HEADER ELECTRON TRANSPORT 12-MAY-11 3RZT TITLE NEUTRON STRUCTURE OF PERDEUTERATED RUBREDOXIN USING RAPID (14 HOURS) TITLE 2 DATA 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,C.-L.CHUNG,K.L.WEISS,M.P.BLAKELEY,D.A.A.MYLES,F.MEILLEUR REVDAT 4 13-SEP-23 3RZT 1 REMARK LINK REVDAT 3 24-JAN-18 3RZT 1 AUTHOR REMARK REVDAT 2 04-JAN-12 3RZT 1 JRNL REVDAT 1 28-DEC-11 3RZT 0 JRNL AUTH P.MUNSHI,S.L.CHUNG,M.P.BLAKELEY,K.L.WEISS,D.A.MYLES, JRNL AUTH 2 F.MEILLEUR JRNL TITL RAPID VISUALIZATION OF HYDROGEN POSITIONS IN PROTEIN NEUTRON JRNL TITL 2 CRYSTALLOGRAPHIC STRUCTURES. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 68 35 2012 JRNL REFN ISSN 0907-4449 JRNL PMID 22194331 JRNL DOI 10.1107/S0907444911048402 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 2010_05_02_2130) 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) : 27.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.530 REMARK 3 COMPLETENESS FOR RANGE (%) : 75.6 REMARK 3 NUMBER OF REFLECTIONS : 4187 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.710 REMARK 3 FREE R VALUE TEST SET COUNT : 197 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 27.2108 - 1.7504 0.76 3990 197 0.2022 0.2490 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 1.20 REMARK 3 K_SOL : 0.60 REMARK 3 B_SOL : 49.51 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.440 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.950 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) : -1.22960 REMARK 3 B22 (A**2) : -2.33480 REMARK 3 B33 (A**2) : -0.53810 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 : 0.013 795 REMARK 3 ANGLE : 1.257 1388 REMARK 3 CHIRALITY : 0.069 55 REMARK 3 PLANARITY : 0.006 125 REMARK 3 DIHEDRAL : 13.083 204 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 3RZT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000065581. REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 08-JUN-07 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 : LADI III REMARK 230 WAVELENGTH OR RANGE (A) : 3.2 - 4.2 REMARK 230 MONOCHROMATOR : NULL REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : IMAGE PLATE REMARK 230 DETECTOR MANUFACTURER : MAATEL QLD: LADI-III REMARK 230 INTENSITY-INTEGRATION SOFTWARE : LAUEGEN REMARK 230 DATA SCALING SOFTWARE : SCALA REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 4187 REMARK 230 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 230 RESOLUTION RANGE LOW (A) : 27.210 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 77.5 REMARK 230 DATA REDUNDANCY : 4.600 REMARK 230 R MERGE (I) : 0.15300 REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 8.4000 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 (%) : 56.2 REMARK 230 DATA REDUNDANCY IN SHELL : 2.60 REMARK 230 R MERGE FOR SHELL (I) : 0.18900 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : 3.600 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 230 SOFTWARE USED : NULL REMARK 230 STARTING MODEL: PDB ENTRY 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 16.96000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.75000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.43500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.75000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.96000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 17.43500 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 0 REMARK 465 GLU A 52 REMARK 465 ASP A 53 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 LYS A 6 CE NZ REMARK 470 LYS A 28 NZ 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 O SER A 46 O DOD A 84 2.07 REMARK 500 O ILE A 11 O DOD A 76 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 66 O DOD A 87 2554 2.13 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 63.58 -155.87 REMARK 500 ILE A 40 -60.59 -92.63 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 123.9 REMARK 620 3 CYS A 38 SG 103.3 102.1 REMARK 620 4 CYS A 41 SG 103.9 107.8 116.7 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 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KYX RELATED DB: PDB REMARK 900 X-RAY AND NEUTRON JOINT REFINEMENT REMARK 900 RELATED ID: 3RYG RELATED DB: PDB REMARK 900 REFINEMENT USING 128 HOURS NEUTRON DATA ONLY REMARK 900 RELATED ID: 3RZ6 RELATED DB: PDB REMARK 900 REFINEMENT USING 40 HOURS 1ST PASS NEUTRON DATA ONLY REMARK 900 RELATED ID: 3RZR RELATED DB: PDB REMARK 900 REFINEMENT USING 40 HOURS NEUTRON DATA ONLY DBREF 3RZT 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 54 1 HETNAM FE FE (III) ION FORMUL 2 FE FE 3+ FORMUL 3 DOD *35(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 5 FE FE A 54 1555 1555 2.41 LINK SG CYS A 8 FE FE A 54 1555 1555 2.24 LINK SG CYS A 38 FE FE A 54 1555 1555 2.35 LINK SG CYS A 41 FE FE A 54 1555 1555 2.22 SITE 1 AC1 4 CYS A 5 CYS A 8 CYS A 38 CYS A 41 CRYST1 33.920 34.870 43.500 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 0.029481 0.000000 0.000000 0.00000 SCALE2 0.000000 0.028678 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022989 0.00000