HEADER OXIDOREDUCTASE 06-MAY-11 3AYG
TITLE CRYSTAL STRUCTURE OF NITRIC OXIDE REDUCTASE COMPLEX WITH HQNO
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: NITRIC OXIDE REDUCTASE;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS;
SOURCE 3 ORGANISM_TAXID: 1422;
SOURCE 4 GENE: NORZ;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3);
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B
KEYWDS OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.MATSUMOTO,T.TOSHA,A.V.PISLIAKOV,T.HINO,H.SUGIMOTI,S.NAGANO,
AUTHOR 2 Y.SUGITA,Y.SHIRO
REVDAT 4 13-MAR-24 3AYG 1 HETSYN
REVDAT 3 29-JUL-20 3AYG 1 COMPND REMARK SEQADV HETNAM
REVDAT 3 2 1 LINK SITE
REVDAT 2 12-JUN-13 3AYG 1 JRNL
REVDAT 1 25-JAN-12 3AYG 0
JRNL AUTH Y.MATSUMOTO,T.TOSHA,A.V.PISLIAKOV,T.HINO,H.SUGIMOTO,
JRNL AUTH 2 S.NAGANO,Y.SUGITA,Y.SHIRO
JRNL TITL CRYSTAL STRUCTURE OF QUINOL-DEPENDENT NITRIC OXIDE REDUCTASE
JRNL TITL 2 FROM GEOBACILLUS STEAROTHERMOPHILUS.
JRNL REF NAT.STRUCT.MOL.BIOL. V. 19 238 2012
JRNL REFN ISSN 1545-9993
JRNL PMID 22266822
JRNL DOI 10.1038/NSMB.2213
REMARK 2
REMARK 2 RESOLUTION. 2.70 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.2
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.60
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 4011837.910
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7
REMARK 3 NUMBER OF REFLECTIONS : 34516
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 SET) : 0.236
REMARK 3 FREE R VALUE : 0.267
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1732
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 6
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.60
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5282
REMARK 3 BIN R VALUE (WORKING SET) : 0.3130
REMARK 3 BIN FREE R VALUE : 0.3340
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 283
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 6078
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 257
REMARK 3 SOLVENT ATOMS : 113
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 45.70
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.00
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -14.69000
REMARK 3 B22 (A**2) : -11.83000
REMARK 3 B33 (A**2) : 26.52000
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 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.36
REMARK 3 ESD FROM SIGMAA (A) : 0.43
REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.43
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.44
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 1.400
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.10
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.850
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 1.250 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.100 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 1.710 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.620 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.30
REMARK 3 BSOL : 52.67
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 : PROTEIN_REP.PARAM
REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 3 : ION.PARAM
REMARK 3 PARAMETER FILE 4 : HEM.PARAM
REMARK 3 PARAMETER FILE 5 : PG_OCTYL_HEPES.PARAM
REMARK 3 PARAMETER FILE 6 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : WATER.TOP
REMARK 3 TOPOLOGY FILE 3 : HEM.TOP
REMARK 3 TOPOLOGY FILE 4 : PG_OCTYL.TOP
REMARK 3 TOPOLOGY FILE 5 : ION.TOP
REMARK 3 TOPOLOGY FILE 6 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
REMARK 4
REMARK 4 3AYG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-MAY-11.
