HEADER OXIDOREDUCTASE 15-JAN-03 1NO3 TITLE REFINED STRUCTURE OF SOYBEAN LIPOXYGENASE-3 WITH 4-NITROCATECHOL AT TITLE 2 2.15 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPOXYGENASE-3; COMPND 3 CHAIN: A; COMPND 4 EC: 1.13.11.12 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GLYCINE MAX; SOURCE 3 ORGANISM_COMMON: SOYBEAN; SOURCE 4 ORGANISM_TAXID: 3847; SOURCE 5 STRAIN: RESNICK CULTIVAR KEYWDS LIPOXYGENASE, 4-NITROCATECHOL, IRON, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR E.SKRZYPCZAK-JANKUN,O.Y.BORBULEVYCH,J.JANKUN REVDAT 6 16-AUG-23 1NO3 1 REMARK LINK REVDAT 5 11-OCT-17 1NO3 1 REMARK REVDAT 4 13-JUL-11 1NO3 1 VERSN REVDAT 3 24-FEB-09 1NO3 1 VERSN REVDAT 2 27-APR-04 1NO3 1 JRNL REVDAT 1 03-JUN-03 1NO3 0 SPRSDE 03-JUN-03 1NO3 1BYT JRNL AUTH E.SKRZYPCZAK-JANKUN,O.Y.BORBULEVYCH,J.JANKUN JRNL TITL SOYBEAN LIPOXYGENASE-3 IN COMPLEX WITH 4-NITROCATECHOL. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 60 613 2004 JRNL REFN ISSN 0907-4449 JRNL PMID 14993710 JRNL DOI 10.1107/S0907444904000861 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.PHAM,J.JANKUN,E.SKRZYPCZAK-JANKUN,R.A.FLOWERS,M.O.FUNK JR. REMARK 1 TITL STRUCTURAL AND THERMOCHEMICAL CHARACTERIZATION OF REMARK 1 TITL 2 LIPOXYGENASE-CATECHOL COMPLEXES REMARK 1 REF BIOCHEMISTRY V. 37 17952 1998 REMARK 1 REFN ISSN 0006-2960 REMARK 1 DOI 10.1021/BI981989T REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 47446 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2543 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3394 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 0.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 170 REMARK 3 BIN FREE R VALUE : 0.2870 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6799 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 494 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 34.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.91000 REMARK 3 B22 (A**2) : 0.63000 REMARK 3 B33 (A**2) : -1.36000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.97000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.259 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.200 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.144 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.532 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6998 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9502 ; 1.979 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 852 ; 7.451 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1035 ; 0.130 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5368 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2990 ; 0.161 ; 0.070 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): 637 ; 0.202 ; 0.400 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): 49 ; 0.148 ; 0.070 