10 20 30 40 50 60 70 80 3BND - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE 14-DEC-07 3BND
TITLE LIPOXYGENASE-1 (SOYBEAN), I553V MUTANT
COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEED LIPOXYGENASE-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: L-1; COMPND 5 EC: 1.13.11.12; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GLYCINE MAX; SOURCE 3 ORGANISM_COMMON: SOYBEAN; SOURCE 4 ORGANISM_TAXID: 3847; SOURCE 5 GENE: LOX1.1, LOX1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PT-7/L-1
KEYWDS DIOXYGENASE, LIPOXYGENASE, METALLOPROTEIN, FATTY ACIDS, FATTY ACID KEYWDS 2 BIOSYNTHESIS, IRON, LIPID SYNTHESIS, METAL-BINDING, OXIDOREDUCTASE, KEYWDS 3 OXYLIPIN BIOSYNTHESIS, ---
EXPDTA X-RAY DIFFRACTION
AUTHOR D.R.TOMCHICK
REVDAT 3 13-JUL-11 3BND 1 VERSN REVDAT 2 24-FEB-09 3BND 1 VERSN REVDAT 1 01-APR-08 3BND 0
JRNL AUTH M.P.MEYER,D.R.TOMCHICK,J.P.KLINMAN JRNL TITL ENZYME STRUCTURE AND DYNAMICS AFFECT HYDROGEN TUNNELING: THE JRNL TITL 2 IMPACT OF A REMOTE SIDE CHAIN (I553) IN SOYBEAN JRNL TITL 3 LIPOXYGENASE-1. JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 1146 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 18216254 JRNL DOI 10.1073/PNAS.0710643105
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.J.KNAPP,J.P.KLINMAN REMARK 1 TITL KINETIC STUDIES OF OXYGEN REACTIVITY IN SOYBEAN REMARK 1 TITL 2 LIPOXYGENASE-1. REMARK 1 REF BIOCHEMISTRY V. 42 11466 2003 REMARK 1 REFN ISSN 0006-2960
REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0066 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 107395 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3349 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7668 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2330 REMARK 3 BIN FREE R VALUE SET COUNT : 250 REMARK 3 BIN FREE R VALUE : 0.2640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6507 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 641 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.09000 REMARK 3 B22 (A**2) : -0.63000 REMARK 3 B33 (A**2) : 0.71000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.37000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.083 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.084 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.255 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6795 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9257 ; 1.502 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 841 ; 5.695 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 307 ;31.885 ;24.202 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1155 ;11.919 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;15.823 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1019 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5204 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3259 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4743 