HEADER OXIDOREDUCTASE 17-JUN-11 3SID TITLE CRYSTAL STRUCTURE OF OXIDIZED SYMERYTHRIN FROM CYANOPHORA PARADOXA, TITLE 2 AZIDE ADDUCT AT 50% OCCUPANCY COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYMERYTHRIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ORF180; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CYANOPHORA PARADOXA; SOURCE 3 ORGANISM_TAXID: 2762; SOURCE 4 GENE: CYANELLE ORF180; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PT7-7 KEYWDS FERRITIN-LIKE SUPERFAMILY, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR R.B.COOLEY,D.J.ARP,P.A.KARPLUS REVDAT 4 30-OCT-24 3SID 1 REMARK REVDAT 3 13-SEP-23 3SID 1 REMARK LINK REVDAT 2 12-OCT-11 3SID 1 JRNL REVDAT 1 31-AUG-11 3SID 0 JRNL AUTH R.B.COOLEY,D.J.ARP,P.A.KARPLUS JRNL TITL SYMERYTHRIN STRUCTURES AT ATOMIC RESOLUTION AND THE ORIGINS JRNL TITL 2 OF RUBRERYTHRINS AND THE FERRITIN-LIKE SUPERFAMILY. JRNL REF J.MOL.BIOL. V. 413 177 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21872605 JRNL DOI 10.1016/J.JMB.2011.08.019 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 65332 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 + TEST SET) : 0.117 REMARK 3 R VALUE (WORKING SET) : 0.115 REMARK 3 FREE R VALUE : 0.156 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3484 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4852 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.1900 REMARK 3 BIN FREE R VALUE SET COUNT : 262 REMARK 3 BIN FREE R VALUE : 0.2390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2730 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 562 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.74000 REMARK 3 B22 (A**2) : -0.74000 REMARK 3 B33 (A**2) : 1.11000 REMARK 3 B12 (A**2) : -0.37000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.052 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.030 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.629 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.981 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3053 ; 0.025 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1999 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4177 ; 2.101 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4943 ; 1.142 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 425 ; 4.832 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 151 ;41.072 ;25.629 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 545 ;13.672 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;17.965 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 469 ; 0.139 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3602 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 608 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1938 ; 2.386 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 771 ; 1.441 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3139 ; 3.304 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1115 ; 4.802 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1019 ; 6.801 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 5052 ; 2.297 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 566 ;13.515 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4976 ; 9.286 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3SID COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1000066238. