HEADER ELECTRON TRANSPORT 11-FEB-15 5AI2 TITLE ANOMALOUS NEUTRON PHASED CRYSTAL STRUCTURE OF 113CD-SUBSTITUTED TITLE 2 PERDEUTERATED PYROCOCCUS FURIOSUS RUBREDOXIN TO 1.75A RESOLUTION AT TITLE 3 295K COMPND MOL_ID: 1; COMPND 2 MOLECULE: RUBREDOXIN; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: PERDEUTERATED, 113-CD SUBSTITUTED, CARBOXYLIC COMPND 5 DEUTERONS SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261 KEYWDS ELECTRON TRANSPORT, NEUTRON ANOMALOUS PHASING, PERDEUTERATED, KEYWDS 2 PYROCOCCUS FURIOSUS, RUBREDOXIN, CADMIUM EXPDTA NEUTRON DIFFRACTION AUTHOR M.G.CUYPERS,E.MOSSOU,S.A.MASON REVDAT 4 08-MAY-24 5AI2 1 REMARK LINK REVDAT 3 24-AUG-16 5AI2 1 JRNL REVDAT 2 11-MAY-16 5AI2 1 REMARK FORMUL HETATM MASTER REVDAT 1 02-MAR-16 5AI2 0 JRNL AUTH M.G.CUYPERS,S.A.MASON,E.MOSSOU,M.HAERTLEIN,V.T.FORSYTH, JRNL AUTH 2 E.P.MITCHELL JRNL TITL MACROMOLECULAR STRUCTURE PHASING BY NEUTRON ANOMALOUS JRNL TITL 2 DIFFRACTION. JRNL REF SCI.REP. V. 6 31487 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27511806 JRNL DOI 10.1038/SREP31487 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 27.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 10050 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 451 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 27.0716 - 2.5236 1.00 3154 179 0.2490 0.3047 REMARK 3 2 2.5236 - 2.0032 1.00 3230 116 0.2216 0.2552 REMARK 3 3 2.0032 - 1.7501 1.00 3215 156 0.2154 0.2765 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.70 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 : 0.003 992 REMARK 3 ANGLE : 0.613 1766 REMARK 3 CHIRALITY : 0.024 63 REMARK 3 PLANARITY : 0.002 184 REMARK 3 DIHEDRAL : 14.246 258 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: USED NEUTRON BOUND COHERENT SCATTERING REMARK 3 LENGTH FOR 113-CD OF -8.0 FM FOR REFINEMENT REMARK 4 REMARK 4 5AI2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1290063011. REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 01-DEC-14 REMARK 230 TEMPERATURE (KELVIN) : 295.0 REMARK 230 PH : 6.50 REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : D19 REMARK 230 WAVELENGTH OR RANGE (A) : 1.17 REMARK 230 MONOCHROMATOR : NULL REMARK 230 OPTICS : BORON CARBIDE BEAM DEFINING REMARK 230 APERTURE REMARK 230 REMARK 230 DETECTOR TYPE : 5ATM 3HE, CURVED 120X30 DEGREES REMARK 230 DETECTOR MANUFACTURER : INSTITUT LAUE LANGEVIN DETECTOR REMARK 230 GROUP REMARK 230 INTENSITY-INTEGRATION SOFTWARE : RETREAT REMARK 230 DATA SCALING SOFTWARE : RETREAT REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 5560 REMARK 230 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 230 RESOLUTION RANGE LOW (A) : 34.440 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 230 DATA REDUNDANCY : 13.40 REMARK 230 R MERGE (I) : 0.14000 REMARK 230 R SYM (I) : 0.04000 REMARK 230 <I/SIGMA(I)> FOR THE DATA SET : NULL 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 (%) : 99.9 REMARK 230 DATA REDUNDANCY IN SHELL : 10.60 REMARK 230 R MERGE FOR SHELL (I) : 0.45700 REMARK 230 R SYM FOR SHELL (I) : 0.14900 REMARK 230 <I/SIGMA(I)> FOR SHELL : 5.400 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: EXPERIMENTAL ANOMALOUS REMARK 230 NEUTRON PHASING REMARK 230 SOFTWARE USED : SHELXCD, SHELXE REMARK 230 STARTING MODEL: NONE REMARK 230 REMARK 230 REMARK: RPIM GIVEN INSTEAD OF RSYM REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 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 17.22000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.89000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.07000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.89000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.22000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 17.07000 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 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 OD2 ASP A 35 D D8U A 1055 1.46 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 64.33 -155.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 DOD A2022 DISTANCE = 6.89 ANGSTROMS REMARK 525 DOD A2050 DISTANCE = 6.43 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 CADMIUM ION (CD): MINIMUM 95 PERCENT PURE 113-CD ISOTOPE IN REMARK 600 CRYSTAL. TRACE AMOUNTS OF FE ONLY DETECTED BY CRYSTAL REMARK 600 X-RAY FLUORESCENCE. 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 A1054 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 5 SG REMARK 620 2 CYS A 8 SG 117.6 REMARK 620 3 CYS A 38 SG 99.4 96.7 REMARK 620 4 CYS A 41 SG 103.9 124.5 111.8 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 CD A 1054 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AI3 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF 113CD-SUBSTITUTED PERDEUTERATED PYROCOCCUS REMARK 900 FURIOSUS RUBREDOXIN TO 1.02A RESOLUTION AT 295K IN A QUARTZ REMARK 900 CAPILLARY DBREF 5AI2 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 CD A1054 1 HET D8U A1055 1 HET D8U A1056 1 HET D8U A1057 1 HETNAM CD CADMIUM ION HETNAM D8U DEUTERIUM(1+) FORMUL 2 CD CD 2+ FORMUL 3 D8U 3(D 1+) FORMUL 6 DOD *48(D2 O) HELIX 1 1 PRO A 19 GLY A 22 5 4 HELIX 2 2 LYS A 28 LEU A 32 5 5 SHEET 1 AA 3 ILE A 11 ASP A 13 0 SHEET 2 AA 3 LYS A 2 CYS A 5 -1 O TRP A 3 N TYR A 12 SHEET 3 AA 3 PHE A 48 LYS A 50 -1 O GLU A 49 N VAL A 4 LINK SG CYS A 5 CD CD A1054 1555 1555 2.73 LINK SG CYS A 8 CD CD A1054 1555 1555 2.74 LINK SG CYS A 38 CD CD A1054 1555 1555 2.72 LINK SG CYS A 41 CD CD A1054 1555 1555 2.73 SITE 1 AC1 4 CYS A 5 CYS A 8 CYS A 38 CYS A 41 CRYST1 34.440 34.140 43.780 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 0.029036 0.000000 0.000000 0.00000 SCALE2 0.000000 0.029291 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022841 0.00000