REMARK 100 THE DEPOSITION ID IS D_1000029852.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 13-FEB-08
REMARK 200 TEMPERATURE (KELVIN) : 90
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SPRING-8
REMARK 200 BEAMLINE : BL41XU
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34516
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700
REMARK 200 RESOLUTION RANGE LOW (A) : 42.600
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : NULL
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.06500
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.87
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.50300
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: MAD
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
REMARK 200 SOFTWARE USED: SHARP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 64.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.42
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 5% ISOPROPANOL, 50MM HEPES, PH 7.0,
REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -X,Y,-Z+1/2
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z
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
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 75.79500
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 75.79500
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 55.25800
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 74.54450
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 55.25800
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 74.54450
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 75.79500
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 55.25800
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 74.54450
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 75.79500
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 55.25800
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 74.54450
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 4480 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 52810 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 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 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 GLU A 2
REMARK 465 VAL A 3
REMARK 465 ASN A 4
REMARK 465 ARG A 5
REMARK 465 THR A 6
REMARK 465 VAL A 7
REMARK 465 SER A 8
REMARK 465 PRO A 9
REMARK 465 ASN A 10
REMARK 465 ILE A 11
REMARK 465 GLN A 12
REMARK 465 THR A 13
REMARK 465 GLY A 14
REMARK 465 ARG A 15
REMARK 465 LYS A 16
REMARK 465 GLU A 117
REMARK 465 ARG A 118
REMARK 465 TYR A 119
REMARK 465 ASN A 120
REMARK 465 LYS A 121
REMARK 465 PRO A 122
REMARK 465 PHE A 123
REMARK 465 LEU A 778
REMARK 465 PRO A 779
REMARK 465 VAL A 780
REMARK 465 ALA A 781
REMARK 465 ASN A 782
REMARK 465 HIS A 783
REMARK 465 TRP A 784
REMARK 465 MET A 785
REMARK 465 LYS A 786
REMARK 465 ASP A 787
REMARK 465 ARG A 788
