HEADER OXIDOREDUCTASE 05-JUN-06 2IUJ TITLE CRYSTAL STRUCTURE OF SOYBEAN LIPOXYGENASE-B COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPOXYGENASE L-5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VEGETATIVE LIPOXYGENASE-B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GLYCINE MAX; SOURCE 3 ORGANISM_COMMON: SOYBEAN; SOURCE 4 ORGANISM_TAXID: 3847; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DIOXYGENASE, METAL-BINDING, OXIDOREDUCTASE, SOYBEAN LIPOXYGENASE-B, KEYWDS 2 FATTY ACID BIOSYNTHESIS, LIPID SYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR B.YOUN,G.E.SELLHORN,R.J.MIRCHEL,B.J.GAFFNEY,H.D.GRIMES,C.KANG REVDAT 5 13-DEC-23 2IUJ 1 REMARK LINK REVDAT 4 28-DEC-11 2IUJ 1 JRNL REMARK VERSN FORMUL REVDAT 3 24-FEB-09 2IUJ 1 VERSN REVDAT 2 20-DEC-06 2IUJ 1 JRNL REVDAT 1 11-OCT-06 2IUJ 0 JRNL AUTH B.YOUN,G.E.SELLHORN,R.J.MIRCHEL,B.J.GAFFNEY,H.D.GRIMES, JRNL AUTH 2 C.KANG JRNL TITL CRYSTAL STRUCTURES OF VEGETATIVE SOYBEAN LIPOXYGENASE VLX-B JRNL TITL 2 AND VLX-D, AND COMPARISONS WITH SEED ISOFORMS LOX-1 AND JRNL TITL 3 LOX-3. JRNL REF PROTEINS V. 65 1008 2006 JRNL REFN ISSN 0887-3585 JRNL PMID 17022084 JRNL DOI 10.1002/PROT.21182 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.5 REMARK 3 NUMBER OF REFLECTIONS : 41906 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) : 0.050 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6692 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 106 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 3.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2IUJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1290028947. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07812 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 480752 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1YGE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 49.99500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.96000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.65500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.96000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 49.99500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.65500 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 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 PRO A 3 REMARK 465 PHE A 4 REMARK 465 GLY A 5 REMARK 465 HIS A 6 REMARK 465 LYS A 7 REMARK 465 ASP A 32 REMARK 465 GLY A 33 REMARK 465 ILE A 34 REMARK 465 VAL A 35 REMARK 465 GLY A 36 REMARK 465 THR A 37 REMARK 465 GLY A 38 REMARK 465 LEU A 39 REMARK 465 ASP A 40 REMARK 465 PHE A 41 REMARK 465 LEU A 42 REMARK 465 GLY A 43 REMARK 465 SER A 44 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 ALA A 45 N REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 134 NE2 HIS A 