HEADER ELECTRON TRANSPORT 19-APR-13 4K9F TITLE NEUTRON STRUCTURE OF PERDEUTERATED RUBREDOXIN REFINED AGAINST 1.75 TITLE 2 RESOLUTION DATA COLLECTED ON THE NEW IMAGINE INSTRUMENT AT HFIR, ORNL COMPND MOL_ID: 1; COMPND 2 MOLECULE: RUBREDOXIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RD; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 186497; SOURCE 4 STRAIN: ATCC 43587 / DSM 3638 / JCM 8422 / VC1; SOURCE 5 GENE: PF1282, RUB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24D KEYWDS IRON, METAL-BINDING, TRANSPORT, ELECTRON TRANSPORT EXPDTA NEUTRON DIFFRACTION AUTHOR P.MUNSHI,F.MEILLEUR,D.MYLES REVDAT 2 13-JUN-18 4K9F 1 REMARK REVDAT 1 04-DEC-13 4K9F 0 JRNL AUTH F.MEILLEUR,P.MUNSHI,L.ROBERTSON,A.D.STOICA,L.CROW, JRNL AUTH 2 A.KOVALEVSKY,T.KORITSANSZKY,B.C.CHAKOUMAKOS,R.BLESSING, JRNL AUTH 3 D.A.MYLES JRNL TITL THE IMAGINE INSTRUMENT: FIRST NEUTRON PROTEIN STRUCTURE AND JRNL TITL 2 NEW CAPABILITIES FOR NEUTRON MACROMOLECULAR CRYSTALLOGRAPHY. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 69 2157 2013 JRNL REFN ISSN 0907-4449 JRNL PMID 24100333 JRNL DOI 10.1107/S0907444913019604 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.630 REMARK 3 COMPLETENESS FOR RANGE (%) : 74.4 REMARK 3 NUMBER OF REFLECTIONS : 4095 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.350 REMARK 3 FREE R VALUE TEST SET COUNT : 424 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 27.1425 - 2.5236 0.88 1506 175 0.1855 0.2201 REMARK 3 2 2.5236 - 2.0033 0.74 1215 134 0.1973 0.2527 REMARK 3 3 2.0033 - 1.7501 0.59 950 115 0.2335 0.2756 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.050 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) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.013 888 REMARK 3 ANGLE : 0.994 1497 REMARK 3 CHIRALITY : 0.079 57 REMARK 3 PLANARITY : 0.005 133 REMARK 3 DIHEDRAL : 9.980 217 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 4K9F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000079057. REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 01-JAN-13 REMARK 230 TEMPERATURE (KELVIN) : 293.0 REMARK 230 PH : NULL REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : NULL REMARK 230 WAVELENGTH OR RANGE (A) : 2.78 - 4.0 REMARK 230 MONOCHROMATOR : HFIR SOURCE REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : IMAGE PLATE REMARK 230 DETECTOR MANUFACTURER : QLD: IMAGINE CG4D HFIR REMARK 230 INTENSITY-INTEGRATION SOFTWARE : LAUEGEN REMARK 230 DATA SCALING SOFTWARE : SCALA REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 4095 REMARK 230 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 230 RESOLUTION RANGE LOW (A) : 27.140 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 76.4 REMARK 230 DATA REDUNDANCY : 3.500 REMARK 230 R MERGE (I) : 0.12700 REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 7.0000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 230 COMPLETENESS FOR SHELL (%) : 54.1 REMARK 230 DATA REDUNDANCY IN SHELL : 2.20 REMARK 230 R MERGE FOR SHELL (I) : 0.18500 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : 3.700 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : NULL REMARK 230 STARTING MODEL: 3KYW 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: 20 MG/ML RUBREDOXIN IN 1.9 M REMARK 280 SODIUM/POTASSIUM PHOSPHATE SITTING DROP EQUILIBRATED AGAINST 3.8 REMARK 280 M SODIUM/POTASSIUM PHOSPHATE RESERVOIR, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K 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 16.91100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.67550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.40150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.67550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.91100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 17.40150 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 ASP A 53 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU A 14 O DOD A 224 2.04 REMARK 500 O ASP A 35 O DOD A 243 2.17 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 68.52 -157.22 REMARK 500 PRO A 39 0.54 -67.69 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 101 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 8 SG REMARK 620 2 CYS A 38 SG 107.6 REMARK 620 3 CYS A 41 SG 116.3 113.4 REMARK 620 4 CYS A 5 SG 119.0 102.5 97.2 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 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KYX RELATED DB: PDB REMARK 900 JOINT XRAY/NEUTRON CRYSTAL STRUCTURE DETERMINATION OF FULLY REMARK 900 PERDEUTERATED RUBREDOXIN AT 295K REMARK 900 RELATED ID: 3RZT RELATED DB: PDB REMARK 900 NEUTRON STRUCTURE OF PERDEUTERATED RUBREDOXIN USING RAPID (14 HOURS) REMARK 900 DATA REMARK 900 RELATED ID: 1VCX RELATED DB: PDB REMARK 900 NEUTRON CRYSTAL STRUCTURE OF THE WILD TYPE RUBREDOXIN FROM REMARK 900 PYROCOCCUS FURIOSUS AT 1.5A RESOLUTION REMARK 900 RELATED ID: 4AR3 RELATED DB: PDB REMARK 900 NEAR-ATOMIC RESOLUTION NEUTRON CRYSTALLOGRAPHY ON THE OXIDISED FORM REMARK 900 PERDEUTERATED PYROCOCCUS FURIOSUS RUBREDOXIN. REMARK 900 RELATED ID: 3RYG RELATED DB: PDB REMARK 900 NEUTRON STRUCTURE OF PERDEUTERATED RUBREDOXIN USING 128 HOURS DATA REMARK 900 RELATED ID: 3SS2 RELATED DB: PDB REMARK 900 NEUTRON STRUCTURE OF PERDEUTERATED RUBREDOXIN USING 48 HOURS DATA DBREF 4K9F A 0 53 UNP P24297 RUBR_PYRFU 1 54 SEQRES 1 A 54 MET ALA LYS TRP VAL CYS LYS ILE CYS GLY TYR ILE TYR SEQRES 2 A 54 ASP GLU ASP ALA GLY ASP PRO ASP ASN GLY ILE SER PRO SEQRES 3 A 54 GLY THR LYS PHE GLU GLU LEU PRO ASP ASP TRP VAL CYS SEQRES 4 A 54 PRO ILE CYS GLY ALA PRO LYS SER GLU PHE GLU LYS LEU SEQRES 5 A 54 GLU ASP HET FE A 101 1 HETNAM FE FE (III) ION FORMUL 2 FE FE 3+ FORMUL 3 DOD *58(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 SG CYS A 8 FE FE A 101 1555 1555 2.10 LINK SG CYS A 38 FE FE A 101 1555 1555 2.12 LINK SG CYS A 41 FE FE A 101 1555 1555 2.20 LINK SG CYS A 5 FE FE A 101 1555 1555 2.37 SITE 1 AC1 4 CYS A 5 CYS A 8 CYS A 38 CYS A 41 CRYST1 33.822 34.803 43.351 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 0.029567 0.000000 0.000000 0.00000 SCALE2 0.000000 0.028733 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023068 0.00000 MASTER 263 0 1 3 3 0 1 6 0 0 0 5 END