REMARK 465 LEU A 789
REMARK 465 LYS A 790
REMARK 465 ASN A 791
REMARK 465 SER A 792
REMARK 465 LEU A 793
REMARK 465 GLU A 794
REMARK 465 HIS A 795
REMARK 465 HIS A 796
REMARK 465 HIS A 797
REMARK 465 HIS A 798
REMARK 465 HIS A 799
REMARK 465 HIS A 800
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 NE ARG A 168 NE2 GLN A 208 2.09
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 NH2 ARG A 294 OD1 ASP A 334 8455 2.03
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 PRO A 333 C - N - CA ANGL. DEV. = 11.8 DEGREES
REMARK 500 ARG A 435 NE - CZ - NH1 ANGL. DEV. = -3.5 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 ASN A 19 50.05 -117.31
REMARK 500 TYR A 84 -55.35 -131.00
REMARK 500 ASP A 152 57.65 -57.21
REMARK 500 THR A 157 167.39 -47.88
REMARK 500 THR A 176 -59.82 -129.06
REMARK 500 TRP A 181 92.54 -171.84
REMARK 500 PRO A 194 164.68 -38.84
REMARK 500 ALA A 199 -84.75 -24.65
REMARK 500 SER A 204 155.50 159.04
REMARK 500 TYR A 239 87.99 -172.54
REMARK 500 LYS A 287 37.13 -99.28
REMARK 500 ARG A 295 57.39 -114.29
REMARK 500 LEU A 346 65.17 -118.05
REMARK 500 TRP A 395 0.18 -68.50
REMARK 500 TYR A 415 33.35 -76.92
REMARK 500 TYR A 430 -23.34 83.54
REMARK 500 ASP A 465 105.96 -59.38
REMARK 500 VAL A 480 -71.25 -52.19
REMARK 500 PRO A 492 -37.35 -34.20
REMARK 500 VAL A 517 -55.62 -127.01
REMARK 500 LEU A 587 41.84 -86.66
REMARK 500 LEU A 588 -63.61 -120.38
REMARK 500 HIS A 643 118.40 -33.58
REMARK 500 VAL A 659 -67.65 -101.20
REMARK 500 THR A 704 -68.87 -128.10
REMARK 500 VAL A 744 -70.34 -57.56
REMARK 500 LYS A 762 47.04 -75.27
REMARK 500 HIS A 766 33.03 -141.79
REMARK 500 PRO A 770 136.20 -38.24
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 CA A 804 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLY A 91 O
REMARK 620 2 TYR A 93 OH 88.1
REMARK 620 3 GLU A 429 OE1 78.9 164.5
REMARK 620 4 GLU A 429 OE2 90.5 141.3 48.4
REMARK 620 5 HEM A 801 O2D 105.9 72.8 118.8 70.4
REMARK 620 6 HEM A 802 O2A 170.3 100.7 91.7 85.1 80.9
REMARK 620 7 HEM A 802 O1A 132.0 88.7 93.5 119.5 118.8 45.2
REMARK 620 8 HOH A 979 O 82.7 77.9 91.8 140.2 149.1 95.1 49.9
REMARK 620 N 1 2 3 4 5 6 7
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 HEM A 801 FE
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 355 NE2
REMARK 620 2 HEM A 801 NA 102.4
REMARK 620 3 HEM A 801 NB 96.8 87.4
REMARK 620 4 HEM A 801 NC 86.1 170.6 87.6
REMARK 620 5 HEM A 801 ND 92.3 92.7 170.7 91.0
REMARK 620 6 HIS A 653 NE2 175.1 79.0 88.0 92.9 82.9
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 803 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 508 ND1
REMARK 620 2 HIS A 559 NE2 119.2
REMARK 620 3 HIS A 560 NE2 106.7 91.1
REMARK 620 4 HOH A 929 O 87.9 86.6 164.2
REMARK 620 5 HOH A 978 O 106.4 125.7 103.0 66.4
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 HEM A 802 FE
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 651 NE2
