HEADER OXIDOREDUCTASE 29-MAR-96 1LNH TITLE LIPOXYGENASE-3(SOYBEAN) NON-HEME FE(II) METALLOPROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPOXYGENASE-3; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GLYCINE MAX; SOURCE 3 ORGANISM_COMMON: SOYBEAN; SOURCE 4 ORGANISM_TAXID: 3847; SOURCE 5 STRAIN: PROVAR CULTIVAR KEYWDS OXIDOREDUCTASE, METALLOPROTEIN, FE(II) COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.SKRZYPCZAK-JANKUN REVDAT 5 09-AUG-23 1LNH 1 REMARK LINK REVDAT 4 24-FEB-09 1LNH 1 VERSN REVDAT 3 01-APR-03 1LNH 1 JRNL REVDAT 2 12-AUG-98 1LNH 1 REMARK JRNL REVDAT 1 02-FEB-97 1LNH 0 JRNL AUTH E.SKRZYPCZAK-JANKUN,L.M.AMZEL,B.A.KROA,M.O.FUNK JR. JRNL TITL STRUCTURE OF SOYBEAN LIPOXYGENASE L3 AND A COMPARISON WITH JRNL TITL 2 ITS L1 ISOENZYME. JRNL REF PROTEINS V. 29 15 1997 JRNL REFN ISSN 0887-3585 JRNL PMID 9294864 JRNL DOI 10.1002/(SICI)1097-0134(199709)29:1<15::AID-PROT2>3.3.CO;2-F REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.SKRZYPCZAK-JANKUN,M.O.FUNK JUNIOR,J.C.BOYINGTON,L.M.AMZEL REMARK 1 TITL LIPOXYGENASE-A MOLECULAR COMPLEX WITH A NON-HEME IRON REMARK 1 REF J.MOL.STRUCT. V. 374 47 1996 REMARK 1 REFN ISSN 0022-2860 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.A.KRAMER,K.R.JOHNSON,W.R.DUNHAM,R.H.SANDS,M.O.FUNK JUNIOR REMARK 1 TITL POSITION 713 IS CRITICAL FOR CATALYSIS BUT NOT IRON BINDING REMARK 1 TITL 2 IN SOYBEAN LIPOXYGENASE 3 REMARK 1 REF BIOCHEMISTRY V. 33 15017 1994 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 3 REMARK 1 AUTH W.C.STALLINGS,B.A.KROA,R.T.CARROLL,A.L.METZGER,M.O.FUNK REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY CHARACTERIZATION OF A REMARK 1 TITL 2 SOYBEAN SEED LIPOXYGENASE REMARK 1 REF J.MOL.BIOL. V. 211 685 1990 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 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) (%) : 82.1 REMARK 3 NUMBER OF REFLECTIONS : 22402 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.265 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 : 6696 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.70 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) : 0.20 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) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 3.550 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.46 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.540 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 1LNH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174774. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 1994 REMARK 200 TEMPERATURE (KELVIN) : 296 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 : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MSC REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23403 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 61.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06200 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) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 43.