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.298 ; 0.400 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): 4254 ; 0.929 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6897 ; 1.652 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2744 ; 2.902 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2605 ; 4.163 ; 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): 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 : 1 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 9 A 859 REMARK 3 ORIGIN FOR THE GROUP (A): 27.5675 4.0796 15.6647 REMARK 3 T TENSOR REMARK 3 T11: 0.0146 T22: 0.0694 REMARK 3 T33: 0.0528 T12: 0.0312 REMARK 3 T13: -0.0271 T23: -0.0554 REMARK 3 L TENSOR REMARK 3 L11: 0.9880 L22: 1.5000 REMARK 3 L33: 1.5250 L12: 0.3550 REMARK 3 L13: -0.3657 L23: -0.3657 REMARK 3 S TENSOR REMARK 3 S11: 0.0003 S12: 0.0128 S13: -0.0089 REMARK 3 S21: 0.0492 S22: 0.0576 S23: 0.1227 REMARK 3 S31: -0.0064 S32: -0.1604 S33: -0.0579 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NO3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000018053. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-97 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : FOCUSSING MIRRORS REMARK 200 OPTICS : FOCUSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50343 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 1.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 1.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.34600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.140 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4 V. 4.2.1 (MOLREP) REMARK 200 STARTING MODEL: PDB ENTRY 1BYT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, CITRATE-PHOSPHATE BUFFER REMARK 280 0.05M, TRIS.HCL, 0.2% SODIUM AZIDE, PH 5.3, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 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 56.45250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 68.76550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.45250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 68.76550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1504 LIES ON A SPECIAL POSITION. 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 LEU A 2 REMARK 465 GLY A 3 REMARK 465 GLY A 4 REMARK 465 LEU A 5 REMARK 465 LEU A 6 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 TYR A 394 CE2 TYR A 394 CD2 -0.098 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 ASP A 25 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 GLY A 37 N - CA - C ANGL. DEV. = -16.1 DEGREES REMARK 500 LEU A 42 CA - CB - CG ANGL. DEV. = 14.9 DEGREES REMARK 500 ASP A 107 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 200 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 205 CB - CG - OD2 ANGL. DEV. = 7.3 DEGREES REMARK 500 ASP A 214 