REMARK 620 2 HEM A 802 NA 89.1
REMARK 620 3 HEM A 802 NB 94.1 90.2
REMARK 620 4 HEM A 802 NC 89.8 178.7 89.1
REMARK 620 5 HEM A 802 ND 85.9 90.4 179.4 90.3
REMARK 620 6 HOH A 978 O 177.8 88.7 86.1 92.3 93.9
REMARK 620 N 1 2 3 4 5
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3AYF RELATED DB: PDB
DBREF 3AYG A 1 792 UNP B3Y963 B3Y963_GEOSE 1 792
SEQADV 3AYG LEU A 793 UNP B3Y963 EXPRESSION TAG
SEQADV 3AYG GLU A 794 UNP B3Y963 EXPRESSION TAG
SEQADV 3AYG HIS A 795 UNP B3Y963 EXPRESSION TAG
SEQADV 3AYG HIS A 796 UNP B3Y963 EXPRESSION TAG
SEQADV 3AYG HIS A 797 UNP B3Y963 EXPRESSION TAG
SEQADV 3AYG HIS A 798 UNP B3Y963 EXPRESSION TAG
SEQADV 3AYG HIS A 799 UNP B3Y963 EXPRESSION TAG
SEQADV 3AYG HIS A 800 UNP B3Y963 EXPRESSION TAG
SEQRES 1 A 800 MET GLU VAL ASN ARG THR VAL SER PRO ASN ILE GLN THR
SEQRES 2 A 800 GLY ARG LYS THR THR ASN SER PHE LEU LYS SER ILE LEU
SEQRES 3 A 800 ILE PHE THR ILE LEU ILE SER SER THR VAL LEU LEU VAL
SEQRES 4 A 800 GLY GLY TYR TRP ILE PHE LYS GLU MET ALA PRO ARG PRO
SEQRES 5 A 800 LYS GLU VAL ARG SER GLU SER GLY GLU VAL LEU MET THR
SEQRES 6 A 800 LYS GLU THR ILE ILE GLY GLY GLN ALA VAL PHE GLN LYS
SEQRES 7 A 800 TYR GLY LEU MET ASP TYR GLY THR VAL LEU GLY HIS GLY
SEQRES 8 A 800 SER TYR MET GLY PRO ASP TYR THR ALA GLU ALA LEU LYS
SEQRES 9 A 800 VAL TYR THR GLU GLY MET GLN ASP TYR LYS ALA LYS GLU
SEQRES 10 A 800 ARG TYR ASN LYS PRO PHE ALA ASP LEU THR ASP ASP GLU
SEQRES 11 A 800 LYS SER ILE ILE ARG GLU GLN VAL ILE LYS GLU MET ARG
SEQRES 12 A 800 LYS ASN ARG TYR ASN PRO VAL THR ASP VAL LEU VAL LEU
SEQRES 13 A 800 THR ASP ALA GLN VAL TYR GLY LEU GLU LYS VAL ARG ASP
SEQRES 14 A 800 TYR TYR ARG ASP VAL PHE THR ASN GLY ASP GLY TRP GLY
SEQRES 15 A 800 LEU LYS LYS GLY LEU ILE LYS GLU SER ASP MET PRO LYS
SEQRES 16 A 800 ALA ASN ARG ALA TRP VAL ALA ASP SER ASP GLN ILE GLN
SEQRES 17 A 800 GLN ILE ALA ASP PHE PHE PHE TRP THR ALA TRP LEU SER
SEQRES 18 A 800 SER THR LEU ARG ILE GLY ASP GLU ILE THR TYR THR ASN
SEQRES 19 A 800 ASN TRP PRO TYR TYR GLU ASP ALA GLY ASN THR MET SER
SEQRES 20 A 800 PHE SER ALA VAL TRP TRP SER GLY ALA SER VAL THR ILE
SEQRES 21 A 800 LEU ILE LEU PHE ILE GLY ILE ILE LEU TYR VAL PHE TYR
SEQRES 22 A 800 ARG TYR GLN LEU SER MET GLN GLU ALA TYR ALA GLU GLY
SEQRES 23 A 800 LYS PHE PRO VAL ILE ASP LEU ARG ARG GLN PRO LEU THR
SEQRES 24 A 800 PRO SER GLN VAL LYS ALA GLY LYS TYR PHE VAL VAL VAL
SEQRES 25 A 800 SER ALA LEU PHE PHE VAL GLN THR MET PHE GLY ALA LEU
SEQRES 26 A 800 LEU ALA HIS TYR TYR THR GLU PRO ASP SER PHE PHE GLY
SEQRES 27 A 800 ILE ASN TRP ILE TYR ASP ILE LEU PRO PHE ASN ILE ALA
SEQRES 28 A 800 LYS GLY TYR HIS LEU GLN LEU ALA ILE PHE TRP ILE ALA
SEQRES 29 A 800 THR ALA TRP LEU GLY MET GLY ILE PHE ILE ALA PRO LEU
SEQRES 30 A 800 VAL GLY GLY GLN GLU PRO LYS LYS GLN GLY LEU LEU VAL
SEQRES 31 A 800 ASP LEU LEU PHE TRP ALA LEU VAL VAL LEU VAL GLY GLY