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 520 ; 0.122 ; 0.200 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): 37 ; 0.206 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.087 ; 0.200 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): 4165 ; 0.845 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6778 ; 1.460 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2630 ; 2.390 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2479 ; 3.885 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7 A 164 REMARK 3 ORIGIN FOR THE GROUP (A): 59.2647 41.8789 9.4838 REMARK 3 T TENSOR REMARK 3 T11: -0.0569 T22: 0.0632 REMARK 3 T33: 0.4553 T12: 0.0264 REMARK 3 T13: 0.1224 T23: 0.0662 REMARK 3 L TENSOR REMARK 3 L11: 2.6619 L22: 2.5011 REMARK 3 L33: 1.3017 L12: -0.0658 REMARK 3 L13: -0.1045 L23: -0.4273 REMARK 3 S TENSOR REMARK 3 S11: 0.0441 S12: 0.0798 S13: -0.2650 REMARK 3 S21: -0.3152 S22: -0.1609 S23: -0.8268 REMARK 3 S31: 0.0651 S32: 0.2423 S33: 0.1169 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 165 A 312 REMARK 3 ORIGIN FOR THE GROUP (A): 27.3309 57.7135 13.9575 REMARK 3 T TENSOR REMARK 3 T11: -0.0450 T22: -0.0377 REMARK 3 T33: -0.0316 T12: -0.0126 REMARK 3 T13: 0.0105 T23: 0.0014 REMARK 3 L TENSOR REMARK 3 L11: 1.2127 L22: 0.3855 REMARK 3 L33: 0.5664 L12: 0.1190 REMARK 3 L13: 0.4189 L23: -0.0778 REMARK 3 S TENSOR REMARK 3 S11: 0.0145 S12: -0.0524 S13: 0.2105 REMARK 3 S21: -0.0290 S22: -0.0684 S23: -0.1729 REMARK 3 S31: -0.1443 S32: 0.0589 S33: 0.0538 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 313 A 389 REMARK 3 ORIGIN FOR THE GROUP (A): 5.9152 42.6613 9.4616 REMARK 3 T TENSOR REMARK 3 T11: 0.0348 T22: 0.0233 REMARK 3 T33: -0.0472 T12: 0.0058 REMARK 3 T13: -0.0133 T23: -0.0068 REMARK 3 L TENSOR REMARK 3 L11: 1.0861 L22: 1.0749 REMARK 3 L33: 0.4698 L12: 0.1948 REMARK 3 L13: -0.1733 L23: 0.0125 REMARK 3 S TENSOR REMARK 3 S11: 0.0094 S12: 0.0023 S13: -0.0044 REMARK 3 S21: -0.0001 S22: -0.0376 S23: -0.0319 REMARK 3 S31: 0.0269 S32: -0.0817 S33: 0.0282 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 390 A 475 REMARK 3 ORIGIN FOR THE GROUP (A): -2.3698 40.2161 18.3331 REMARK 3 T TENSOR REMARK 3 T11: 0.0646 T22: 0.0685 REMARK 3 T33: -0.0321 T12: -0.0086 REMARK 3 T13: 0.0149 T23: -0.0055 REMARK 3 L TENSOR REMARK 3 L11: 1.2539 L22: 1.9184 REMARK 3 L33: 1.0665 L12: 0.4982 REMARK 3 L13: -0.1063 L23: 0.1852 REMARK 3 S TENSOR REMARK 3 S11: 0.0473 S12: -0.1079 S13: 0.0420 REMARK 3 S21: 0.1207 S22: -0.0948 S23: 0.1767 REMARK 3 S31: -0.0558 S32: -0.1167 S33: 0.0475 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 476 A 666 REMARK 3 ORIGIN FOR THE GROUP (A): 24.9001 36.0062 19.1517 REMARK 3 T TENSOR REMARK 3 T11: 0.0292 T22: 0.0567 REMARK 3 T33: 0.0453 T12: -0.0002 REMARK 3 T13: -0.0169 T23: 0.0740 REMARK 3 L TENSOR REMARK 3 L11: 1.2966 L22: 0.6685 REMARK 3 L33: 0.3444 L12: 0.2016 REMARK 3 L13: -0.0585 L23: -0.0883 