HEADER OXIDOREDUCTASE 20-JUL-01 1JMX TITLE CRYSTAL STRUCTURE OF A QUINOHEMOPROTEIN AMINE DEHYDROGENASE TITLE 2 FROM PSEUDOMONAS PUTIDA COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMINE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: AMINE DEHYDROGENASE; COMPND 6 CHAIN: B; COMPND 7 MOL_ID: 3; COMPND 8 MOLECULE: AMINE DEHYDROGENASE; COMPND 9 CHAIN: G SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 303; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 6 ORGANISM_TAXID: 303; SOURCE 7 MOL_ID: 3; SOURCE 8 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 9 ORGANISM_TAXID: 303 KEYWDS AMINE DEHYDROGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.SATOH,I.MIYAHARA,K.HIROTSU REVDAT 5 24-FEB-09 1JMX 1 VERSN REVDAT 4 01-APR-03 1JMX 1 JRNL REVDAT 3 18-DEC-02 1JMX 1 REMARK REVDAT 2 06-MAR-02 1JMX 1 JRNL REVDAT 1 16-JAN-02 1JMX 0 JRNL AUTH A.SATOH,J.K.KIM,I.MIYAHARA,B.DEVREESE, JRNL AUTH 2 I.VANDENBERGHE,A.HACISALIHOGLU,T.OKAJIMA,S.KURODA, JRNL AUTH 3 O.ADACHI,J.A.DUINE,J.VAN BEEUMEN,K.TANIZAWA, JRNL AUTH 4 K.HIROTSU JRNL TITL CRYSTAL STRUCTURE OF QUINOHEMOPROTEIN AMINE JRNL TITL 2 DEHYDROGENASE FROM PSEUDOMONAS PUTIDA. JRNL TITL 3 IDENTIFICATION OF A NOVEL QUINONE COFACTOR ENCAGED JRNL TITL 4 BY MULTIPLE THIOETHER CROSS-BRIDGES. JRNL REF J.BIOL.CHEM. V. 277 2830 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 11704672 JRNL DOI 10.1074/JBC.M109090200 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 64940 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3292 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 : 7067 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 87 REMARK 3 SOLVENT ATOMS : 457 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.61 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 1JMX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUL-01. REMARK 100 THE RCSB ID CODE IS RCSB013952. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-01 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-18B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 89255 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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: MIR REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG MME2000, NICKEL CHLORIDE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.0K 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 83.60500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.18500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 83.60500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 46.18500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -95.