SEQRES 32 A 800 SER MET ILE GLY GLN TRP LEU GLY VAL ASN GLY TYR LEU
SEQRES 33 A 800 GLY ASN GLU TRP PHE LEU LEU GLY HIS GLN GLY TRP GLU
SEQRES 34 A 800 TYR ILE GLU LEU GLY ARG ILE TRP GLN ILE ILE LEU VAL
SEQRES 35 A 800 VAL GLY MET LEU LEU TRP LEU PHE ILE VAL PHE ARG GLY
SEQRES 36 A 800 VAL LYS ARG GLY LEU LYS ARG GLU SER ASP LYS GLY GLY
SEQRES 37 A 800 LEU ILE HIS LEU LEU PHE TYR SER ALA ILE ALA VAL PRO
SEQRES 38 A 800 PHE PHE TYR ILE PHE ALA PHE PHE ILE GLN PRO ASP THR
SEQRES 39 A 800 ASN PHE THR MET ALA ASP PHE TRP ARG TRP TRP ILE ILE
SEQRES 40 A 800 HIS LEU TRP VAL GLU GLY ILE PHE GLU VAL PHE ALA VAL
SEQRES 41 A 800 VAL VAL ILE GLY PHE LEU LEU VAL GLN LEU ARG LEU VAL
SEQRES 42 A 800 THR LYS LYS SER THR VAL ARG ALA LEU TYR PHE GLN PHE
SEQRES 43 A 800 THR ILE LEU LEU GLY SER GLY VAL ILE GLY ILE GLY HIS
SEQRES 44 A 800 HIS TYR TYR TYR ASN GLY SER PRO GLU VAL TRP ILE ALA
SEQRES 45 A 800 LEU GLY ALA VAL PHE SER ALA LEU GLU VAL ILE PRO LEU
SEQRES 46 A 800 THR LEU LEU ILE LEU GLU ALA TYR GLU GLN TYR LYS MET
SEQRES 47 A 800 MET ARG ASP GLY GLY ALA ASN PHE PRO TYR LYS ALA THR
SEQRES 48 A 800 PHE TRP PHE LEU ILE SER THR ALA ILE TRP ASN LEU VAL
SEQRES 49 A 800 GLY ALA GLY VAL PHE GLY PHE LEU ILE ASN LEU PRO ALA
SEQRES 50 A 800 VAL SER TYR PHE GLU HIS GLY GLN PHE LEU THR PRO ALA
SEQRES 51 A 800 HIS GLY HIS ALA ALA MET MET GLY VAL TYR GLY MET PHE
SEQRES 52 A 800 ALA ILE ALA VAL LEU LEU TYR SER LEU ARG ASN ILE VAL
SEQRES 53 A 800 LYS PRO GLU ALA TRP ASN ASP LYS TRP LEU LYS PHE SER
SEQRES 54 A 800 CYS TRP MET LEU ASN ILE GLY LEU ALA GLY MET VAL VAL
SEQRES 55 A 800 ILE THR LEU LEU PRO VAL GLY ILE LEU GLN MET LYS GLU
SEQRES 56 A 800 ALA PHE ILE HIS GLY TYR TRP ALA SER ARG SER PRO SER
SEQRES 57 A 800 PHE LEU GLN GLN ASP VAL VAL GLN ASN LEU LEU LEU VAL
SEQRES 58 A 800 ARG ALA VAL PRO ASP THR ILE PHE LEU ILE GLY VAL VAL
SEQRES 59 A 800 ALA LEU LEU VAL PHE ALA ILE LYS ALA LEU PHE HIS LEU
SEQRES 60 A 800 ARG LYS PRO THR HIS GLY GLU GLY GLU GLU LEU PRO VAL
SEQRES 61 A 800 ALA ASN HIS TRP MET LYS ASP ARG LEU LYS ASN SER LEU
SEQRES 62 A 800 GLU HIS HIS HIS HIS HIS HIS
HET HEM A 801 43
HET HEM A 802 43
HET ZN A 803 1
HET CA A 804 1
HET BOG A 805 20
HET BOG A 806 20
HET BOG A 807 20
HET LOP A 809 45
HET LOP A 810 45
HET HQO A 811 19
HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE
HETNAM ZN ZINC ION
HETNAM CA CALCIUM ION
HETNAM BOG OCTYL BETA-D-GLUCOPYRANOSIDE
HETNAM LOP (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-
HETNAM 2 LOP [(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
HETNAM HQO 2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE
HETSYN HEM HEME
HETSYN BOG BETA-OCTYLGLUCOSIDE; OCTYL BETA-D-GLUCOSIDE; OCTYL D-
HETSYN 2 BOG GLUCOSIDE; OCTYL GLUCOSIDE
HETSYN LOP LAURYL OLEYL PHOSPHATIDYL ETHANOLAMINE
HETSYN HQO 2-HEPTYL-1-OXY-QUINOLIN-4-OL
FORMUL 2 HEM 2(C34 H32 FE N4 O4)
FORMUL 4 ZN ZN 2+
FORMUL 5 CA CA 2+