REMARK 3 S TENSOR REMARK 3 S11: 0.0474 S12: -0.2306 S13: -0.2486 REMARK 3 S21: 0.0473 S22: -0.1019 S23: -0.2345 REMARK 3 S31: 0.0389 S32: 0.0516 S33: 0.0545 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 667 A 839 REMARK 3 ORIGIN FOR THE GROUP (A): 19.0480 38.7340 6.1092 REMARK 3 T TENSOR REMARK 3 T11: 0.0257 T22: -0.0045 REMARK 3 T33: -0.0191 T12: 0.0018 REMARK 3 T13: 0.0237 T23: 0.0141 REMARK 3 L TENSOR REMARK 3 L11: 1.1853 L22: 1.0860 REMARK 3 L33: 0.6341 L12: 0.1772 REMARK 3 L13: -0.0643 L23: -0.2323 REMARK 3 S TENSOR REMARK 3 S11: -0.0099 S12: 0.0170 S13: -0.1585 REMARK 3 S21: -0.0767 S22: -0.0432 S23: -0.1890 REMARK 3 S31: 0.0449 S32: 0.0003 S33: 0.0532 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 3BND COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JAN-08. REMARK 100 THE RCSB ID CODE IS RCSB045729.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-04 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 : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97921 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-3 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 110778 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 27.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.63300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1F8N REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, SODIUM ACETATE, PH 5.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 46.50200 REMARK 290 SMTRY3 2 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 1 REMARK 465 PHE A 2 REMARK 465 SER A 3 REMARK 465 ALA A 4 REMARK 465 GLY A 5 REMARK 465 HIS A 6 REMARK 465 GLU A 19 REMARK 465 LEU A 20 REMARK 465 GLU A 21 REMARK 465 VAL A 22 REMARK 465 ASN A 23 REMARK 465 PRO A 24 REMARK 465 ASP A 25 REMARK 465 GLY A 26 REMARK 465 SER A 27 REMARK 465 ALA A 28 REMARK 465 VAL A 29 REMARK 465 ASP A 30 REMARK 465 ILE A 117 REMARK 465 SER A 118 REMARK 465 ASN A 119 REMARK 465 GLN A 120
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 SER A 90 CB SER A 90 OG 0.108 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 309 C - N - CA ANGL. DEV. = -9.8 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 LEU A 36 -158.39 -91.00 REMARK 500 LEU A 74 -75.78 -142.50 REMARK 500 TRP A 87 86.81 -165.98 REMARK 500 MET A 91 7.33 -63.97 REMARK 500 GLU A 294 -95.81 -109.30 REMARK 500 VAL A 312 -57.29 73.25 REMARK 500 GLN A 322 -64.37 -124.32 REMARK 500 ALA A 352 16.92 -143.77 REMARK 500 LEU A 390 41.83 -106.21 REMARK 500 HIS A 499 -71.74 -97.68 REMARK 500 THR A 503 -80.13 -112.25 REMARK 500 SER A 560 -134.44 58.35 REMARK 500 ASP A 607 68.05 -102.56 REMARK 500 SER A 687 -86.72 -105.45 REMARK 500 ASN A 729 72.62 -150.81 REMARK 500 THR A 739 130.05 -39.60 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 HOH A1508 DISTANCE = 5.21 ANGSTROMS