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, G REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 25070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 62200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -203.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, G, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 304.71370 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 73.52568 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 ALA A 1 REMARK 465 ALA B 1 REMARK 465 ASP B 2 REMARK 465 THR B 3 REMARK 465 LYS B 220 REMARK 465 ASP B 221 REMARK 465 ASP B 222 REMARK 465 LYS B 223 REMARK 465 GLN B 224 REMARK 465 ASP B 225 REMARK 465 PRO B 226 REMARK 465 MET G 1 REMARK 465 SER G 2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 423 CG CD OE1 OE2 REMARK 480 ARG A 424 CG CD NE CZ NH1 NH2 REMARK 480 SER B 96 OG REMARK 480 PHE B 97 CG CD1 CD2 CE1 CE2 CZ REMARK 480 ILE B 99 CG1 CG2 CD1 REMARK 480 SER B 100 OG 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 CYS G 7 CB CYS G 7 SG -0.233 REMARK 500 GLY G 6 C CYS G 7 N 0.410 REMARK 500 TRP G 15 C GLU G 16 N 0.261 REMARK 500 GLU G 16 C VAL G 17 N 0.384 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 CYS G 7 CB - CA - C ANGL. DEV. = 8.2 DEGREES REMARK 500 CYS G 7 CA - CB - SG ANGL. DEV. = -18.7 DEGREES REMARK 500 GLY G 6 O - C - N ANGL. DEV. = -13.7 DEGREES REMARK 500 CYS G 7 C - N - CA ANGL. DEV. = 19.4 DEGREES REMARK 500 CYS G 7 CA - C - N ANGL. DEV. = -28.5 DEGREES REMARK 500 CYS G 7 O - C - N ANGL. DEV. = 26.9 DEGREES REMARK 500 THR G 8 C - N - CA ANGL. DEV. = -17.0 DEGREES REMARK 500 GLU G 16 N - CA - CB ANGL. DEV. = -15.8 DEGREES REMARK 500 GLU G 16 CA - CB - CG ANGL. DEV. = 15.1 DEGREES REMARK 500 TRP G 15 O - C - N ANGL. DEV. = -11.5 DEGREES REMARK 500 GLU G 16 CA - C - N ANGL. DEV. = -18.0 DEGREES REMARK 500 CYS G 41 CA - CB - SG ANGL. DEV. = -21.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 21 71.47 14.09 REMARK 500 ARG A 26 -62.76 73.66 REMARK 500 CYS A 103 -69.12 -108.54 REMARK 500 ALA A 139 -44.78 -142.05 REMARK 500 TYR A 236 -25.85 -147.26 REMARK 500 GLU A 323 108.01 -166.81 REMARK 500 GLU A 326 143.85 -174.23 REMARK 500 GLU A 381 -148.75 49.62 REMARK 500 ASN A 460 49.22 -81.85 REMARK 500 THR A 484 -166.64 -121.84 REMARK 500 ASN B 21 50.90 165.54 REMARK 500 ASP B 41 -135.11 62.55 REMARK 500 TYR B 151 -115.37 -127.87 REMARK 500 LEU B 184 -73.49 -112.58 REMARK 500 GLN B 204 73.10 -107.54 REMARK 500 THR B 228 -24.23 74.90 REMARK 500 GLN B 248 131.11 -177.86 REMARK 500 ALA B 251 151.85 173.07 REMARK 500 LEU B 274 -89.54 -173.30 REMARK 500 THR B 314 -109.43 74.30 REMARK 500 PHE B 315 -154.79 -88.03 REMARK 500 SER B 340 -129.21 52.57 REMARK 500 TRP G 15 -51.11 -134.40 REMARK 500 SER G 52 -59.72 -131.54 REMARK 500 TYR G 54 66.27 -117.12 REMARK 500 ALA G 61 50.80 -141.45 REMARK 500 PRO G 76 75.00 -69.