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 234 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 234 NE - CZ - NH2 ANGL. DEV. = -6.0 DEGREES REMARK 500 GLY A 239 C - N - CA ANGL. DEV. = -15.8 DEGREES REMARK 500 ARG A 240 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 240 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ASP A 246 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 293 CB - CG - OD2 ANGL. DEV. = 7.7 DEGREES REMARK 500 ASP A 305 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 338 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 396 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 459 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP A 592 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 607 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 607 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ASP A 787 CB - CG - OD2 ANGL. DEV. = 9.1 DEGREES REMARK 500 PHE A 848 C - N - CA ANGL. DEV. = -15.1 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 THR A 30 43.42 -68.44 REMARK 500 GLN A 38 -169.99 -119.35 REMARK 500 LEU A 40 78.91 -65.95 REMARK 500 ASP A 41 91.69 -20.93 REMARK 500 LEU A 42 91.66 -23.61 REMARK 500 VAL A 43 27.32 -75.43 REMARK 500 LEU A 47 94.61 71.33 REMARK 500 ARG A 56 58.23 -107.96 REMARK 500 VAL A 128 -62.23 -95.87 REMARK 500 ASP A 134 -155.25 -84.58 REMARK 500 ILE A 135 -45.79 -132.34 REMARK 500 PHE A 230 73.93 -118.26 REMARK 500 LEU A 294 -86.37 -127.72 REMARK 500 ASN A 295 8.00 -162.54 REMARK 500 SER A 312 -91.31 -93.98 REMARK 500 ASP A 320 -62.93 -12.20 REMARK 500 PRO A 329 -93.50 -10.99 REMARK 500 ASP A 338 -76.07 -76.89 REMARK 500 GLU A 340 -83.76 -80.86 REMARK 500 ALA A 370 10.25 -140.29 REMARK 500 ASP A 390 -138.15 -86.60 REMARK 500 SER A 391 9.31 -65.42 REMARK 500 GLN A 392 -164.49 -63.90 REMARK 500 TYR A 394 14.32 -54.79 REMARK 500 HIS A 397 -136.40 -101.51 REMARK 500 PRO A 408 -85.93 -120.40 REMARK 500 ASN A 409 -61.54 -132.64 REMARK 500 GLN A 475 67.07 -151.17 REMARK 500 SER A 479 58.70 -95.87 REMARK 500 HIS A 518 -68.53 -99.62 REMARK 500 HIS A 518 -67.89 -99.67 REMARK 500 THR A 522 -78.52 -114.75 REMARK 500 PRO A 617 -56.73 -25.77 REMARK 500 VAL A 674 -55.73 -126.97 REMARK 500 MET A 688 66.04 -116.72 REMARK 500 SER A 706 -89.33 -104.90 REMARK 500 LYS A 737 -32.31 -37.03 REMARK 500 ASN A 788 -79.28 -42.89 REMARK 500 PRO A 789 -131.13 -137.32 REMARK 500 CYS A 828 -51.82 -122.13 REMARK 500 PHE A 848 52.53 -113.94 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 234 0.07 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 FE A 858 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 518 NE2 REMARK 620 2 HIS A 523 NE2 81.9 REMARK 620 3 HIS A 709 NE2 105.9 104.7 REMARK 620 4 ILE A 857 OXT 155.7 106.6 94.1 REMARK 620 5 HOH A1533 O 75.2 126.2 128.2 81.7 REMARK 620 N 1 2 3 4 