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 840 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 499 NE2 REMARK 620 2 HIS A 504 NE2 92.0 REMARK 620 3 HIS A 690 NE2 99.7 98.3 REMARK 620 4 ASN A 694 OD1 81.8 169.7 90.9 REMARK 620 5 ILE A 839 OXT 171.7 92.2 86.8 92.9 REMARK 620 6 HOH A 841 O 86.9 91.9 167.6 79.6 85.8 REMARK 620 N 1 2 3 4 5
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 840
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F8N RELATED DB: PDB REMARK 900 WILD TYPE PROTEIN REMARK 900 RELATED ID: 3BNB RELATED DB: PDB REMARK 900 I553L MUTANT REMARK 900 RELATED ID: 3BNC RELATED DB: PDB REMARK 900 I553G MUTANT REMARK 900 RELATED ID: 3BNE RELATED DB: PDB REMARK 900 I553V MUTANT
DBREF 3BND A 1 839 UNP P08170 LOX1_SOYBN 1 839
SEQADV 3BND GLU A 160 UNP P08170 SER 160 ENGINEERED SEQADV 3BND VAL A 553 UNP P08170 ILE 553 ENGINEERED
SEQRES 1 A 839 MET PHE SER ALA GLY HIS LYS ILE LYS GLY THR VAL VAL SEQRES 2 A 839 LEU MET PRO LYS ASN GLU LEU GLU VAL ASN PRO ASP GLY SEQRES 3 A 839 SER ALA VAL ASP ASN LEU ASN ALA PHE LEU GLY ARG SER SEQRES 4 A 839 VAL SER LEU GLN LEU ILE SER ALA THR LYS ALA ASP ALA SEQRES 5 A 839 HIS GLY LYS GLY LYS VAL GLY LYS ASP THR PHE LEU GLU SEQRES 6 A 839 GLY ILE ASN THR SER LEU PRO THR LEU GLY ALA GLY GLU SEQRES 7 A 839 SER ALA PHE ASN ILE HIS PHE GLU TRP ASP GLY SER MET SEQRES 8 A 839 GLY ILE PRO GLY ALA PHE TYR ILE LYS ASN TYR MET GLN SEQRES 9 A 839 VAL GLU PHE PHE LEU LYS SER LEU THR LEU GLU ALA ILE SEQRES 10 A 839 SER ASN GLN GLY THR ILE ARG PHE VAL CYS ASN SER TRP SEQRES 11 A 839 VAL TYR ASN THR LYS LEU TYR LYS SER VAL ARG ILE PHE SEQRES 12 A 839 PHE ALA ASN HIS THR TYR VAL PRO SER GLU THR PRO ALA SEQRES 13 A 839 PRO LEU VAL GLU TYR ARG GLU GLU GLU LEU LYS SER LEU SEQRES 14 A 839 ARG GLY ASN GLY THR GLY GLU ARG LYS GLU TYR ASP ARG SEQRES 15 A 839 ILE TYR ASP TYR ASP VAL TYR ASN ASP LEU GLY ASN PRO SEQRES 16 A 839 ASP LYS SER GLU LYS LEU ALA ARG PRO VAL LEU GLY GLY SEQRES 17 A 839 SER SER THR PHE PRO TYR PRO ARG ARG GLY ARG THR GLY SEQRES 18 A 839 ARG GLY PRO THR VAL THR ASP PRO ASN THR GLU LYS GLN SEQRES 19 A 839 GLY GLU VAL PHE TYR VAL PRO ARG ASP GLU ASN LEU GLY SEQRES 20 A 839 HIS LEU LYS SER LYS ASP ALA LEU GLU ILE GLY THR LYS SEQRES 21 A 839 SER LEU SER GLN ILE VAL GLN PRO ALA PHE GLU SER ALA SEQRES 22 A 839 PHE ASP LEU LYS SER THR PRO ILE GLU PHE HIS SER PHE SEQRES 23 A 839 GLN ASP VAL HIS ASP LEU TYR GLU GLY GLY ILE LYS LEU SEQRES 24 A 839 PRO ARG ASP VAL ILE SER THR ILE ILE PRO LEU PRO VAL SEQRES 25 A 839 ILE LYS GLU LEU TYR ARG THR ASP GLY GLN HIS ILE LEU SEQRES 26 A 839 LYS PHE PRO GLN PRO HIS VAL VAL GLN VAL SER GLN SER SEQRES 27 A 839 ALA TRP MET THR ASP GLU GLU PHE ALA ARG GLU MET ILE SEQRES 28 A 839 ALA GLY VAL ASN PRO CYS VAL ILE ARG GLY LEU GLU GLU SEQRES 29 A 839 PHE PRO PRO LYS SER ASN LEU ASP PRO ALA ILE TYR GLY SEQRES 30 A 839 ASP GLN SER SER LYS ILE THR ALA ASP SER LEU ASP LEU SEQRES 31 A 839 ASP GLY TYR THR MET ASP GLU ALA LEU GLY SER ARG ARG SEQRES 32 A 839 LEU PHE MET LEU ASP TYR