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLU G 16 -14.19 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 A2064 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH B 427 DISTANCE = 5.14 ANGSTROMS REMARK 525 HOH B 491 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A2235 DISTANCE = 5.72 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 HEC A1001 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 104 NE2 REMARK 620 2 HIS A 126 NE2 179.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A1002 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 16 NE2 REMARK 620 2 MET A 44 SD 178.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A2001 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 367 OE1 REMARK 620 2 HOH A2151 O 87.4 REMARK 620 3 HOH A2068 O 174.6 88.4 REMARK 620 4 HOH A2248 O 93.1 160.2 89.7 REMARK 620 5 HIS B 11 NE2 92.3 87.1 90.8 112.6 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 NI A 2001 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 1001 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 1002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JMZ RELATED DB: PDB REMARK 900 1JMZ CONTAINS THE SAME PROTEIN COMPLEXED WITH INHIBITOR DBREF 1JMX A 1 494 UNP Q8VW85 Q8VW85_PSEPU 49 542 DBREF 1JMX B 1 349 UNP Q8VW82 Q8VW82_PSEPU 31 379 DBREF 1JMX G 2 79 UNP P0A182 QADG_PSEPU 1 78 SEQRES 1 A 494 ALA GLU GLN GLY PRO SER LEU LEU GLN ASN LYS CYS MET SEQRES 2 A 494 GLY CYS HIS ILE PRO GLU GLY ASN ASP THR TYR SER ARG SEQRES 3 A 494 ILE SER HIS GLN ARG LYS THR PRO GLU GLY TRP LEU MET SEQRES 4 A 494 SER ILE ALA ARG MET GLN VAL MET HIS GLY LEU GLN ILE SEQRES 5 A 494 SER ASP ASP ASP ARG ARG THR LEU VAL LYS TYR LEU ALA SEQRES 6 A 494 ASP LYS GLN GLY LEU ALA PRO SER GLU THR ASP GLY VAL SEQRES 7 A 494 ARG TYR ALA MET GLU ARG ARG LEU ASN THR VAL GLU GLN SEQRES 8 A 494 PHE ASP THR GLN LEU SER GLU THR CYS GLY ARG CYS HIS SEQRES 9 A 494 SER GLY ALA ARG VAL ALA LEU GLN ARG ARG PRO ALA LYS SEQRES 10 A 494 GLU TRP GLU HIS LEU VAL ASN PHE HIS LEU GLY GLN TRP SEQRES 11 A 494 PRO SER LEU GLU TYR GLN ALA GLN ALA ARG ASP ARG ASP SEQRES 12 A 494 TRP LEU PRO ILE ALA LEU GLN GLN VAL VAL PRO ASP LEU SEQRES 13 A 494 ALA LYS