PDB Short entry for 1JYB HEADER ELECTRON TRANSPORT 11-SEP-01 1JYB TITLE CRYSTAL STRUCTURE OF RUBRERYTHRIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RUBRERYTHRIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS; SOURCE 3 ORGANISM_TAXID: 881 KEYWDS ALPHA HELIX BUNDLE, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR W.R.CHANG,M.LI,M.Y.LIU REVDAT 5 13-MAR-24 1JYB 1 REMARK LINK REVDAT 4 13-JUL-11 1JYB 1 VERSN REVDAT 3 24-FEB-09 1JYB 1 VERSN REVDAT 2 24-JUN-03 1JYB 1 JRNL REVDAT 1 11-SEP-02 1JYB 0 JRNL AUTH M.LI,M.Y.LIU,J.LEGALL,L.L.GUI,J.LIAO,T.JIANG,J.P.ZHANG, JRNL AUTH 2 D.C.LIANG,W.R.CHANG JRNL TITL CRYSTAL STRUCTURE STUDIES ON RUBRERYTHRIN: ENZYMATIC JRNL TITL 2 ACTIVITY IN RELATION TO THE ZINC MOVEMENT. JRNL REF J.BIOL.INORG.CHEM. V. 8 149 2003 JRNL REFN ISSN 0949-8257 JRNL PMID 12459910 JRNL DOI 10.1007/S00775-002-0400-0 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 86.4 REMARK 3 NUMBER OF REFLECTIONS : 8671 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 867 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1514 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 69 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : 2.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JYB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-SEP-01. REMARK 100 THE DEPOSITION ID IS D_1000014327. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-99 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : CONVENTIONAL CU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE 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 : 14352 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.37600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG1500, TRIS, PH 7.0, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 24.83500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.77600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.87700 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 24.83500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.77600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.87700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.83500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 40.77600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.87700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 24.83500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 40.77600 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 49.87700 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED BY REMARK 300 THE TWO FOLD AXIS: -X, -Y, Z 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 REMARK 350 TOTAL BURIED SURFACE AREA: 3660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -117.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 13170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -269.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 56 NE2 HIS A 56 CD2 -0.067 REMARK 500 HIS A 84 NE2 HIS A 84 CD2 -0.086 REMARK 500 HIS A 95 NE2 HIS A 95 CD2 -0.068 REMARK 500 HIS A 96 NE2 HIS A 96 CD2 -0.072 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 24 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 24 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ASP A 44 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 GLY A 78 CA - C - N ANGL. DEV. = -15.8 DEGREES REMARK 500 GLY A 78 O - C - N ANGL. DEV. = 16.9 DEGREES REMARK 500 GLU A 97 OE1 - CD - OE2 ANGL. DEV. = -16.3 DEGREES REMARK 500 TYR A 114 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 GLU A 128 OE1 - CD - OE2 ANGL. DEV. = -8.6 DEGREES REMARK 500 ARG A 134 CB - CG - CD ANGL. DEV. = -16.3 DEGREES REMARK 500 ARG A 134 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 134 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 140 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 146 NE - CZ - NH1 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 146 NE - CZ - NH2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG A 150 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 150 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 TRP A 156 CD1 - CG - CD2 ANGL. DEV. = 7.5 DEGREES REMARK 500 TRP A 156 CE2 - CD2 - CG ANGL. DEV. = -6.9 DEGREES REMARK 500 TRP A 191 CD1 - CG - CD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 TRP A 191 CE2 - CD2 - CG ANGL. DEV. = -5.6 DEGREES 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 PHE A 39 78.05 -114.60 REMARK 500 ILE A 79 115.16 73.58 REMARK 500 ALA A 81 -154.68 -118.81 REMARK 500 GLU A 100 -65.55 -106.85 REMARK 500 TYR A 114 66.64 -108.51 REMARK 500 THR A 154 -168.03 -126.