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.11700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.390 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: FOR MOLECULAR REPLACEMENT: 1SBL FOR SOYBEAN REMARK 200 LIPOXYGENASE-1. THE MODEL WAS TRUNCATED TO INCLUDE ONLY THE REMARK 200 ATOMS (7854) COMMON WITH LIPOXYGENASE-3 SEQUENCE (ENTRY 1SBL WAS REMARK 200 REPLACED LATER IN PDB BY 2SBL WITH BETTER REFINED MODEL). REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.3 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 56.40000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 68.70000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.40000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 68.70000 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 400 REMARK 400 COMPOUND REMARK 400 THE NUMBERING OF THE SECONDARY STRUCTURE ELEMENTS HAS REMARK 400 SYMBOLS AFTER SOYBEAN LIPOXYGENASE L1 AS IN PDB ENTRY 2SBL REMARK 400 (BOYINGTON ET AL., 1993, SCIENCE, 260, 1482-1486). REMARK 400 THERE ARE SOME KINKS IN 3 HELICES: H2 - AT 283, REMARK 400 H9 - AT 521-522, H18 - AT 706, 714-715. 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 465 HIS A 7 REMARK 465 ARG A 8 REMARK 465 GLY A 33 REMARK 465 GLY A 34 REMARK 465 ILE A 35 REMARK 465 ILE A 36 REMARK 465 GLY A 37 REMARK 465 GLN A 38 REMARK 465 GLY A 39 REMARK 465 LEU A 40 REMARK 465 ASP A 41 REMARK 465 LEU A 42 REMARK 465 VAL A 43 REMARK 465 GLY A 44 REMARK 465 SER A 45 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 138 NE2 HIS A 138 CD2 -0.075 REMARK 500 HIS A 142 NE2 HIS A 142 CD2 -0.067 REMARK 500 HIS A 185 NE2 HIS A 185 CD2 -0.067 REMARK 500 HIS A 219 NE2 HIS A 219 CD2 -0.071 REMARK 500 HIS A 429 NE2 HIS A 429 CD2 -0.067 REMARK 500 HIS A 430 NE2 HIS A 430 CD2 -0.075 REMARK 500 HIS A 473 NE2 HIS A 473 CD2 -0.070 REMARK 500 HIS A 523 NE2 HIS A 523 CD2 -0.078 REMARK 500 HIS A 536 NE2 HIS A 536 CD2 -0.070 REMARK 500 HIS A 541 NE2 HIS A 541 CD2 -0.068 REMARK 500 HIS A 550 NE2 HIS A 550 CD2 -0.069 REMARK 500 HIS A 618 NE2 HIS A 618 CD2 -0.069 REMARK 500 HIS A 645 NE2 HIS A 645 CD2 -0.075 REMARK 500 HIS A 709 NE2 HIS A 709 CD2 -0.074 REMARK 500 HIS A 776 NE2 HIS A 776 CD2 -0.068 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 LEU A 18 CA - CB - CG ANGL. DEV. = 16.0 DEGREES REMARK 500 ARG A 20 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP A 48 CA - C - N ANGL. DEV. = -15.3 DEGREES REMARK 500 ARG A 56 CA - CB - CG ANGL. DEV. = -14.6 DEGREES REMARK 500 THR A 91 N - CA - CB ANGL. DEV. = -15.8 DEGREES REMARK 500 TRP A 105 CD1 - CG - CD2 ANGL. DEV. = 7.6 DEGREES REMARK 500 TRP A 105 CG - CD1 - NE1 ANGL. DEV. = -6.1 DEGREES REMARK 500 TRP A 105 CE2 - CD2 - CG ANGL. DEV. = -6.6 DEGREES REMARK 500 ASP A 134 N - CA - C ANGL. DEV. = 19.6 DEGREES REMARK 500 TRP A 148 CD1 - CG - CD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 TRP A 148 CB - CG - CD1 ANGL. DEV. = -8.3 DEGREES REMARK 500 TRP A 148 CE2 - CD2 - CG ANGL. DEV. = -5.9 DEGREES REMARK 500 TRP A 148 CG - CD2 - CE3 ANGL. DEV. = 6.8 DEGREES REMARK 500 PRO A 169 CA - CB - CG ANGL. DEV. = -12.3 DEGREES REMARK 500 THR A 172 CA - C - N ANGL. DEV. = 18.5 DEGREES REMARK 500 ARG A 180 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 LEU A 187 CA - CB - CG ANGL. DEV. = 15.1 DEGREES REMARK 500 TRP A 198 CD1 - CG - CD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 TRP A 198 CE2 - CD2 - CG ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 200 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 200 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 VAL A 206 N - CA - CB ANGL. DEV. = -15.9 DEGREES REMARK 500 ARG A 221 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 234 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 