ARG TYR PRO LEU GLU SER ALA ALA TRP ALA GLU SEQRES 14 A 494 TRP GLN LYS ALA ARG PRO LYS ALA ASP ALA LEU PRO GLY SEQRES 15 A 494 GLN TRP ALA PHE SER GLY HIS MET LEU ALA LYS GLY ASP SEQRES 16 A 494 VAL ARG GLY VAL MET SER VAL THR PRO ASP GLN GLY ASP SEQRES 17 A 494 THR PHE LYS VAL GLU VAL LYS GLY ALA TYR ALA ASP GLY SEQRES 18 A 494 THR PRO PHE ASN GLY SER GLY SER ALA ILE LEU TYR ASN SEQRES 19 A 494 GLY TYR GLU TRP ARG GLY ASN VAL LYS VAL GLY ASP ALA SEQRES 20 A 494 ASN LEU ARG GLN VAL PHE ALA ALA LEU ASP GLY GLU MET SEQRES 21 A 494 LYS GLY ARG MET PHE GLU ALA GLU HIS ASP GLU ARG GLY SEQRES 22 A 494 LEU ASP PHE THR ALA VAL LYS GLU GLY LYS ALA ARG LEU SEQRES 23 A 494 LEU ALA VAL GLN PRO ALA PHE ILE LYS ALA GLY GLY GLU SEQRES 24 A 494 SER GLU ILE THR LEU VAL GLY SER GLY LEU ALA GLY LYS SEQRES 25 A 494 PRO ASP LEU GLY ALA GLY VAL GLU VAL THR GLU VAL LEU SEQRES 26 A 494 GLU GLN THR PRO THR LEU VAL ARG LEU LYS ALA ARG ALA SEQRES 27 A 494 ALA ALA ASP ALA LYS PRO GLY GLN ARG GLU VAL ALA VAL SEQRES 28 A 494 GLY THR LEU LYS GLY VAL ASN LEU ALA VAL TYR ASP LYS SEQRES 29 A 494 VAL GLU GLU VAL LYS VAL VAL PRO ALA PHE SER ILE ALA SEQRES 30 A 494 ARG ILE GLY GLU ASN GLY ALA SER VAL PRO LYS VAL GLN SEQRES 31 A 494 GLY ARG PHE GLU ALA GLU ALA TRP GLY LYS ASP ALA ASN SEQRES 32 A 494 GLY GLN PRO LEU ARG ILE GLY TYR LEU PRO ALA SER TRP SEQRES 33 A 494 LYS VAL GLU PRO PHE ASN GLU ARG ALA VAL GLU ASP GLU SEQRES 34 A 494 ASP VAL LYS PHE ALA GLY LYS MET GLN ALA ASP GLY VAL SEQRES 35 A 494 PHE VAL PRO GLY GLY ALA GLY PRO ASN PRO GLU ARG LYS SEQRES 36 A 494 MET MET THR ASN ASN ALA GLY ASN LEU LYS VAL ILE ALA SEQRES 37 A 494 THR LEU ALA ASP GLY GLY GLN THR GLY GLU GLY HIS MET SEQRES 38 A 494 ILE VAL THR VAL GLN ARG TRP ASN ASN PRO PRO LEU PRO SEQRES 1 B 349 ALA ASP THR GLY PRO ALA LEU LYS ALA GLY HIS GLU TYR SEQRES 2 B 349 MET ILE VAL THR ASN TYR PRO ASN ASN LEU HIS VAL VAL SEQRES 3 B 349 ASP VAL ALA SER ASP THR VAL TYR LYS SER CYS VAL MET SEQRES 4 B 349 PRO ASP LYS PHE GLY PRO GLY THR ALA MET MET ALA PRO SEQRES 5 B 349 ASP ASN ARG THR ALA TYR VAL LEU ASN ASN HIS TYR GLY SEQRES 6 B 349 ASP ILE TYR GLY ILE ASP LEU ASP THR CYS LYS ASN THR SEQRES 7 B 349 PHE HIS ALA ASN LEU SER SER VAL PRO GLY GLU VAL GLY SEQRES 8 B 349 ARG SER MET TYR SER PHE ALA ILE SER PRO ASP GLY LYS SEQRES 9 B 349 GLU VAL TYR ALA THR VAL ASN PRO THR GLN ARG LEU ASN SEQRES 10 B 349 ASP HIS TYR VAL VAL LYS PRO PRO ARG LEU GLU VAL PHE SEQRES 11 B 349 SER THR ALA ASP GLY LEU GLU ALA LYS PRO VAL ARG THR SEQRES 12 B 349 PHE PRO MET PRO ARG GLN VAL TYR LEU MET ARG ALA ALA