134 CD2 -0.071 REMARK 500 HIS A 138 NE2 HIS A 138 CD2 -0.069 REMARK 500 HIS A 261 NE2 HIS A 261 CD2 -0.072 REMARK 500 HIS A 392 NE2 HIS A 392 CD2 -0.069 REMARK 500 HIS A 400 NE2 HIS A 400 CD2 -0.069 REMARK 500 HIS A 424 NE2 HIS A 424 CD2 -0.073 REMARK 500 HIS A 425 NE2 HIS A 425 CD2 -0.069 REMARK 500 HIS A 468 NE2 HIS A 468 CD2 -0.071 REMARK 500 HIS A 508 NE2 HIS A 508 CD2 -0.070 REMARK 500 HIS A 513 NE2 HIS A 513 CD2 -0.070 REMARK 500 HIS A 536 NE2 HIS A 536 CD2 -0.078 REMARK 500 HIS A 545 NE2 HIS A 545 CD2 -0.068 REMARK 500 HIS A 613 NE2 HIS A 613 CD2 -0.067 REMARK 500 HIS A 771 NE2 HIS A 771 CD2 -0.082 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 MET A 15 CG - SD - CE ANGL. DEV. = -11.9 DEGREES REMARK 500 GLY A 74 CA - C - N ANGL. DEV. = -13.7 DEGREES REMARK 500 TRP A 101 CD1 - CG - CD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 TRP A 101 CE2 - CD2 - CG ANGL. DEV. = -6.7 DEGREES REMARK 500 TRP A 101 CG - CD2 - CE3 ANGL. DEV. = 5.9 DEGREES REMARK 500 TRP A 144 CD1 - CG - CD2 ANGL. DEV. = 8.8 DEGREES REMARK 500 TRP A 144 CG - CD1 - NE1 ANGL. DEV. = -6.2 DEGREES REMARK 500 TRP A 144 CE2 - CD2 - CG ANGL. DEV. = -7.2 DEGREES REMARK 500 TRP A 144 CG - CD2 - CE3 ANGL. DEV. = 6.4 DEGREES REMARK 500 VAL A 145 CG1 - CB - CG2 ANGL. DEV. = -9.9 DEGREES REMARK 500 ARG A 184 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 184 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 186 N - CA - C ANGL. DEV. = 22.4 DEGREES REMARK 500 TRP A 194 CD1 - CG - CD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 TRP A 194 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 230 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 239 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 LEU A 253 CA - CB - CG ANGL. DEV. = 15.4 DEGREES REMARK 500 ARG A 255 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 TRP A 353 CD1 - CG - CD2 ANGL. DEV. = 7.1 DEGREES REMARK 500 TRP A 353 CE2 - CD2 - CG ANGL. DEV. = -6.2 DEGREES REMARK 500 THR A 397 CA - C - N ANGL. DEV. = -13.9 DEGREES REMARK 500 TRP A 493 CD1 - CG - CD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 TRP A 493 CB - CG - CD1 ANGL. DEV. = -8.3 DEGREES REMARK 500 TRP A 493 CE2 - CD2 - CG ANGL. DEV. = -6.4 DEGREES REMARK 500 TRP A 493 CG - CD2 - CE3 ANGL. DEV. = 6.5 DEGREES REMARK 500 TRP A 514 CD1 - CG - CD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 TRP A 514 CE2 - CD2 - CG ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG A 530 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 TYR A 546 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 TRP A 573 CD1 - CG - CD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 TRP A 573 CE2 - CD2 - CG ANGL. DEV. = -5.8 DEGREES REMARK 500 TYR A 576 