FORMUL 6 BOG 3(C14 H28 O6)
FORMUL 9 LOP 2(C35 H68 N O8 P)
FORMUL 11 HQO C16 H21 N O2
FORMUL 12 HOH *113(H2 O)
HELIX 1 1 ASN A 19 MET A 48 1 30
HELIX 2 2 THR A 65 TYR A 79 1 15
HELIX 3 3 GLY A 80 TYR A 84 5 5
HELIX 4 4 ASP A 97 ALA A 115 1 19
HELIX 5 5 THR A 127 ARG A 143 1 17
HELIX 6 6 THR A 157 GLY A 178 1 22
HELIX 7 7 LYS A 189 MET A 193 5 5
HELIX 8 8 ASP A 205 THR A 223 1 19
HELIX 9 9 TYR A 239 GLY A 243 5 5
HELIX 10 10 SER A 247 TYR A 275 1 29
HELIX 11 11 ASP A 292 GLN A 296 5 5
HELIX 12 12 THR A 299 TYR A 330 1 32
HELIX 13 13 ASN A 340 LEU A 346 1 7
HELIX 14 14 PRO A 347 GLY A 380 1 34
HELIX 15 15 LYS A 385 GLY A 414 1 30
HELIX 16 16 GLU A 419 GLY A 424 1 6
HELIX 17 17 GLY A 434 GLU A 463 1 30
HELIX 18 18 GLY A 468 ILE A 485 1 18
HELIX 19 19 PHE A 486 ILE A 490 5 5
HELIX 20 20 ASN A 495 HIS A 508 1 14
HELIX 21 21 TRP A 510 VAL A 517 1 8
HELIX 22 22 VAL A 517 LEU A 530 1 14
HELIX 23 23 THR A 534 ILE A 557 1 24
HELIX 24 24 GLY A 558 TYR A 562 5 5
HELIX 25 25 GLU A 568 LEU A 580 1 13
HELIX 26 26 GLU A 581 LEU A 587 1 7
HELIX 27 27 LEU A 588 GLY A 602 1 15
HELIX 28 28 TYR A 608 GLY A 625 1 18
HELIX 29 29 GLY A 627 ILE A 633 1 7
HELIX 30 30 LEU A 635 HIS A 643 1 9
HELIX 31 31 PHE A 646 VAL A 676 1 31
HELIX 32 32 LYS A 677 TRP A 681 5 5
HELIX 33 33 ASP A 683 THR A 704 1 22
HELIX 34 34 THR A 704 GLY A 720 1 17
HELIX 35 35 GLY A 720 ARG A 725 1 6
HELIX 36 36 SER A 726 GLN A 732 1 7
HELIX 37 37 GLN A 732 VAL A 741 1 10
HELIX 38 38 ARG A 742 LYS A 762 1 21
HELIX 39 39 ALA A 763 LEU A 767 5 5
SHEET 1 A 4 VAL A 62 MET A 64 0
SHEET 2 A 4 GLU A 54 ARG A 56 -1 N VAL A 55 O MET A 64
SHEET 3 A 4 VAL A 153 VAL A 155 1 O LEU A 154 N ARG A 56
SHEET 4 A 4 TYR A 147 ASN A 148 -1 N ASN A 148 O VAL A 153
SHEET 1 B 2 THR A 86 VAL A 87 0
SHEET 2 B 2 HIS A 90 GLY A 91 -1 O HIS A 90 N VAL A 87
LINK O GLY A 91 CA CA A 804 1555 1555 2.46
LINK OH TYR A 93 CA CA A 804 1555 1555 2.69
LINK NE2 HIS A 355 FE HEM A 801 1555 1555 2.01
LINK OE1 GLU A 429 CA CA A 804 1555 1555 2.68
LINK OE2 GLU A 429 CA CA A 804 1555 1555 2.69
LINK ND1 HIS A 508 ZN ZN A 803 1555 1555 2.19
LINK NE2 HIS A 559 ZN ZN A 803 1555 1555 2.19
LINK NE2 HIS A 560 ZN ZN A 803 1555 1555 2.25
LINK NE2 HIS A 651 FE HEM A 802 1555 1555 2.19
LINK NE2 HIS A 653 FE HEM A 801 1555 1555 2.28
LINK O2D HEM A 801 CA CA A 804 1555 1555 2.78
LINK O2A HEM A 802 CA CA A 804 1555 1555 2.60
LINK O1A HEM A 802 CA CA A 804 1555 1555 3.09
LINK FE HEM A 802 O HOH A 978 1555 1555 2.74
LINK ZN ZN A 803 O HOH A 929 1555 1555 2.63
LINK ZN ZN A 803 O HOH A 978 1555 1555 2.12
LINK CA CA A 804 O HOH A 979 1555 1555 2.50
CISPEP 1 TRP A 236 PRO A 237 0 0.04
CRYST1 110.516 149.089 151.590 90.00 90.00 90.00 C 2 2 21 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 0.009048 0.000000 0.000000 0.00000
SCALE2 0.000000 0.006707 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006597 0.00000