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97650 REMARK 200 MONOCHROMATOR : SI(220) ASYMMETRIC CUT SINGLE REMARK 200 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68857 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07400 REMARK 200 FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.00 REMARK 200 R MERGE FOR SHELL (I) : 0.44100 REMARK 200 R SYM FOR SHELL (I) : 0.44100 REMARK 200 FOR SHELL : 5.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 3QHB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.1M BISTRIS, 0.35M REMARK 280 NH4CL, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 279K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.96000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.48000 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 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 1 REMARK 465 GLY A 2 REMARK 465 LEU A 3 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 LEU B 3 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 ASN A 4 CG OD1 ND2 REMARK 470 GLU A 150 CD OE1 OE2 REMARK 470 GLU A 178 CG CD OE1 OE2 REMARK 470 ASN B 4 CG OD1 ND2 REMARK 470 GLU B 8 CG CD OE1 OE2 REMARK 470 LYS B 88 CG CD CE NZ REMARK 470 GLU B 150 CD OE1 OE2 REMARK 470 GLU B 178 CG CD OE1 OE2 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 HOH B 423 O HOH B 445 1.73 REMARK 500 OE1 GLU B 50 O HOH B 529 1.93 REMARK 500 OE2 GLU A 50 O HOH A 523 1.93 REMARK 500 O HOH A 239 O HOH A 540 1.99 REMARK 500 SD MET B 38 O HOH B 496 2.01 REMARK 500 O HOH B 271 O HOH B 298 2.08 REMARK 500 O HOH A 516 O HOH A 562 2.16 REMARK 500 O HOH A 332 O HOH A 405 2.16 REMARK 500 O HOH A 202 O HOH A 263 2.18 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 SD MET A 149 O HOH A 297 3565 2.03 REMARK 500 SD MET B 149 O HOH B 258 3555 2.06 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 50 CG GLU A 50 CD 0.102 REMARK 500 GLN A 76 CD GLN A 76 NE2 -0.153 REMARK 500 TYR A 136 CE1 TYR A 136 CZ -0.098 REMARK 500 GLU A 145 CG GLU A 145 CD 0.109 REMARK 500 GLU B 50 CG GLU B 50 CD 0.110 REMARK 500 TYR B 136 CG TYR B 136 CD1 -0.085 REMARK 500 TYR B 136 CE1 TYR B 136 CZ -0.088 REMARK 500 GLU B 145 CG GLU B 145 CD 0.094 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 TYR A 136 CD1 - CE1 - CZ ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP B 27 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 TYR B 136 CB - CG - CD2 ANGL. DEV. = 4.4 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 CYS A 43 -58.95 -122.83 REMARK 500 CYS A 43 -64.64 -128.40 REMARK 500 LYS A 134 -64.71 -127.14 REMARK 500 ASN A 148 79.41 -100.79 REMARK 500 ASN A 148 77.14 -100.79 REMARK 500 CYS B 43 -57.51 -124.72 REMARK 500 CYS B 43 -64.96 -129.17 REMARK 500 LYS B 134 -66.29 -124.76 REMARK 500 ASN B 148 75.58 -101.36 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 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 37 OE2 REMARK 620 2 GLU A 37 OE1 31.0 REMARK 620 3 GLU A 40 OE1 85.4 97.2 REMARK 620 4 GLU A 71 OE1 101.4 74.1 84.6 REMARK 620 5 GLU A 131 OE2 80.7 108.9 91.6 175.5 REMARK 620 6 GLU A 162 OE2 91.7 81.4 176.5 98.1 85.8 REMARK 620 7 HOH A 183 O 166.9 162.0 90.6 90.6 87.0 91.7 REMARK 620 8 HOH A 204 O 71.1 99.7 89.9 171.1 9.7 87.2 96.5 REMARK 620 9 AZI A 300 N3 168.3 160.7 91.0 89.3 88.3 91.4 1.4 97.8 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 200 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 71 OE2 REMARK 620 2 GLU A 128 OE2 102.1 REMARK 620 3 GLU A 128 OE1 160.3 58.7 REMARK 620 4 GLU A 162 OE1 111.9 146.0 87.3 REMARK 620 5 HIS A 165 ND1 86.4 97.7 99.5 86.6 REMARK 620 6 HOH A 183 O 86.1 86.6 88.5 93.6 172.0 REMARK 620 7 AZI A 300 N3 85.2 87.4 89.5 93.3 171.0 1.