HIS ASP ILE PHE MET PRO TYR SEQRES 33 A 839 VAL ARG GLN ILE ASN GLN LEU ASN SER ALA LYS THR TYR SEQRES 34 A 839 ALA THR ARG THR ILE LEU PHE LEU ARG GLU ASP GLY THR SEQRES 35 A 839 LEU LYS PRO VAL ALA ILE GLU LEU SER LEU PRO HIS SER SEQRES 36 A 839 ALA GLY ASP LEU SER ALA ALA VAL SER GLN VAL VAL LEU SEQRES 37 A 839 PRO ALA LYS GLU GLY VAL GLU SER THR ILE TRP LEU LEU SEQRES 38 A 839 ALA LYS ALA TYR VAL ILE VAL ASN ASP SER CYS TYR HIS SEQRES 39 A 839 GLN LEU MET SER HIS TRP LEU ASN THR HIS ALA ALA MET SEQRES 40 A 839 GLU PRO PHE VAL ILE ALA THR HIS ARG HIS LEU SER VAL SEQRES 41 A 839 LEU HIS PRO ILE TYR LYS LEU LEU THR PRO HIS TYR ARG SEQRES 42 A 839 ASN ASN MET ASN ILE ASN ALA LEU ALA ARG GLN SER LEU SEQRES 43 A 839 ILE ASN ALA ASN GLY ILE VAL GLU THR THR PHE LEU PRO SEQRES 44 A 839 SER LYS TYR SER VAL GLU MET SER SER ALA VAL TYR LYS SEQRES 45 A 839 ASN TRP VAL PHE THR ASP GLN ALA LEU PRO ALA ASP LEU SEQRES 46 A 839 ILE LYS ARG GLY VAL ALA ILE LYS ASP PRO SER THR PRO SEQRES 47 A 839 HIS GLY VAL ARG LEU LEU ILE GLU ASP TYR PRO TYR ALA SEQRES 48 A 839 ALA ASP GLY LEU GLU ILE TRP ALA ALA ILE LYS THR TRP SEQRES 49 A 839 VAL GLN GLU TYR VAL PRO LEU TYR TYR ALA ARG ASP ASP SEQRES 50 A 839 ASP VAL LYS ASN ASP SER GLU LEU GLN HIS TRP TRP LYS SEQRES 51 A 839 GLU ALA VAL GLU LYS GLY HIS GLY ASP LEU LYS ASP LYS SEQRES 52 A 839 PRO TRP TRP PRO LYS LEU GLN THR LEU GLU ASP LEU VAL SEQRES 53 A 839 GLU VAL CYS LEU ILE ILE ILE TRP ILE ALA SER ALA LEU SEQRES 54 A 839 HIS ALA ALA VAL ASN PHE GLY GLN TYR PRO TYR GLY GLY SEQRES 55 A 839 LEU ILE MET ASN ARG PRO THR ALA SER ARG ARG LEU LEU SEQRES 56 A 839 PRO GLU LYS GLY THR PRO GLU TYR GLU GLU MET ILE ASN SEQRES 57 A 839 ASN HIS GLU LYS ALA TYR LEU ARG THR ILE THR SER LYS SEQRES 58 A 839 LEU PRO THR LEU ILE SER LEU SER VAL ILE GLU ILE LEU SEQRES 59 A 839 SER THR HIS ALA SER ASP GLU VAL TYR LEU GLY GLN ARG SEQRES 60 A 839 ASP ASN PRO HIS TRP THR SER ASP SER LYS ALA LEU GLN SEQRES 61 A 839 ALA PHE GLN LYS PHE GLY ASN LYS LEU LYS GLU ILE GLU SEQRES 62 A 839 GLU LYS LEU VAL ARG ARG ASN ASN ASP PRO SER LEU GLN SEQRES 63 A 839 GLY ASN ARG LEU GLY PRO VAL GLN LEU PRO TYR THR LEU SEQRES 64 A 839 LEU TYR PRO SER SER GLU GLU GLY LEU THR PHE ARG GLY SEQRES 65 A 839 ILE PRO ASN SER ILE SER ILE
HET FE A 840 1
HETNAM FE FE (III) ION
FORMUL 2 FE FE 3+ FORMUL 3 HOH *641(H2 O)
HELIX 1 1 ASN A 31 LEU A 36 5 6 HELIX 2 2 ASP A 88 GLY A 92 5 5 HELIX 3 3 ASN A 133 TYR A 137 5 5 HELIX 4 4 VAL A 150 THR A 154 5 5 HELIX 5 5 PRO A 155 PRO A 157 5 3 HELIX 6 6 LEU A 158 GLY A 171 1 14 HELIX 7 7 SER A 198 ALA A 202 5 5 HELIX 8 8 PRO A 241 ASN A 245 5 5 HELIX 9 9 LYS A 250 ALA A 254 5 5 HELIX 10 10 LEU A 255 ILE A 265 1 11 HELIX 11 11 ILE A 265 LEU A 276 1 12 HELIX 12 12 SER A 285 ASP A 291 1 7 HELIX 13 13 LEU A 292 GLU A 294 5 3 HELIX 14 14 PRO A 300 ILE A 308 1 9 HELIX 15 15 VAL A 312 LEU A 316 5 5 HELIX 16 16 PRO A 330 GLN A 334 5 5 HELIX 17 17 SER A 338 