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES REMARK 500 TRP A 588 CD1 - CG - CD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 TRP A 588 CE2 - CD2 - CG ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG A 602 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 602 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 TRP A 632 CD1 - CG - CD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 TRP A 632 CE2 - CD2 - CG ANGL. DEV. = -6.6 DEGREES REMARK 500 TRP A 632 CG - CD2 - CE3 ANGL. DEV. = 5.6 DEGREES REMARK 500 TRP A 638 CD1 - CG - CD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 TRP A 638 CB - CG - CD1 ANGL. DEV. = -9.6 DEGREES REMARK 500 TRP A 638 CE2 - CD2 - CG ANGL. DEV. = -6.5 DEGREES REMARK 500 TRP A 638 CG - CD2 - CE3 ANGL. DEV. = 6.8 DEGREES REMARK 500 TRP A 662 CD1 - CG - CD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 TRP A 662 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES REMARK 500 TRP A 663 CD1 - CG - CD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 TRP A 663 CE2 - CD2 - CG ANGL. DEV. = -6.3 DEGREES REMARK 500 TRP A 679 CD1 - CG - CD2 ANGL. DEV. = 6.8 DEGREES REMARK 500 TRP A 679 CE2 - CD2 - CG ANGL. DEV. = -6.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 65 ANGLE DEVIATIONS. 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 GLN A 9 -71.29 -48.23 REMARK 500 ASN A 26 -62.60 -105.86 REMARK 500 SER A 27 136.00 -31.84 REMARK 500 ILE A 28 158.97 88.79 REMARK 500 SER A 30 -56.59 -163.81 REMARK 500 LEU A 46 46.00 -105.50 REMARK 500 THR A 48 96.27 25.40 REMARK 500 LEU A 52 -146.67 -151.19 REMARK 500 ALA A 53 81.47 -62.40 REMARK 500 SER A 54 132.82 79.60 REMARK 500 SER A 55 -48.81 173.23 REMARK 500 LYS A 75 119.68 33.43 REMARK 500 ARG A 80 4.09 -57.91 REMARK 500 LYS A 82 8.10 -172.40 REMARK 500 THR A 84 140.12 -21.36 REMARK 500 THR A 87 43.45 -97.95 REMARK 500 ASP A 102 -85.33 -134.40 REMARK 500 SER A 103 -34.56 -173.47 REMARK 500 ALA A 110 154.67 163.80 REMARK 500 ASP A 130 26.24 35.34 REMARK 500 ASN A 133 -7.21 67.84 REMARK 500 CYS A 141 -74.13 -96.80 REMARK 500 ASN A 160 26.59 -71.98 REMARK 500 GLU A 167 0.01 -165.76 REMARK 500 PRO A 169 127.30 -38.22 REMARK 500 ASP A 186 -15.39 19.52 REMARK 500 ARG A 196 53.36 -141.59 REMARK 500 LYS A 211 42.15 -92.22 REMARK 500 SER A 274 1.09 -69.85 REMARK 500 ASP A 297 -73.34 -98.05 REMARK 500 ILE A 326 47.73 -75.38 REMARK 500 LYS A 327 -119.87 -80.72 REMARK 500 GLU A 328 39.25 -88.41 REMARK 500 GLN A 336 73.52 71.80 REMARK 500 LEU A 338 143.49 173.50 REMARK 500 VAL A 345 7.34 -64.95 REMARK 500 MET A 346 -2.13 -143.45 REMARK 500 GLU A 362 0.75 -64.20 REMARK 500 LEU A 380 105.45 137.85 REMARK 500 TYR A 389 -31.70 -132.92 REMARK 500 HIS A 392 41.45 -101.91 REMARK 500 LYS A 398 -48.95 47.56 REMARK 500 PRO A 403 -156.59 -108.62 REMARK 500 HIS A 425 -98.18 -92.64 REMARK 500 ALA A 437 3.98 -58.78 REMARK 500 ASN A 438 -137.06 -149.46 REMARK 500 THR A 439 0.66 -62.03 REMARK 500 ALA A 461 159.79 178.05 REMARK 500 HIS A 468 106.52 82.65 REMARK 500 PRO A 483 150.94 -45.71 REMARK 500 REMARK 500 THIS ENTRY HAS 71 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 85 PRO A 86 -48.40 REMARK 500 THR A 321 PRO A 322 -56.04 REMARK 500 PHE A 378 PRO A 379 35.11 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 A1854 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 513 NE2 REMARK 620 2 HIS A 518 NE2 86.5 REMARK 620 3 HIS A 704 NE2 95.8 90.6 REMARK 620 4 ILE A 853 O 161.1 75.2 89.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 1854 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IUK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SOYBEAN LIPOXYGENASE-D DBREF 2IUJ A 1 853 UNP Q43446 Q43446_SOYBN 1 853 SEQRES 1 A 853 MET PHE PRO PHE GLY HIS LYS GLY GLN LYS ILE LYS GLY SEQRES 2 A 853 THR MET VAL VAL MET GLN LYS ASN VAL LEU ASP ILE ASN SEQRES 3 A 853 SER ILE THR SER VAL ASP GLY ILE VAL GLY THR GLY LEU SEQRES 4 A 853 ASP PHE LEU GLY SER ALA LEU ASP THR VAL THR PHE LEU SEQRES 5 A 853 ALA SER SER ILE SER ILE GLN LEU ILE SER ALA THR LYS SEQRES 6 A 853 ALA ASP GLY GLY LYS GLY LYS VAL GLY LYS ALA THR ASN SEQRES 7 A 853 LEU ARG GLY LYS ILE THR LEU PRO THR ILE GLY ALA LYS SEQRES 8 A 853 GLU GLU ALA TYR ASP ALA GLN PHE ASP TRP ASP SER ASP SEQRES 9 A 853 PHE GLY ILE PRO GLY ALA PHE TYR ILE LYS ASN TYR MET SEQRES 10 A 853 GLN ASN GLU PHE TYR LEU LYS SER LEU ILE LEU GLU ASP SEQRES 11 A 853 ILE PRO ASN HIS GLY THR ILE HIS PHE ILE CYS ASN SER SEQRES 12 A 853 TRP VAL TYR ASN SER LYS HIS TYR LYS THR ASP ARG ILE SEQRES 13 A 853 PHE PHE ALA ASN ASN THR TYR LEU PRO SER GLU THR PRO SEQRES 14 A 853 ALA PRO LEU VAL LYS TYR ARG GLU GLU GLU LEU LYS ASN SEQRES 15 A 853 VAL ARG GLY ASP GLY THR GLY GLU ARG LYS GLU TRP ASP SEQRES 16 A 853 ARG ILE TYR ASP TYR ASP VAL TYR ASN ASP LEU GLY ASP SEQRES 17 A 853 PRO ASP LYS GLY GLU LYS TYR ALA ARG PRO VAL LEU GLY SEQRES 18 A 853 GLY SER ALA LEU PRO TYR PRO ARG ARG GLY ARG THR GLY SEQRES 19 A 853 ARG GLY LYS THR ARG LYS ASP PRO ASN SER GLU LYS PRO SEQRES 20 A 853 GLY ASP PHE VAL TYR LEU PRO ARG ASP GLU ALA PHE GLY SEQRES 21 A 853 HIS LEU LYS SER SER ASP PHE LEU ALA TYR GLY ILE LYS SEQRES 22 A 853 SER VAL ALA GLN ASP VAL LEU PRO VAL LEU THR ASP ALA SEQRES 23 A 853 PHE ASP GLY ASN LEU LEU SER LEU ASP PHE ASP ASN PHE SEQRES 24 A 853 ALA GLU VAL ARG LYS LEU TYR GLU GLY GLY VAL THR LEU SEQRES 25 A 853 PRO THR ASN PHE LEU SER ASN ILE THR PRO ILE PRO ILE SEQRES 26 A 853 ILE LYS GLU LEU PHE ARG THR ASP GLY GLU GLN PHE LEU SEQRES 27 A 853 LYS TYR PRO PRO PRO LYS VAL MET GLN VAL ASP LYS SER SEQRES 