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 200 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 37 OE1 REMARK 620 2 GLU B 37 OE1 29.5 REMARK 620 3 GLU B 40 OE1 85.8 97.0 REMARK 620 4 GLU B 71 OE1 98.5 72.2 86.0 REMARK 620 5 GLU B 131 OE1 83.9 110.2 94.2 177.5 REMARK 620 6 GLU B 162 OE2 91.3 82.4 175.1 98.4 81.5 REMARK 620 7 HOH B 181 O 169.9 160.6 90.9 90.7 86.8 91.2 REMARK 620 8 HOH B 198 O 74.0 101.7 87.0 170.1 11.9 88.3 96.4 REMARK 620 9 AZI B 300 N1 169.6 160.5 92.5 91.5 86.0 89.6 1.7 95.8 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 71 OE2 REMARK 620 2 GLU B 128 OE2 101.0 REMARK 620 3 GLU B 128 OE1 160.0 59.6 REMARK 620 4 GLU B 162 OE1 112.6 146.3 86.7 REMARK 620 5 HIS B 165 ND1 86.9 97.0 99.6 87.7 REMARK 620 6 HOH B 181 O 85.9 87.6 88.4 92.0 172.0 REMARK 620 7 AZI B 300 N1 88.1 86.1 86.0 92.2 174.5 2.5 REMARK 620 N 1 2 3 4 5 6 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 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE B 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI B 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QHB RELATED DB: PDB REMARK 900 OXIDIZED SYMERYTHRIN FROM C. PARADOXA REMARK 900 RELATED ID: 3QHC RELATED DB: PDB REMARK 900 SYMERYTHRIN FROM C. PARADOXA, REDUCED WITH DITHIONITE DBREF 3SID A 1 180 UNP P48329 YCX8_CYAPA 1 180 DBREF 3SID B 1 180 UNP P48329 YCX8_CYAPA 1 180 SEQRES 1 A 180 MET GLY LEU ASN TYR ASN GLN GLU ASP PHE MET GLY LEU SEQRES 2 A 180 ASP ARG PHE PHE GLN ASP ALA VAL SER HIS ASN ASN THR SEQRES 3 A 180 ASP ALA ASN ALA ALA SER SER ILE GLU VAL GLU MET TYR SEQRES 4 A 180 GLU CYS ASP CYS MET TYR PRO THR PHE ALA GLU ILE ALA SEQRES 5 A 180 ARG ARG SER GLY GLN PRO GLU ILE GLY ALA MET PHE ASP SEQRES 6 A 180 ALA ILE ALA LYS GLU GLU GLY MET HIS ALA GLN LEU LEU SEQRES 7 A 180 THR LYS LEU TYR SER GLU LEU GLU VAL LYS ASP SER ALA SEQRES 8 A 180 GLU THR LEU GLU ALA LYS ARG LEU VAL SER THR ILE GLU SEQRES 9 A 180 SER GLN ILE ASP ALA VAL ALA SER ASP SER ARG GLY LEU SEQRES 10 A 180 ARG ARG ALA LEU GLU THR ALA LEU GLU VAL GLU THR ILE SEQRES 11 A 180 GLU SER GLN LYS THR TYR PRO ALA PHE ALA LYS LEU ALA SEQRES 12 A 180 ALA GLU GLN GLY ASN MET GLU VAL ALA THR ALA PHE GLU SEQRES 13 A 180 ALA ILE VAL LYS SER GLU THR LYS HIS ALA ASN TRP VAL SEQRES 14 A 180 LYS ARG ALA LEU GLU ASN LEU LEU GLU VAL ALA SEQRES 1 B 180 MET GLY LEU ASN TYR ASN GLN GLU ASP PHE MET GLY LEU SEQRES 2 B 180 ASP ARG PHE PHE GLN ASP ALA VAL SER HIS ASN ASN THR SEQRES 3 B 180 ASP ALA ASN ALA ALA SER SER ILE GLU VAL GLU MET TYR SEQRES 4 B 180 GLU CYS ASP CYS MET TYR PRO THR PHE ALA GLU ILE ALA SEQRES 5 B 180 ARG ARG SER GLY GLN PRO GLU ILE GLY ALA MET PHE ASP SEQRES 6 B 180 ALA ILE ALA LYS GLU GLU GLY MET HIS ALA GLN LEU LEU SEQRES 7 B 180 THR LYS LEU TYR SER GLU LEU GLU VAL LYS ASP SER ALA SEQRES 8 B 180 GLU THR LEU GLU ALA LYS ARG LEU VAL SER THR ILE GLU SEQRES 9 B 180 SER GLN ILE ASP ALA VAL ALA SER ASP SER ARG GLY LEU SEQRES 10 B 180 ARG ARG ALA LEU GLU THR ALA LEU GLU VAL GLU THR ILE SEQRES 11 B 180 GLU SER GLN LYS THR TYR PRO ALA PHE ALA LYS LEU ALA SEQRES 12 B 180 ALA GLU GLN GLY ASN MET GLU VAL ALA THR ALA PHE GLU SEQRES 13 B 180 ALA ILE VAL LYS SER GLU THR LYS HIS ALA ASN TRP VAL SEQRES 14 B 180 LYS ARG ALA LEU GLU ASN LEU LEU GLU VAL