234 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 THR A 238 CA - C - N ANGL. DEV. = 12.2 DEGREES REMARK 500 ARG A 240 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 TYR A 311 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 TRP A 358 CD1 - CG - CD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 TRP A 358 CB - CG - CD1 ANGL. DEV. = -8.1 DEGREES REMARK 500 TRP A 358 CE2 - CD2 - CG ANGL. DEV. = -6.2 DEGREES REMARK 500 TRP A 358 CG - CD2 - CE3 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASN A 375 N - CA - CB ANGL. DEV. = -10.9 DEGREES REMARK 500 VAL A 393 N - CA - C ANGL. DEV. = 17.0 DEGREES REMARK 500 HIS A 397 CA - CB - CG ANGL. DEV. = 13.9 DEGREES REMARK 500 ARG A 423 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 439 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 451 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 463 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 HIS A 473 CA - CB - CG ANGL. DEV. = 11.3 DEGREES REMARK 500 TRP A 498 CD1 - CG - CD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 TRP A 498 CG - CD1 - NE1 ANGL. DEV. = -6.2 DEGREES REMARK 500 TRP A 498 CE2 - CD2 - CG ANGL. DEV. = -6.1 DEGREES REMARK 500 CYS A 511 CA - CB - SG ANGL. DEV. = -14.1 DEGREES REMARK 500 TRP A 519 CD1 - CG - CD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 TRP A 519 CE2 - CD2 - CG ANGL. DEV. = -5.8 DEGREES REMARK 500 THR A 522 N - CA - CB ANGL. DEV. = -12.2 DEGREES REMARK 500 TRP A 578 CE2 - CD2 - CG ANGL. DEV. = -5.3 DEGREES REMARK 500 ARG A 580 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 MET A 585 CG - SD - CE ANGL. DEV. = -10.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 100 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 HIS A 10 142.01 167.89 REMARK 500 VAL A 29 0.51 -58.20 REMARK 500 THR A 66 -75.00 -138.27 REMARK 500 ALA A 70 -68.58 3.87 REMARK 500 ASN A 71 64.57 -118.97 REMARK 500 LYS A 73 72.72 -54.29 REMARK 500 LYS A 78 123.27 -3.59 REMARK 500 SER A 88 -63.52 -146.22 REMARK 500 LEU A 89 129.25 55.78 REMARK 500 PRO A 90 -8.95 -52.68 REMARK 500 PHE A 115 143.33 -170.79 REMARK 500 ASP A 134 -136.45 -73.95 REMARK 500 ILE A 135 -55.50 -151.90 REMARK 500 PRO A 136 -172.49 -64.82 REMARK 500 LYS A 156 -9.44 54.05 REMARK 500 SER A 157 -124.32 -135.81 REMARK 500 ASN A 164 -16.70 -31.50 REMARK 500 PRO A 169 9.29 -66.22 REMARK 500 THR A 172 -87.89 -21.67 REMARK 500 PRO A 173 109.34 -52.71 REMARK 500 ASP A 190 171.05 59.76 REMARK 500 PHE A 230 75.01 -118.05 REMARK 500 ARG A 260 154.49 -42.92 REMARK 500 ASP A 261 -12.85 73.48 REMARK 500 SER A 270 -19.49 93.81 REMARK 500 LEU A 294 -96.39 -99.56 REMARK 500 ASN A 295 -15.69 -178.92 REMARK 500 SER A 312 -62.72 -99.40 REMARK 500 LYS A 316 104.97 -55.05 REMARK 500 ILE A 321 -62.84 -105.56 REMARK 500 ILE A 325 61.41 -106.49 REMARK 500 SER A 326 -75.48 -132.65 REMARK 500 VAL A 330 -34.95 74.00 REMARK 500 GLU A 333 -30.12 71.13 REMARK 500 GLN A 341 32.42 29.06 REMARK 500 ASP A 390 -161.41 -47.00 REMARK 500 SER A 391 4.69 -52.74 REMARK 500 GLN A 392 37.71 -88.65 REMARK 500 VAL A 393 41.21 22.83 REMARK 500 HIS A 397 -147.20 174.70 REMARK 500 GLN A 400 39.82 -80.84 REMARK 500 THR A 402 80.07 -61.50 REMARK 500 GLU A 404 35.66 -82.83 REMARK 500 HIS A 405 62.11 -163.03 REMARK 500 GLU A 407 72.57 75.87 REMARK 500 ASN A 409 -42.08 -169.91 REMARK 500 GLU