SEQRES 13 B 349 ASP ASP GLY SER LEU TYR VAL ALA GLY PRO ASP ILE TYR SEQRES 14 B 349 LYS MET ASP VAL LYS THR GLY LYS TYR THR VAL ALA LEU SEQRES 15 B 349 PRO LEU ARG ASN TRP ASN ARG LYS GLY TYR SER ALA PRO SEQRES 16 B 349 ASP VAL LEU TYR PHE TRP PRO HIS GLN SER PRO ARG HIS SEQRES 17 B 349 GLU PHE SER MET LEU TYR THR ILE ALA ARG PHE LYS ASP SEQRES 18 B 349 ASP LYS GLN ASP PRO ALA THR ALA ASP LEU LEU TYR GLY SEQRES 19 B 349 TYR LEU SER VAL ASP LEU LYS THR GLY LYS THR HIS THR SEQRES 20 B 349 GLN GLU PHE ALA ASP LEU THR GLU LEU TYR PHE THR GLY SEQRES 21 B 349 LEU ARG SER PRO LYS ASP PRO ASN GLN ILE TYR GLY VAL SEQRES 22 B 349 LEU ASN ARG LEU ALA LYS TYR ASP LEU LYS GLN ARG LYS SEQRES 23 B 349 LEU ILE LYS ALA ALA ASN LEU ASP HIS THR TYR TYR CYS SEQRES 24 B 349 VAL ALA PHE ASP LYS LYS GLY ASP LYS LEU TYR LEU GLY SEQRES 25 B 349 GLY THR PHE ASN ASP LEU ALA VAL PHE ASN PRO ASP THR SEQRES 26 B 349 LEU GLU LYS VAL LYS ASN ILE LYS LEU PRO GLY GLY ASP SEQRES 27 B 349 MET SER THR THR THR PRO GLN VAL PHE ILE ARG SEQRES 1 G 79 MET SER ALA VAL ALA GLY CYS THR ALA THR THR ASP PRO SEQRES 2 G 79 GLY TRP GLU VAL ASP ALA PHE GLY GLY VAL SER SER LEU SEQRES 3 G 79 CYS GLN PRO MET GLU ALA ASP LEU TYR GLY CYS SER ASP SEQRES 4 G 79 PRO CYS TRP TRQ PRO ALA GLN VAL PRO ASP MET MET SER SEQRES 5 G 79 THR TYR GLN ASP TRP ASN ALA GLN ALA SER ASN SER ALA SEQRES 6 G 79 GLU ASP TRP ARG ASN LEU GLY THR VAL PHE PRO LYS ASP SEQRES 7 G 79 LYS MODRES 1JMX TRQ G 43 TRP HET TRQ G 43 16 HET NI A2001 1 HET HEC A1001 43 HET HEC A1002 43 HETNAM TRQ 2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1H-INDOL-3-YL)- HETNAM 2 TRQ PROPIONIC ACID HETNAM NI NICKEL (II) ION HETNAM HEC HEME C FORMUL 3 TRQ C11 H10 N2 O4 FORMUL 4 NI NI 2+ FORMUL 5 HEC 2(C34 H34 FE N4 O4) FORMUL 7 HOH *457(H2 O) HELIX 1 1 GLN A 3 MET A 13 1 11 HELIX 2 2 ARG A 26 GLN A 30 5 5 HELIX 3 3 THR A 33 GLY A 49 1 17 HELIX 4 4 SER A 53 GLN A 68 1 16 HELIX 5 5 ALA A 71 THR A 75 5 5 HELIX 6 6 ASP A 93 GLY A 101 1 9 HELIX 7 7 GLY A 106 LEU A 111 1 6 HELIX 8 8 PRO A 115 TRP A 130 1 16 HELIX 9 9 PRO A 131 GLN A 136 5 6 HELIX 10 10 ASP A 143 GLN A 151 1 9 HELIX 11 11 GLN A 151 TYR A 160 1 10 HELIX 12 12 SER A 164 ARG A 174 1 11 HELIX 13 13 LYS A 176 LEU A 180 5 5 HELIX 14 14 ASN A 422 ASP A 428 1 7 HELIX 15 15 GLU A 429 ALA A 434 1 6 HELIX 16 16 ARG A 454 THR A 458 5 5 HELIX 17 17 ALA B 133 GLU B 137 5 5 HELIX 18 18 PRO G 29 ALA G 32 5 4 HELIX 19 19 ASP G 33 ASP G 39 1 7 HELIX 20 20 ASN G 63 TRP G 68 1 6 HELIX 21 21 ARG G 69 LEU G 71 5 3 SHEET 1 A 2 PRO A 18 GLY A 20 0 SHEET 2 A 2 THR A 23 TYR