ALA HET FE A 200 1 HET FE A 201 1 HET AZI A 300 3 HET FE B 200 1 HET FE B 201 1 HET AZI B 300 3 HETNAM FE FE (III) ION HETNAM AZI AZIDE ION FORMUL 3 FE 4(FE 3+) FORMUL 5 AZI 2(N3 1-) FORMUL 9 HOH *562(H2 O) HELIX 1 1 ASP A 9 PHE A 17 5 9 HELIX 2 2 ASN A 25 CYS A 43 1 19 HELIX 3 3 CYS A 43 SER A 55 1 13 HELIX 4 4 GLN A 57 TYR A 82 1 26 HELIX 5 5 SER A 90 GLN A 106 1 17 HELIX 6 6 GLN A 106 ASP A 113 1 8 HELIX 7 7 SER A 114 LYS A 134 1 21 HELIX 8 8 LYS A 134 GLN A 146 1 13 HELIX 9 9 ASN A 148 GLU A 178 1 31 HELIX 10 10 ASP B 9 PHE B 17 5 9 HELIX 11 11 ASN B 25 CYS B 43 1 19 HELIX 12 12 CYS B 43 SER B 55 1 13 HELIX 13 13 GLN B 57 TYR B 82 1 26 HELIX 14 14 SER B 90 GLN B 106 1 17 HELIX 15 15 GLN B 106 ASP B 113 1 8 HELIX 16 16 SER B 114 LYS B 134 1 21 HELIX 17 17 LYS B 134 GLN B 146 1 13 HELIX 18 18 ASN B 148 GLU B 178 1 31 LINK CD1 PHE A 17 CG1 VAL A 127 1555 1555 1.66 LINK CD1 PHE B 17 CG1 VAL B 127 1555 1555 1.66 LINK OE2AGLU A 37 FE FE A 201 1555 1555 1.98 LINK OE1BGLU A 37 FE FE A 201 1555 1555 2.25 LINK OE1 GLU A 40 FE FE A 201 1555 1555 2.07 LINK OE2 GLU A 71 FE FE A 200 1555 1555 2.01 LINK OE1 GLU A 71 FE FE A 201 1555 1555 2.10 LINK OE2 GLU A 128 FE FE A 200 1555 1555 2.17 LINK OE1 GLU A 128 FE FE A 200 1555 1555 2.28 LINK OE2BGLU A 131 FE FE A 201 1555 1555 2.28 LINK OE1 GLU A 162 FE FE A 200 1555 1555 2.03 LINK OE2 GLU A 162 FE FE A 201 1555 1555 2.11 LINK ND1 HIS A 165 FE FE A 200 1555 1555 2.19 LINK O HOH A 183 FE FE A 200 1555 1555 2.19 LINK O HOH A 183 FE FE A 201 1555 1555 2.03 LINK FE FE A 200 N3 AZI A 300 1555 1555 2.15 LINK FE FE A 201 O HOH A 204 1555 1555 1.94 LINK FE FE A 201 N3 AZI A 300 1555 1555 2.01 LINK FE FE A 201 N2 AZI A 300 1555 1555 2.70 LINK OE1AGLU B 37 FE FE B 200 1555 1555 1.97 LINK OE1BGLU B 37 FE FE B 200 1555 1555 2.27 LINK OE1 GLU B 40 FE FE B 200 1555 1555 2.12 LINK OE1 GLU B 71 FE FE B 200 1555 1555 2.07 LINK OE2 GLU B 71 FE FE B 201 1555 1555 2.03 LINK OE2 GLU B 128 FE FE B 201 1555 1555 2.20 LINK OE1 GLU B 128 FE FE B 201 1555 1555 2.27 LINK OE1BGLU B 131 FE FE B 200 1555 1555 2.23 LINK OE2 GLU B 162 FE FE B 200 1555 1555 2.10 LINK OE1 GLU B 162 FE FE B 201 1555 1555 2.04 LINK ND1 HIS B 165 FE FE B 201 1555 1555 2.20 LINK O HOH B 181 FE FE B 200 1555 1555 2.00 LINK O HOH B 181 FE FE B 201 1555 1555 2.19 LINK O HOH B 198 FE FE B 200 1555 1555 1.98 LINK FE FE B 200 N1 AZI B 300 1555 1555 2.08 LINK FE FE B 200 N2 AZI B 300 1555 1555 2.73 LINK FE FE B 201 N1 AZI B 300 1555 1555 2.15 SITE 1 AC1 7 GLU A 71 GLU A 128 GLU A 162 HIS A 165 SITE 2 AC1 7 HOH A 183 FE A 201 AZI A 300 SITE 1 AC2 9 GLU A 37 GLU A 40 GLU A 71 GLU A 131 SITE 2 AC2 9 GLU A 162 HOH A 183 FE A 200 HOH A 204 SITE 3 AC2 9 AZI A 300 SITE 1 AC3 10 GLU A 40 GLU A 71 VAL A 127 GLU A 128 SITE 2 AC3 10 GLU A 131 GLU A 162 HOH A 183 FE A 200 SITE 3 AC3 10 FE A 201 HOH A 204 SITE 1 AC4 9 GLU B 37 GLU B 40 GLU B 71 GLU B 131 SITE 2 AC4 9 GLU B 162 HOH B 181 HOH B 198 FE B 201 SITE 3 AC4 9 AZI B 300 SITE 1 AC5 7 GLU B 71 GLU B 128 GLU B 162 HIS B 165 SITE 2 AC5 7 HOH B 181 FE B 200 AZI B 300 SITE 1 AC6 10 GLU B 40 GLU B 71 VAL B 127 GLU B 128 SITE 2 AC6 10 GLU B 131 GLU B 162 HOH B 181 HOH B 198 SITE 3 AC6 10 FE B 200 FE B 201 CRYST1 82.009 82.009 46.440 90.00 90.00 120.00 P 32 6 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 0.012194 0.007040 0.000000 0.00000 SCALE2 0.000000 0.014080 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021533 0.00000