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 858 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 4NC A 859 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BYT RELATED DB: PDB REMARK 900 UNREFINED MODEL OF SOYBEAN LIPOXYGENASE-3 WITH 4-NITROCATECHOL REMARK 900 RELATED ID: 1N8Q RELATED DB: PDB REMARK 900 COMPLEX OF SOYBEAN LIPOXYGENASE-3 WITH PROTOCATECHUIC ACID DBREF 1NO3 A 1 857 UNP P09186 LOX3_SOYBN 1 857 SEQRES 1 A 857 MET LEU GLY GLY LEU LEU HIS ARG GLY HIS LYS ILE LYS SEQRES 2 A 857 GLY THR VAL VAL LEU MET ARG LYS ASN VAL LEU ASP VAL SEQRES 3 A 857 ASN SER VAL THR SER VAL GLY GLY ILE ILE GLY GLN GLY SEQRES 4 A 857 LEU ASP LEU VAL GLY SER THR LEU ASP THR LEU THR ALA SEQRES 5 A 857 PHE LEU GLY ARG SER VAL SER LEU GLN LEU ILE SER ALA SEQRES 6 A 857 THR LYS ALA ASP ALA ASN GLY LYS GLY LYS LEU GLY LYS SEQRES 7 A 857 ALA THR PHE LEU GLU GLY ILE ILE THR SER LEU PRO THR SEQRES 8 A 857 LEU GLY ALA GLY GLN SER ALA PHE LYS ILE ASN PHE GLU SEQRES 9 A 857 TRP ASP ASP GLY SER GLY ILE PRO GLY ALA PHE TYR ILE SEQRES 10 A 857 LYS ASN PHE MET GLN THR GLU PHE PHE LEU VAL SER LEU SEQRES 11 A 857 THR LEU GLU ASP ILE PRO ASN HIS GLY SER ILE HIS PHE SEQRES 12 A 857 VAL CYS ASN SER TRP ILE TYR ASN ALA LYS LEU PHE LYS SEQRES 13 A 857 SER ASP ARG ILE PHE PHE ALA ASN GLN THR TYR LEU PRO SEQRES 14 A 857 SER GLU THR PRO ALA PRO LEU VAL LYS TYR ARG GLU GLU SEQRES 15 A 857 GLU LEU HIS ASN LEU ARG GLY ASP GLY THR GLY GLU ARG SEQRES 16 A 857 LYS GLU TRP GLU ARG ILE TYR ASP TYR ASP VAL TYR ASN SEQRES 17 A 857 ASP LEU GLY ASP PRO ASP LYS GLY GLU ASN HIS ALA ARG SEQRES 18 A 857 PRO VAL LEU GLY GLY ASN ASP THR PHE PRO TYR PRO ARG SEQRES 19 A 857 ARG GLY ARG THR GLY ARG LYS PRO THR ARG LYS ASP PRO SEQRES 20 A 857 ASN SER GLU SER ARG SER ASN ASP VAL TYR LEU PRO ARG SEQRES 21 A 857 ASP GLU ALA PHE GLY HIS LEU LYS SER SER ASP PHE LEU SEQRES 22 A 857 THR TYR GLY LEU LYS SER VAL SER GLN ASN VAL LEU PRO SEQRES 23 A 857 LEU LEU GLN SER ALA PHE ASP LEU ASN PHE THR PRO ARG SEQRES 24 A 857 GLU PHE ASP SER PHE ASP GLU VAL HIS GLY LEU TYR SER SEQRES 25 A 857 GLY GLY ILE LYS LEU PRO THR ASP ILE ILE SER LYS ILE SEQRES 26 A 857 SER PRO LEU PRO VAL LEU LYS GLU ILE PHE ARG THR ASP SEQRES 27 A 857 GLY GLU GLN ALA LEU LYS PHE PRO PRO PRO LYS VAL ILE SEQRES 28 A 857 GLN VAL SER LYS SER ALA TRP MET THR ASP GLU GLU PHE SEQRES 29 A 857 ALA ARG GLU MET LEU ALA GLY VAL ASN PRO ASN LEU ILE SEQRES 30 A 857 ARG CYS LEU LYS ASP PHE PRO PRO ARG SER LYS LEU ASP SEQRES 31 A 857 SER GLN VAL TYR GLY ASP HIS THR SER GLN ILE THR LYS SEQRES 32 A 857 GLU HIS LEU GLU PRO ASN LEU GLU GLY LEU THR VAL ASP SEQRES 33 A 857 GLU ALA ILE GLN ASN LYS ARG LEU PHE LEU LEU ASP HIS SEQRES 34 A 857 HIS ASP PRO ILE MET PRO TYR LEU ARG ARG ILE ASN ALA SEQRES 35 A 857 THR SER THR LYS ALA TYR ALA THR ARG THR ILE LEU PHE SEQRES 36 A 857 LEU LYS ASN ASP