HEADER ELECTRON TRANSPORT 17-MAR-04 1VCX TITLE NEUTRON CRYSTAL STRUCTURE OF THE WILD TYPE RUBREDOXIN FROM PYROCOCCUS TITLE 2 FURIOSUS AT 1.5A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RUBREDOXIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PF RD; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21-DE3; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PT7-7 KEYWDS NEUTRON STRUCTURE, HYDROGEN ATOM POSITION, HYDRATION WATER STRUCTURE, KEYWDS 2 HYDROGEN/DEUTERIUM EXCHANGE, IRON-SULFUR CORE, N-TERMINAL REGION, KEYWDS 3 ELECTRON TRANSPORT EXPDTA NEUTRON DIFFRACTION AUTHOR K.KURIHARA,I.TANAKA,T.CHATAKE,M.W.W.ADAMS,F.E.JENNEY JR.,N.MOISEEVA, AUTHOR 2 R.BAU,N.NIIMURA REVDAT 7 25-OCT-23 1VCX 1 REMARK LINK REVDAT 6 18-JUL-18 1VCX 1 REMARK REVDAT 5 11-JUL-18 1VCX 1 REMARK REVDAT 4 07-MAR-18 1VCX 1 REMARK REVDAT 3 13-JUL-11 1VCX 1 VERSN REVDAT 2 24-FEB-09 1VCX 1 VERSN REVDAT 1 10-AUG-04 1VCX 0 JRNL AUTH K.KURIHARA,I.TANAKA,T.CHATAKE,M.W.W.ADAMS,F.E.JENNEY JR., JRNL AUTH 2 N.MOISEEVA,R.BAU,N.NIIMURA JRNL TITL NEUTRON CRYSTALLOGRAPHIC STUDY ON RUBREDOXIN FROM PYROCOCCUS JRNL TITL 2 FURIOSUS BY BIX-3, A SINGLE-CRYSTAL DIFFRACTOMETER FOR JRNL TITL 3 BIOMACROMOLECULES JRNL REF PROC.NATL.ACAD.SCI.USA V. 101 11215 2004 JRNL REFN ISSN 0027-8424 JRNL PMID 15272083 JRNL DOI 10.1073/PNAS.0403807101 REMARK 2 REMARK 2 RESOLUTION. 1.50 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 : MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 103355.670 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 80.5 REMARK 3 NUMBER OF REFLECTIONS : 7286 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) : 0.186 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.800 REMARK 3 FREE R VALUE TEST SET COUNT : 789 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 52.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 416 REMARK 3 BIN R VALUE (WORKING SET) : 0.2710 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 48 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.043 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 413 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 37 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.35000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : 0.32000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : 0.15 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) : 0.19 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.240 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.200 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) : 1.330 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.190 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.890 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.490 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.05 REMARK 3 BSOL : 100.0 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 : PROTEIN.PARAM REMARK 3 PARAMETER FILE 2 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN-ALLHDG.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: X-PLOR 3.851 WAS ALSO USED FOR THE REMARK 3 REFINEMENT. THE STANDARD TOPOLOGY AND PARAMETER FILES WERE REMARK 3 CHANGED FOR HYDROGEN AND DEUTERIUM ATOM PARAMETERS TO MEET THE REMARK 3 REQUIREMENTS OF THE NEUTRON STRUCTURE REFINEMENT. REMARK 4 REMARK 4 1VCX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-MAR-04. REMARK 100 THE DEPOSITION ID IS D_1000006475. REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 24-AUG-99 REMARK 230 TEMPERATURE (KELVIN) : 298.0 REMARK 230 PH : 8.00 REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : 1G-A REMARK 230 WAVELENGTH OR RANGE (A) : 2.33 REMARK 230 MONOCHROMATOR : ELASTICALLY-BENT PERFECT SI(111) REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : IMAGE PLATE REMARK 230 DETECTOR MANUFACTURER : MACSCIENCE DIP100 REMARK 230 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 230 DATA SCALING SOFTWARE : SCALEPACK REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 7417 REMARK 230 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 230 RESOLUTION RANGE LOW (A) : 30.000 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 81.9 REMARK 230 DATA REDUNDANCY : 3.300 REMARK 230 R MERGE (I) : NULL REMARK 230 R SYM (I) : 0.09600 REMARK 230 FOR THE DATA SET : 8.5000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 230 COMPLETENESS FOR SHELL (%) : 53.1 REMARK 230 DATA REDUNDANCY IN SHELL : 1.70 REMARK 230 R MERGE FOR SHELL (I) : NULL REMARK 230 R SYM FOR SHELL (I) : 0.23200 REMARK 230 FOR SHELL : 3.100 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : X-PLOR, CNS REMARK 230 STARTING MODEL: PDB ENTRY 1BRF REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM DIHYDROGEN PHOSPHATE, REMARK 280 DIPOTASSIUM HYDROGEN PHOSPHATE, PH 8.0, MACROSEEDING, REMARK 280 TEMPERATURE 298K 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 17.16000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.11500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.65500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.11500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.16000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 17.65500 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O DOD A 105 O DOD A 130 2555 1.86 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 18 68.39 -154.80 REMARK 500 REMARK 500 REMARK: NULL 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 FE A 54 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 5 SG REMARK 620 2 CYS A 8 SG 116.8 REMARK 620 3 CYS A 38 SG 105.1 104.6 REMARK 620 4 CYS A 41 SG 103.7 118.5 107.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 54 DBREF 1VCX A 1 53 UNP P24297 RUBR_PYRFU 1 53 SEQRES 1 A 53 ALA LYS TRP VAL CYS LYS ILE CYS GLY TYR ILE TYR ASP SEQRES 2 A 53 GLU ASP ALA GLY ASP PRO ASP ASN GLY ILE SER PRO GLY SEQRES 3 A 53 THR LYS PHE GLU GLU LEU PRO ASP ASP TRP VAL CYS PRO SEQRES 4 A 53 ILE CYS GLY ALA PRO LYS SER GLU PHE GLU LYS LEU GLU SEQRES 5 A 53 ASP HET FE A 54 1 HETNAM FE FE (III) ION FORMUL 2 FE FE 3+ FORMUL 3 DOD *37(D2 O) HELIX 1 1 ASP A 18 GLY A 22 5 5 HELIX 2 2 LYS A 28 LEU A 32 5 5 HELIX 3 3 PRO A 44 SER A 46 5 3 SHEET 1 A 3 ILE A 11 ASP A 13 0 SHEET 2 A 3 LYS A 2 CYS A 5 -1 N TRP A 3 O TYR A 12 SHEET 3 A 3 PHE A 48 LYS A 50 -1 O GLU A 49 N VAL A 4 LINK O ILE A 11 O DOD A 120 1555 1555 1.81 LINK SG CYS A 5 FE FE A 54 1555 1555 2.24 LINK SG CYS A 8 FE FE A 54 1555 1555 2.25 LINK SG CYS A 38 FE FE A 54 1555 1555 2.24 LINK SG CYS A 41 FE FE A 54 1555 1555 2.25 SITE 1 AC1 4 CYS A 5 CYS A 8 CYS A 38 CYS A 41 CRYST1 34.320 35.310 44.230 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 0.029138 0.000000 0.000000 0.00000 SCALE2 0.000000 0.028321 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022609 0.00000