A 24 -1 O THR A 23 N GLU A 19 SHEET 1 B 2 ARG A 31 LYS A 32 0 SHEET 2 B 2 GLN A 112 ARG A 113 -1 N ARG A 113 O ARG A 31 SHEET 1 C 9 GLY A 182 MET A 190 0 SHEET 2 C 9 GLY A 194 PRO A 204 -1 N GLY A 194 O MET A 190 SHEET 3 C 9 THR A 209 TYR A 218 -1 N LYS A 211 O THR A 203 SHEET 4 C 9 PRO A 223 TYR A 233 -1 N PHE A 224 O GLY A 216 SHEET 5 C 9 GLU A 237 VAL A 244 -1 O GLU A 237 N TYR A 233 SHEET 6 C 9 ALA A 247 LEU A 256 -1 O ALA A 247 N VAL A 244 SHEET 7 C 9 GLU A 259 GLU A 266 -1 O GLU A 259 N LEU A 256 SHEET 8 C 9 HIS A 269 LYS A 280 -1 O HIS A 269 N GLU A 266 SHEET 9 C 9 GLY A 182 MET A 190 -1 O ALA A 185 N VAL A 279 SHEET 1 D 4 ARG A 285 GLN A 290 0 SHEET 2 D 4 GLU A 299 SER A 307 -1 O THR A 303 N GLN A 290 SHEET 3 D 4 LEU A 331 ALA A 338 -1 O VAL A 332 N LEU A 304 SHEET 4 D 4 VAL A 319 GLN A 327 -1 N GLU A 320 O ARG A 337 SHEET 1 E 4 PHE A 293 LYS A 295 0 SHEET 2 E 4 LEU A 354 TYR A 362 1 O ALA A 360 N ILE A 294 SHEET 3 E 4 GLY A 345 VAL A 351 -1 N GLY A 345 O VAL A 361 SHEET 4 E 4 PRO A 313 ASP A 314 -1 N ASP A 314 O ALA A 350 SHEET 1 F 3 GLU A 367 VAL A 371 0 SHEET 2 F 3 GLU A 394 LYS A 400 -1 O GLU A 394 N VAL A 371 SHEET 3 F 3 PRO A 406 TYR A 411 -1 O LEU A 407 N GLY A 399 SHEET 1 G 4 PHE A 374 ARG A 378 0 SHEET 2 G 4 THR A 476 THR A 484 1 O HIS A 480 N SER A 375 SHEET 3 G 4 GLY A 462 LEU A 470 -1 O GLY A 462 N VAL A 483 SHEET 4 G 4 ALA A 414 PRO A 420 -1 N SER A 415 O THR A 469 SHEET 1 H 3 GLY A 391 ARG A 392 0 SHEET 2 H 3 VAL A 442 PRO A 445 -1 N PHE A 443 O GLY A 391 SHEET 3 H 3 GLY A 435 MET A 437 -1 O LYS A 436 N VAL A 444 SHEET 1 I 4 GLN B 345 ILE B 348 0 SHEET 2 I 4 GLU B 12 ASN B 18 -1 N TYR B 13 O PHE B 347 SHEET 3 I 4 ASN B 22 ASP B 27 -1 O ASN B 22 N ASN B 18 SHEET 4 I 4 THR B 32 VAL B 38 -1 O THR B 32 N ASP B 27 SHEET 1 J 4 THR B 47 MET B 50 0 SHEET 2 J 4 THR B 56 ASN B 61 -1 N TYR B 58 O MET B 49 SHEET 3 J 4 ASP B 66 ASP B 71 -1 O ASP B 66 N ASN B 61 SHEET 4 J 4 ASN B 77 ASN B 82 -1 N THR B 78 O GLY B 69 SHEET 1 K 8 GLU B 89 ARG B 92 0 SHEET 2 K 8 GLU B 105 ARG B 115 -1 N ASN B 111 O ARG B 92 SHEET 3 K 8 PHE B 97 ILE B 99 -1 O ALA B 98 N TYR B 107 SHEET 4 K 8 GLU B 105 ARG B 115 -1 N TYR B 107 O ALA B 98 SHEET 5 K 8 TYR B 120 VAL B 122 -1 O VAL B 121 N GLN B 114 SHEET 6 K 8 GLU B 105 ARG B 115 -1 N GLN B 114 O VAL B 121 SHEET 7 K 8 ARG B 126 SER B 131 -1 O ARG B 126 N VAL B 110 SHEET 8 K 8 ARG B 142 PRO B 145 -1 O ARG B 142 N VAL B 129 SHEET 1 L 4 MET B 153 ALA B 155 0 SHEET 2 L 4 LEU B 161 ALA B 164 -1 N TYR B 162 O ARG B 154 SHEET 3 L 4 ILE B 168 MET B 171 -1 N TYR B 169 O VAL B 163 