GLY THR LEU ARG PRO LEU ALA ILE GLU SEQRES 37 A 857 LEU SER LEU PRO HIS PRO GLN GLY ASP GLN SER GLY ALA SEQRES 38 A 857 PHE SER GLN VAL PHE LEU PRO ALA ASP GLU GLY VAL GLU SEQRES 39 A 857 SER SER ILE TRP LEU LEU ALA LYS ALA TYR VAL VAL VAL SEQRES 40 A 857 ASN ASP SER CYS TYR HIS GLN LEU VAL SER HIS TRP LEU SEQRES 41 A 857 ASN THR HIS ALA VAL VAL GLU PRO PHE ILE ILE ALA THR SEQRES 42 A 857 ASN ARG HIS LEU SER VAL VAL HIS PRO ILE TYR LYS LEU SEQRES 43 A 857 LEU HIS PRO HIS TYR ARG ASP THR MET ASN ILE ASN GLY SEQRES 44 A 857 LEU ALA ARG LEU SER LEU VAL ASN ASP GLY GLY VAL ILE SEQRES 45 A 857 GLU GLN THR PHE LEU TRP GLY ARG TYR SER VAL GLU MET SEQRES 46 A 857 SER ALA VAL VAL TYR LYS ASP TRP VAL PHE THR ASP GLN SEQRES 47 A 857 ALA LEU PRO ALA ASP LEU ILE LYS ARG GLY MET ALA ILE SEQRES 48 A 857 GLU ASP PRO SER CYS PRO HIS GLY ILE ARG LEU VAL ILE SEQRES 49 A 857 GLU ASP TYR PRO TYR THR VAL ASP GLY LEU GLU ILE TRP SEQRES 50 A 857 ASP ALA ILE LYS THR TRP VAL HIS GLU TYR VAL PHE LEU SEQRES 51 A 857 TYR TYR LYS SER ASP ASP THR LEU ARG GLU ASP PRO GLU SEQRES 52 A 857 LEU GLN ALA CYS TRP LYS GLU LEU VAL GLU VAL GLY HIS SEQRES 53 A 857 GLY ASP LYS LYS ASN GLU PRO TRP TRP PRO LYS MET GLN SEQRES 54 A 857 THR ARG GLU GLU LEU VAL GLU ALA CYS ALA ILE ILE ILE SEQRES 55 A 857 TRP THR ALA SER ALA LEU HIS ALA ALA VAL ASN PHE GLY SEQRES 56 A 857 GLN TYR PRO TYR GLY GLY LEU ILE LEU ASN ARG PRO THR SEQRES 57 A 857 LEU SER ARG ARG PHE MET PRO GLU LYS GLY SER ALA GLU SEQRES 58 A 857 TYR GLU GLU LEU ARG LYS ASN PRO GLN LYS ALA TYR LEU SEQRES 59 A 857 LYS THR ILE THR PRO LYS PHE GLN THR LEU ILE ASP LEU SEQRES 60 A 857 SER VAL ILE GLU ILE LEU SER ARG HIS ALA SER ASP GLU SEQRES 61 A 857 VAL TYR LEU GLY GLU ARG ASP ASN PRO ASN TRP THR SER SEQRES 62 A 857 ASP THR ARG ALA LEU GLU ALA PHE LYS ARG PHE GLY ASN SEQRES 63 A 857 LYS LEU ALA GLN ILE GLU ASN LYS LEU SER GLU ARG ASN SEQRES 64 A 857 ASN ASP GLU LYS LEU ARG ASN ARG CYS GLY PRO VAL GLN SEQRES 65 A 857 MET PRO TYR THR LEU LEU LEU PRO SER SER LYS GLU GLY SEQRES 66 A 857 LEU THR PHE ARG GLY ILE PRO ASN SER ILE SER ILE HET FE A 858 1 HET 4NC A 859 11 HETNAM FE FE (III) ION HETNAM 4NC 4-NITROCATECHOL FORMUL 2 FE FE 3+ FORMUL 3 4NC C6 H5 N O4 FORMUL 4 HOH *494(H2 O) HELIX 1 1 LYS A 21 ASP A 25 1 5 HELIX 2 2 ASP A 25 THR A 30 1 6 HELIX 3 3 THR A 49 LEU A 54 5 6 HELIX 4 4 ASN A 151 PHE A 155 5 5 HELIX 5 5 LEU A 168 THR A 172 5 5 HELIX 6 6 PRO A 173 PRO A 175 5 3 HELIX 7 7 LEU A 176 GLY A 189 1 14 HELIX 8 8 ASP A 212 ALA A 220 5 9 HELIX 9 9 PRO A 259 ALA A 263 5 5 HELIX 10 10 LYS A 268 ASP A 271 5 4 HELIX 11 11 PHE A 272 ASN A 283 1 12 HELIX 12 12 ASN A 283 ASP A 293 1 11 HELIX 13 13 SER A 303 GLY A 309 1 7 HELIX 14 14 LEU A 310 SER A 312 5 3 HELIX 15 15 PRO A 318 SER A 326 1 9 HELIX 16 16 VAL A 330 PHE A 335 1 6 HELIX 17 17 PRO A 348 GLN A 352 5 5 HELIX 