28 A 853 ALA TRP MET THR ASP GLU GLU PHE ALA ARG GLU THR ILE SEQRES 29 A 853 ALA GLY LEU ASN PRO ASN VAL ILE LYS ILE ILE GLU GLU SEQRES 30 A 853 PHE PRO LEU SER SER LYS LEU ASP THR GLN ALA TYR GLY SEQRES 31 A 853 ASP HIS THR CYS ILE ILE THR LYS GLU HIS LEU GLU PRO SEQRES 32 A 853 ASN LEU GLY GLY LEU THR VAL GLU GLN ALA ILE GLN ASN SEQRES 33 A 853 LYS LYS LEU PHE ILE LEU ASP HIS HIS ASP TYR LEU ILE SEQRES 34 A 853 PRO TYR LEU ARG LYS ILE ASN ALA ASN THR THR LYS THR SEQRES 35 A 853 TYR ALA THR ARG THR ILE PHE PHE LEU LYS ASN ASP GLY SEQRES 36 A 853 THR LEU THR PRO LEU ALA ILE GLU LEU SER LYS PRO HIS SEQRES 37 A 853 PRO GLN GLY GLU GLU TYR GLY PRO VAL SER GLU VAL TYR SEQRES 38 A 853 VAL PRO SER SER GLU GLY VAL GLU ALA TYR ILE TRP LEU SEQRES 39 A 853 LEU ALA LYS ALA TYR VAL VAL VAL ASN ASP ALA CYS TYR SEQRES 40 A 853 HIS GLN ILE ILE SER HIS TRP LEU ASN THR HIS ALA VAL SEQRES 41 A 853 VAL GLU PRO PHE VAL ILE ALA THR ASN ARG HIS LEU SER SEQRES 42 A 853 VAL VAL HIS PRO ILE TYR LYS LEU LEU PHE PRO HIS TYR SEQRES 43 A 853 ARG ASP THR MET ASN ILE ASN SER LEU ALA ARG LYS SER SEQRES 44 A 853 LEU VAL ASN ALA ASP GLY ILE ILE GLU LYS THR PHE LEU SEQRES 45 A 853 TRP GLY ARG TYR SER LEU GLU MET SER ALA VAL ILE TYR SEQRES 46 A 853 LYS ASP TRP VAL PHE THR ASP GLN ALA LEU PRO ASN ASP SEQRES 47 A 853 LEU VAL LYS ARG GLY VAL ALA VAL LYS ASP PRO SER ALA SEQRES 48 A 853 PRO HIS GLY VAL ARG LEU LEU ILE GLU ASP TYR PRO TYR SEQRES 49 A 853 ALA SER ASP GLY LEU GLU ILE TRP ASP ALA ILE LYS SER SEQRES 50 A 853 TRP VAL GLU GLU TYR VAL SER PHE TYR TYR LYS SER ASP SEQRES 51 A 853 GLU GLU LEU GLN LYS ASP PRO GLU LEU GLN ALA TRP TRP SEQRES 52 A 853 LYS GLU LEU VAL GLU VAL GLY HIS GLY ASP LEU LYS ASP SEQRES 53 A 853 LYS PRO TRP TRP GLN LYS MET GLN THR ARG GLU GLU LEU SEQRES 54 A 853 VAL GLU ALA SER ALA THR LEU ILE TRP ILE ALA SER ALA SEQRES 55 A 853 LEU HIS ALA ALA VAL ASN PHE GLY GLN TYR PRO TYR GLY SEQRES 56 A 853 GLY LEU ILE LEU ASN ARG PRO THR ILE SER ARG ARG PHE SEQRES 57 A 853 MET PRO GLU LYS GLY SER PRO GLU TYR ASP ALA LEU ALA SEQRES 58 A 853 LYS ASN PRO GLU LYS GLU PHE LEU LYS THR ILE THR GLY SEQRES 59 A 853 LYS LYS GLU THR LEU ILE ASP LEU THR ILE ILE GLU ILE SEQRES 60 A 853 LEU SER ARG HIS ALA SER ASP GLU PHE TYR LEU GLY GLN SEQRES 61 A 853 ARG ASP GLY GLY ASP TYR TRP THR SER ASP ALA GLY PRO SEQRES 62 A 853 LEU GLU ALA PHE LYS ARG PHE GLY LYS ASN LEU GLU GLU SEQRES 63 A 853 ILE GLU LYS LYS LEU ILE GLU LYS ASN ASN ASP GLU THR SEQRES 64 A 853 LEU ARG ASN ARG TYR GLY PRO ALA LYS MET PRO TYR THR SEQRES 65 A 853 LEU LEU TYR PRO SER SER GLU GLU GLY LEU THR PHE ARG SEQRES 66 A 853 GLY ILE PRO ASN SER ILE SER ILE HET FE A1854 1 HETNAM FE FE (III) ION FORMUL 2 FE FE 3+ FORMUL 3 HOH *106(H2 O) HELIX 1 1 ASN A 21 LEU A 23 5 3 HELIX 2 2 