SHEET 4 L 4 TYR B 178 LEU B 182 -1 O THR B 179 N LYS B 170 SHEET 1 M 3 GLU B 209 ARG B 218 0 SHEET 2 M 3 ASP B 230 ASP B 239 -1 N ASP B 230 O ARG B 218 SHEET 3 M 3 THR B 245 ASP B 252 -1 N HIS B 246 O SER B 237 SHEET 1 N 4 TYR B 257 ARG B 262 0 SHEET 2 N 4 GLN B 269 LEU B 274 -1 N TYR B 271 O LEU B 261 SHEET 3 N 4 ARG B 276 ASP B 281 -1 O ARG B 276 N LEU B 274 SHEET 4 N 4 LYS B 286 ASN B 292 -1 O LYS B 286 N ASP B 281 SHEET 1 O 4 CYS B 299 PHE B 302 0 SHEET 2 O 4 LEU B 309 GLY B 312 -1 N TYR B 310 O ALA B 301 SHEET 3 O 4 ASP B 317 ASN B 322 -1 O ALA B 319 N LEU B 311 SHEET 4 O 4 GLU B 327 LYS B 333 -1 O GLU B 327 N ASN B 322 SSBOND 1 CYS B 37 CYS B 75 1555 1555 2.03 LINK SG CYS A 100 CAB HEC A1001 1555 1555 1.70 LINK SG CYS A 103 CAC HEC A1001 1555 1555 1.82 LINK NE2 HIS A 104 FE HEC A1001 1555 1555 2.04 LINK NE2 HIS A 126 FE HEC A1001 1555 1555 2.14 LINK SG CYS A 12 CAB HEC A1002 1555 1555 1.83 LINK SG CYS A 15 CAC HEC A1002 1555 1555 1.79 LINK NE2 HIS A 16 FE HEC A1002 1555 1555 2.04 LINK OE1 GLU A 367 NI NI A2001 1555 1555 1.93 LINK SG CYS G 27 CB ASP G 33 1555 1555 1.74 LINK SG CYS G 41 CB ASP G 49 1555 1555 1.77 LINK SG CYS G 37 CE3 TRQ G 43 1555 1555 1.84 LINK SG CYS G 7 CG GLU G 16 1555 1555 2.08 LINK FE HEC A1002 SD MET A 44 1555 1555 2.45 LINK NI NI A2001 O HOH A2151 1555 1555 2.64 LINK NI NI A2001 O HOH A2068 1555 1555 2.09 LINK NI NI A2001 O HOH A2248 1555 1555 2.21 LINK C TRP G 42 N TRQ G 43 1555 1555 1.32 LINK C TRQ G 43 N PRO G 44 1555 1555 1.35 LINK NI NI A2001 NE2 HIS B 11 1555 4646 2.25 CISPEP 1 GLN A 290 PRO A 291 0 -0.05 CISPEP 2 VAL A 371 PRO A 372 0 -0.11 CISPEP 3 GLY B 44 PRO B 45 0 -0.11 CISPEP 4 ASP G 12 PRO G 13 0 -0.21 CISPEP 5 GLN G 28 PRO G 29 0 -0.57 SITE 1 AC1 5 GLU A 367 HOH A2068 HOH A2151 HOH A2248 SITE 2 AC1 5 HIS B 11 SITE 1 AC2 21 LYS A 32 SER A 40 ARG A 43 THR A 99 SITE 2 AC2 21 CYS A 100 CYS A 103 HIS A 104 ARG A 108 SITE 3 AC2 21 VAL A 109 GLN A 112 LEU A 122 HIS A 126 SITE 4 AC2 21 TRP A 130 GLN A 136 ASN A 489 PRO A 491 SITE 5 AC2 21 HEC A1002 HOH A2058 HOH A2102 HOH G 80 SITE 6 AC2 21 HOH G 82 SITE 1 AC3 20 LYS A 11 CYS A 12 CYS A 15 HIS A 16 SITE 2 AC3 20 ARG A 26 ILE A 27 GLN A 30 ARG A 43 SITE 3 AC3 20 MET A 44 HIS A 48 LEU A 50 ARG A 114 SITE 4 AC3 20 PHE A 125 HEC A1001 HOH A2003 HOH A2035 SITE 5 AC3 20 LEU B 116 ASN B 117 ASP B 118 HIS B 119 CRYST1 167.210 92.370 79.300 90.00 112.00 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 0.005981 0.000000 0.002416 0.00000 SCALE2 0.000000 0.010826 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013601 0.00000