18 18 SER A 356 MET A 359 5 4 HELIX 19 19 THR A 360 GLY A 371 1 12 HELIX 20 20 LYS A 403 GLU A 407 5 5 HELIX 21 21 THR A 414 ASN A 421 1 8 HELIX 22 22 ILE A 433 PRO A 435 5 3 HELIX 23 23 TYR A 436 ASN A 441 1 6 HELIX 24 24 GLY A 476 GLY A 480 5 5 HELIX 25 25 GLU A 491 VAL A 516 1 26 HELIX 26 26 THR A 522 LEU A 537 1 16 HELIX 27 27 HIS A 541 HIS A 548 1 8 HELIX 28 28 PRO A 549 ARG A 552 5 4 HELIX 29 29 ASP A 553 LEU A 565 1 13 HELIX 30 30 GLY A 570 PHE A 576 1 7 HELIX 31 31 TRP A 578 ARG A 580 5 3 HELIX 32 32 TYR A 581 LYS A 591 1 11 HELIX 33 33 ASP A 592 TRP A 593 5 2 HELIX 34 34 VAL A 594 GLN A 598 5 5 HELIX 35 35 ALA A 599 ARG A 607 1 9 HELIX 36 36 TYR A 627 TYR A 652 1 26 HELIX 37 37 SER A 654 GLU A 660 1 7 HELIX 38 38 ASP A 661 VAL A 674 1 14 HELIX 39 39 HIS A 676 LYS A 680 5 5 HELIX 40 40 THR A 690 SER A 706 1 17 HELIX 41 41 SER A 706 PHE A 714 1 9 HELIX 42 42 GLY A 715 GLY A 721 1 7 HELIX 43 43 SER A 739 ASN A 748 1 10 HELIX 44 44 ASN A 748 ILE A 757 1 10 HELIX 45 45 PRO A 759 SER A 774 1 16 HELIX 46 46 ASP A 794 ASN A 820 1 27 HELIX 47 47 LEU A 824 CYS A 828 5 5 SHEET 1 A 5 GLY A 84 ILE A 86 0 SHEET 2 A 5 GLN A 96 TRP A 105 -1 O ALA A 98 N ILE A 86 SHEET 3 A 5 HIS A 10 ARG A 20 -1 O HIS A 10 N TRP A 105 SHEET 4 A 5 PHE A 125 GLU A 133 -1 O PHE A 126 N MET A 19 SHEET 5 A 5 ILE A 141 ILE A 149 -1 O ILE A 141 N LEU A 132 SHEET 1 B 6 GLY A 74 LEU A 76 0 SHEET 2 B 6 VAL A 58 ALA A 68 -1 N SER A 64 O LYS A 75 SHEET 3 B 6 THR A 80 PHE A 81 -1 N THR A 80 O LEU A 60 SHEET 4 B 6 VAL A 58 ALA A 68 -1 O LEU A 60 N THR A 80 SHEET 5 B 6 PRO A 112 ASN A 119 -1 N GLY A 113 O ILE A 63 SHEET 6 B 6 ARG A 159 PHE A 162 -1 O ARG A 159 N ILE A 117 SHEET 1 C 2 TYR A 204 ASP A 205 0 SHEET 2 C 2 ARG A 235 GLY A 236 -1 N ARG A 235 O ASP A 205 SHEET 1 D 5 ARG A 378 CYS A 379 0 SHEET 2 D 5 LEU A 424 HIS A 429 -1 N LEU A 426 O ARG A 378 SHEET 3 D 5 ALA A 449 LEU A 456 -1 O THR A 450 N HIS A 429 SHEET 4 D 5 LEU A 462 LEU A 471 -1 O ARG A 463 N PHE A 455 SHEET 5 D 5 PHE A 482 PHE A 486 -1 O PHE A 482 N LEU A 471 SHEET 1 E 2 ALA A 610 GLU A 612 0 SHEET 2 E 2 ILE A 620 LEU A 622 -1 N ARG A 621 O ILE A 611 LINK NE2AHIS A 518 FE FE A 858 1555 1555 2.44 LINK NE2 HIS A 523 FE FE A 858 1555 1555 2.16 LINK NE2 HIS A 709 FE FE A 858 1555 1555 2.16 LINK OXT ILE A 857 FE FE A 858 1555 1555 2.15 LINK FE FE A 858 O HOH A1533 1555 1555 2.06 CISPEP 1 PHE A 383 PRO A 384 0 -6.26 SITE 1 AC1 6 HIS A 518 HIS A 523 HIS A 709 ASN A 713 SITE 2 AC1 6 ILE A 857 HOH A1533 SITE 1 AC2 9 GLN A 514 HIS A 518 TRP A 519 HIS A 523 SITE 2 AC2 9 ILE A 557 LEU A 565 ILE A 572 LEU A 773 SITE 3 AC2 9 ILE A 857 CRYST1 112.905 137.531 61.880 90.00 95.48 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008857 0.000000 0.000850 0.00000 SCALE2 0.000000 0.007271 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016235 0.00000