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 8 0.09 SIDE CHAIN 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 ZN A 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 20 OE2 REMARK 620 2 GLU A 20 OE1 53.4 REMARK 620 3 GLU A 53 OE1 69.9 92.7 REMARK 620 4 GLU A 97 OE2 111.2 83.1 173.3 REMARK 620 5 GLU A 128 OE1 77.5 128.1 84.2 102.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 600 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 53 OE2 REMARK 620 2 GLU A 94 OE1 162.2 REMARK 620 3 GLU A 94 OE2 106.7 61.7 REMARK 620 4 GLU A 128 OE2 97.7 95.5 155.2 REMARK 620 5 HIS A 131 ND1 83.1 110.9 98.1 80.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 158 SG REMARK 620 2 CYS A 161 SG 113.8 REMARK 620 3 CYS A 174 SG 112.9 102.5 REMARK 620 4 CYS A 177 SG 105.9 113.4 108.3 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 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 601 DBREF 1JYB A 1 191 UNP P24931 RUBY_DESVH 1 191 SEQRES 1 A 191 MET LYS SER LEU LYS GLY SER ARG THR GLU LYS ASN ILE SEQRES 2 A 191 LEU THR ALA PHE ALA GLY GLU SER GLN ALA ARG ASN ARG SEQRES 3 A 191 TYR ASN TYR PHE GLY GLY GLN ALA LYS LYS ASP GLY PHE SEQRES 4 A 191 VAL GLN ILE SER ASP ILE PHE ALA GLU THR ALA ASP GLN SEQRES 5 A 191 GLU ARG GLU HIS ALA LYS ARG LEU PHE LYS PHE LEU GLU SEQRES 6 A 191 GLY GLY ASP LEU GLU ILE VAL ALA ALA PHE PRO ALA GLY SEQRES 7 A 191 ILE ILE ALA ASP THR HIS ALA ASN LEU ILE ALA SER ALA SEQRES 8 A 191 ALA GLY GLU HIS HIS GLU TYR THR GLU MET TYR PRO SER SEQRES 9 A 191 PHE ALA ARG ILE ALA ARG GLU GLU GLY TYR GLU GLU ILE SEQRES 10 A 191 ALA ARG VAL PHE ALA SER ILE ALA VAL ALA GLU GLU PHE SEQRES 11 A 191 HIS GLU LYS ARG PHE LEU ASP PHE ALA ARG ASN ILE LYS SEQRES 12 A 191 GLU GLY ARG VAL PHE LEU ARG GLU GLN ALA THR LYS TRP SEQRES 13 A 191 ARG CYS ARG ASN CYS GLY TYR VAL HIS GLU GLY THR GLY SEQRES 14 A 191 ALA PRO GLU LEU CYS PRO ALA CYS ALA HIS PRO LYS ALA SEQRES 15 A 191 HIS PHE GLU LEU LEU GLY ILE ASN TRP HET FE A 600 1 HET FE A 401 1 HET ZN A 601 1 HETNAM FE FE (III) ION HETNAM ZN ZINC ION FORMUL 2 FE 2(FE 3+) FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *69(H2 O) HELIX 1 1 SER A 7 GLY A 38 1 32 HELIX 2 2 PHE A 39 LYS A 62 1 24 HELIX 3 3 ASP A 82 GLU A 100 1 19 HELIX 4 4 GLU A 100 GLU A 112 1 13 HELIX 5 5 TYR A 114 GLY A 145 1 32 HELIX 6 6 PRO A 180 ALA A 182 5 3 SHEET 1 A 3 VAL A 164 GLY A 169 0 SHEET 2 A 3 LEU A 149 CYS A 158 -1 N THR A 154 O GLY A 167 SHEET 3 A 3 PHE A 184 LEU A 186 -1 O GLU A 185 N ARG A 157 LINK OE2 GLU A 20 ZN ZN A 601 1555 1555 2.63 LINK OE1 GLU A 20 ZN ZN A 601 1555 1555 2.25 LINK OE2 GLU A 53 FE FE A 600 1555 1555 2.24 LINK OE1 GLU A 53 ZN ZN A 601 1555 1555 2.17 LINK OE1 GLU A 94 FE FE A 600 1555 1555 2.10 LINK OE2 GLU A 94 FE FE A 600 1555 1555 2.09 LINK OE2 GLU A 97 ZN ZN A 601 1555 1555 2.09 LINK OE2 GLU A 128 FE FE A 600 1555 1555 2.21 LINK OE1 GLU A 128 ZN ZN A 601 1555 1555 2.29 LINK ND1 HIS A 131 FE FE A 600 1555 1555 2.46 LINK SG CYS A 158 FE FE A 401 1555 1555 2.27 LINK SG CYS A 161 FE FE A 401 1555 1555 2.26 LINK SG CYS A 174 FE FE A 401 1555 1555 2.27 LINK SG CYS A 177 FE FE A 401 1555 1555 2.29 SITE 1 AC1 5 GLU A 53 GLU A 94 GLU A 128 HIS A 131 SITE 2 AC1 5 ZN A 601 SITE 1 AC2 4 CYS A 158 CYS A 161 CYS A 174 CYS A 177 SITE 1 AC3 5 GLU A 20 GLU A 53 GLU A 97 GLU A 128 SITE 2 AC3 5 FE A 600 CRYST1 49.670 81.552 99.754 90.00 90.00 90.00 I 2 2 2 8 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 0.020133 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012262 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010025 0.00000