LEU A 164 THR A 168 5 5 HELIX 3 3 LEU A 172 GLY A 185 1 14 HELIX 4 4 ASP A 208 GLY A 212 5 5 HELIX 5 5 PRO A 254 ALA A 258 5 5 HELIX 6 6 LYS A 263 ASP A 266 5 4 HELIX 7 7 PHE A 267 GLN A 277 1 11 HELIX 8 8 ASP A 278 GLY A 289 1 12 HELIX 9 9 ASN A 298 GLY A 309 1 12 HELIX 10 10 PRO A 313 ILE A 320 1 8 HELIX 11 11 PRO A 343 GLN A 347 5 5 HELIX 12 12 THR A 355 GLU A 362 1 8 HELIX 13 13 THR A 409 ASN A 416 1 8 HELIX 14 14 LEU A 428 PRO A 430 5 3 HELIX 15 15 TYR A 431 ALA A 437 1 7 HELIX 16 16 GLY A 471 GLY A 475 5 5 HELIX 17 17 GLY A 487 ILE A 511 1 25 HELIX 18 18 GLY A 8 ASN A 516 1 496 HELIX 19 19 THR A 517 LEU A 532 1 16 HELIX 20 20 HIS A 536 PHE A 543 1 8 HELIX 21 21 PRO A 544 ARG A 547 5 4 HELIX 22 22 ASP A 548 LEU A 560 1 13 HELIX 23 23 GLY A 565 PHE A 571 1 7 HELIX 24 24 TRP A 573 ARG A 575 5 3 HELIX 25 25 TYR A 576 LYS A 586 1 11 HELIX 26 26 PHE A 590 GLN A 593 5 4 HELIX 27 27 ALA A 594 GLY A 603 1 10 HELIX 28 28 TYR A 622 TYR A 647 1 26 HELIX 29 29 SER A 649 GLN A 654 1 6 HELIX 30 30 ASP A 656 VAL A 669 1 14 HELIX 31 31 HIS A 671 LYS A 675 5 5 HELIX 32 32 THR A 685 PHE A 709 1 25 HELIX 33 33 GLN A 711 GLY A 716 1 6 HELIX 34 34 SER A 734 ASN A 743 1 10 HELIX 35 35 ASN A 743 LYS A 750 1 8 HELIX 36 36 GLY A 754 LEU A 768 1 15 HELIX 37 37 ASP A 790 ASN A 815 1 26 HELIX 38 38 LEU A 820 TYR A 824 5 5 SHEET 1 AA 4 GLU A 93 ASP A 100 0 SHEET 2 AA 4 LYS A 10 GLN A 19 -1 O ILE A 11 N PHE A 99 SHEET 3 AA 4 PHE A 121 LEU A 128 -1 O TYR A 122 N MET A 18 SHEET 4 AA 4 ILE A 137 VAL A 145 -1 O ILE A 137 N LEU A 128 SHEET 1 AB 4 GLY A 71 ASN A 78 0 SHEET 2 AB 4 ILE A 56 ALA A 66 -1 O ILE A 58 N THR A 77 SHEET 3 AB 4 PRO A 108 ASN A 115 -1 N GLY A 109 O ILE A 61 SHEET 4 AB 4 ARG A 155 PHE A 158 -1 O ARG A 155 N ILE A 113 SHEET 1 AC 2 TYR A 200 ASP A 201 0 SHEET 2 AC 2 ARG A 230 GLY A 231 -1 O ARG A 230 N ASP A 201 SHEET 1 AD 5 LYS A 373 ILE A 374 0 SHEET 2 AD 5 LEU A 419 ILE A 421 -1 O ILE A 421 N LYS A 373 SHEET 3 AD 5 THR A 447 LEU A 451 -1 O PHE A 449 N PHE A 420 SHEET 4 AD 5 LEU A 457 LYS A 466 -1 O THR A 458 N PHE A 450 SHEET 5 AD 5 VAL A 477 TYR A 481 -1 O VAL A 477 N LYS A 466 SHEET 1 AE 2 ALA A 605 LYS A 607 0 SHEET 2 AE 2 VAL A 615 LEU A 617 -1 O ARG A 616 N VAL A 606 LINK NE2 HIS A 513 FE FE A1854 1555 1555 2.39 LINK NE2 HIS A 518 FE FE A1854 1555 1555 2.29 LINK NE2 HIS A 704 FE FE A1854 1555 1555 2.36 LINK O ILE A 853 FE FE A1854 1555 1555 2.28 CISPEP 1 GLY A 475 PRO A 476 0 7.57 SITE 1 AC1 5 HIS A 513 HIS A 518 HIS A 704 ASN A 708 SITE 2 AC1 5 ILE A 853 CRYST1 99.990 105.310 105.920 90.00 90.00 90.00 P 21 21 21 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 0.010001 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009496 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009441 0.00000