MET A 341 5 4 HELIX 18 18 THR A 342 GLY A 353 1 12 HELIX 19 19 ASP A 372 GLY A 377 1 6 HELIX 20 20 THR A 384 LEU A 388 5 5 HELIX 21 21 THR A 394 SER A 401 1 8 HELIX 22 22 TYR A 409 GLN A 422 1 14 HELIX 23 23 GLU A 472 MET A 497 1 26 HELIX 24 24 THR A 503 LEU A 518 1 16 HELIX 25 25 HIS A 522 THR A 529 1 8 HELIX 26 26 PRO A 530 ARG A 533 5 4 HELIX 27 27 ASN A 534 LEU A 546 1 13 HELIX 28 28 GLY A 551 PHE A 557 1 7 HELIX 29 29 PRO A 559 LYS A 561 5 3 HELIX 30 30 TYR A 562 LYS A 572 1 11 HELIX 31 31 ASN A 573 TRP A 574 5 2 HELIX 32 32 VAL A 575 GLN A 579 5 5 HELIX 33 33 ALA A 580 ARG A 588 1 9 HELIX 34 34 TYR A 608 TYR A 633 1 26 HELIX 35 35 ARG A 635 ASN A 641 1 7 HELIX 36 36 ASP A 642 LYS A 655 1 14 HELIX 37 37 HIS A 657 LYS A 661 5 5 HELIX 38 38 THR A 671 SER A 687 1 17 HELIX 39 39 SER A 687 PHE A 695 1 9 HELIX 40 40 GLY A 696 GLY A 702 1 7 HELIX 41 41 THR A 720 ASN A 729 1 10 HELIX 42 42 ASN A 729 ILE A 738 1 10 HELIX 43 43 SER A 740 SER A 755 1 16 HELIX 44 44 ASP A 775 ASN A 801 1 27 HELIX 45 45 ASP A 802 SER A 804 5 3 HELIX 46 46 LEU A 805 LEU A 810 1 6
SHEET 1 A 5 GLY A 66 ASN A 68 0 SHEET 2 A 5 SER A 79 PHE A 85 -1 O ASN A 82 N GLY A 66 SHEET 3 A 5 ILE A 8 PRO A 16 -1 N GLY A 10 O ILE A 83 SHEET 4 A 5 PHE A 107 LEU A 114 -1 O PHE A 108 N MET A 15 SHEET 5 A 5 ILE A 123 VAL A 131 -1 O SER A 129 N LEU A 109 SHEET 1 B 3 GLY A 56 VAL A 58 0 SHEET 2 B 3 VAL A 40 ALA A 50 -1 N LYS A 49 O LYS A 57 SHEET 3 B 3 THR A 62 PHE A 63 -1 O THR A 62 N LEU A 42 SHEET 1 C 4 GLY A 56 VAL A 58 0 SHEET 2 C 4 VAL A 40 ALA A 50 -1 N LYS A 49 O LYS A 57 SHEET 3 C 4 PRO A 94 ASN A 101 -1 O GLY A 95 N ILE A 45 SHEET 4 C 4 ARG A 141 PHE A 144 -1 O PHE A 143 N PHE A 97 SHEET 1 D 2 TYR A 186 ASP A 187 0 SHEET 2 D 2 ARG A 217 GLY A 218 -1 O ARG A 217 N ASP A 187 SHEET 1 E 3 ILE A 297 LYS A 298 0 SHEET 2 E 3 ILE A 324 LYS A 326 -1 O LEU A 325 N ILE A 297 SHEET 3 E 3 ARG A 318 THR A 319 -1 N ARG A 318 O LYS A 326 SHEET 1 F 5 ARG A 360 GLY A 361 0 SHEET 2 F 5 LEU A 404 ASP A 408 -1 O MET A 406 N ARG A 360 SHEET 3 F 5 ALA A 430 LEU A 437 -1 O LEU A 435 N PHE A 405 SHEET 4 F 5 LEU A 443 SER A 451 -1 O GLU A 449 N ARG A 432 SHEET 5 F 5 GLN A 465 VAL A 467 -1 O GLN A 465 N LEU A 450 SHEET 1 G 2 ALA A 591 LYS A 593 0 SHEET 2 G 2 VAL A 601 LEU A 603 -1 O ARG A 602 N ILE A 592
LINK NE2 HIS A 499 FE FE A 840 1555 1555 2.17 LINK NE2 HIS A 504 FE FE A 840 1555 1555 2.30 LINK NE2 HIS A 690 FE FE A 840 1555 1555 2.20 LINK OD1 ASN A 694 FE FE A 840 1555 1555 2.51 LINK OXT ILE A 839 FE FE A 840 1555 1555 2.24 LINK FE FE A 840 O HOH A 841 1555 1555 2.14
CISPEP 1 PHE A 365 PRO A 366 0 0.83
SITE 1 AC1 6 HIS A 499 HIS A 504 HIS A 690 ASN A 694 SITE 2 AC1 6 ILE A 839 HOH A 841
CRYST1 94.012 93.004 49.351 90.00 90.61 90.00 P 1 21 1 2
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 0.010637 0.000000 0.000113 0.00000
SCALE2 0.000000 0.010752 0.000000 0.00000
SCALE3 0.000000 0.000000 0.020264 0.00000