A 6 LYS A 8 0 SHEET 2 A 2 VAL A 15 LYS A 17 -1 N VAL A 16 O TYR A 7 SHEET 1 B 2 VAL B 6 LYS B 8 0 SHEET 2 B 2 VAL B 15 LYS B 17 -1 N VAL B 16 O TYR B 7 LINK SG CYS A 9 CD CD A 37 1555 1555 2.52 LINK SG CYS A 12 CD CD A 37 1555 1555 2.55 LINK SG CYS A 28 CD CD A 37 1555 1555 2.54 LINK SG CYS A 29 CD CD A 37 1555 1555 2.54 LINK SG CYS B 9 CD CD B 37 1555 1555 2.54 LINK SG CYS B 12 CD CD B 37 1555 1555 2.54 LINK SG CYS B 28 CD CD B 37 1555 1555 2.55 LINK SG CYS B 29 CD CD B 37 1555 1555 2.54 SITE 1 CDA 4 CYS A 9 CYS A 12 CYS A 28 CYS A 29 SITE 1 CDB 4 CYS B 9 CYS B 12 CYS B 28 CYS B 29 SITE 1 AC1 4 CYS A 9 CYS A 12 CYS A 28 CYS A 29 SITE 1 AC2 4 CYS B 9 CYS B 12 CYS B 28 CYS B 29 CRYST1 27.950 27.950 130.940 90.00 90.00 120.00 P 31 2 1 12 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 0.035778 0.020656 0.000000 0.00000 SCALE2 0.000000 0.041313 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007637 0.00000 MTRIX1 1 -0.939027 -0.226955 -0.258303 47.12950 1 MTRIX2 1 -0.228768 -0.148457 0.962094 -24.85730 1 MTRIX3 1 -0.256699 0.962524 0.087485 33.36160 1