A 411 -17.48 -142.53 REMARK 500 TYR A 448 56.19 -141.27 REMARK 500 ALA A 449 99.83 -13.15 REMARK 500 HIS A 473 56.09 29.11 REMARK 500 REMARK 500 THIS ENTRY HAS 79 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 ASN A 788 PRO A 789 133.54 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 TYR A 581 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE IRON BINDING SITE CONSISTS OF HIS 518, HIS 523, HIS 709 REMARK 600 AND ILE 857(C-TERMINAL) THAT ARE COVALENTLY BOUND TO IRON REMARK 600 FE 858, WHILE ASN 713 AND H2O 901 ARE IN A DISTANCE GREATER REMARK 600 THAN THE SUM OF THE VAN DER WAALS RADII. 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 FE2 A 858 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 518 NE2 REMARK 620 2 HIS A 523 NE2 91.6 REMARK 620 3 HIS A 709 NE2 100.7 86.5 REMARK 620 4 ILE A 857 OXT 171.6 94.5 85.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: FE REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: IRON BINDING SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A 858 DBREF 1LNH 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 FE2 A 858 1 HETNAM FE2 FE (II) ION FORMUL 2 FE2 FE 2+ FORMUL 3 HOH *170(H2 O) HELIX 1 1 LYS A 21 LEU A 24 1 4 HELIX 2 H1 ALA A 174 ARG A 188 1AFTER L1 15 HELIX 3 H2 LEU A 273 ASP A 293 1(KINK AT 283) 21 HELIX 4 H3 PHE A 304 HIS A 308 1 5 HELIX 5 H4 THR A 319 ILE A 322 1 4 HELIX 6 H6 ASP A 361 ALA A 370 1 10 HELIX 7 H7 VAL A 415 GLN A 420 1 6 HELIX 8 H8 MET A 434 ILE A 440 1 7 HELIX 9 H9 GLY A 492 HIS A 536 1INTRNL PI 516-20 (KINK 521-2) 45 HELIX 10 H10 PRO A 542 LEU A 547 1 6 HELIX 11 H11 THR A 554 SER A 564 1 11 HELIX 12 H12 VAL A 571 THR A 575 1 5 HELIX 13 H13 SER A 582 TYR A 590 1 9 HELIX 14 H14 LEU A 600 LYS A 606 1 7 HELIX 15 H15 PRO A 628 PHE A 649 1 22 HELIX 16 H16 ASP A 655 ARG A 659 1 5 HELIX 17 H17 PRO A 662 GLU A 673 1 12 HELIX 18 H18 GLU A 693 GLY A 720 1KINK AT 706 AND 714-715 28 HELIX 19 H19 ALA A 740 LYS A 747 1 8 HELIX 20 H20 PRO A 749 THR A 756 1 8 HELIX 21 H21 LYS A 760 LEU A 773 1 14 HELIX 22 H22 THR A 795 ASN A 820 1 26 SHEET 1 S1 8 LYS A 11 ARG A 20 0 SHEET 2 S1 8 VAL A 58 SER A 64 -1 SHEET 3 S1 8 LEU A 76 PHE A 81 -1 SHEET 4 S1 8 GLN A 96 GLU A 104 -1 SHEET 5 S1 8 PRO A 112 ASN A 119 -1 SHEET 6 S1 8 PHE A 125 GLU A 133 -1 SHEET 7 S1 8 ILE A 141 ILE A 149 -1 SHEET 8 S1 8 ARG A 159 PHE A 162 -1 SHEET 1 S2 2 TYR A 204 ASP A 205 0 SHEET 2 S2 2 ARG A 235 GLY A 236 -1 SHEET 1 S3 2 ARG A 336 THR A 337 0 SHEET 2 S3 2 LEU A 343 LYS A 344 -1 SHEET 1 S4 5 ARG A 378 CYS A 379 0 SHEET 2 S4 5 LEU A 424 ASP A 428 -1 SHEET 3 S4 5 THR A 450 LEU A 456 -1 SHEET 4 S4 5 LEU A 462 PRO A 472 -1 SHEET 5 S4 5 ALA A 481 PHE A 486 -1 SHEET 1 S5 2 ALA A 610 GLU A 612 0 SHEET 2 S5 2 ILE A 620 LEU A 622 -1 LINK NE2 HIS A 518 FE FE2 A 858 1555 1555 2.23 LINK NE2 HIS A 523 FE FE2 A 858 1555 1555 2.21 LINK NE2 HIS A 709 FE FE2 A 858 1555 1555 2.26 LINK OXT ILE A 857 FE FE2 A 858 1555 1555 2.13 CISPEP 1 PHE A 383 PRO A 384 0 -11.55 SITE 1 FE 7 FE2 A 858 HIS A 518 HIS A 523 HIS A 709 SITE 2 FE 7 ASN A 713 ILE A 857 HOH A 901 SITE 1 AC1 5 HIS A 518 HIS A 523 HIS A 709 ASN A 713 SITE 2 AC1 5 ILE A 857 CRYST1 112.800 137.400 61.850 90.00 95.50 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 0.008865 0.000000 0.000854 0.00000 SCALE2 0.000000 0.007278 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016243 0.00000