HEADER OXIDOREDUCTASE 15-MAY-03 1PBY TITLE STRUCTURE OF THE PHENYLHYDRAZINE ADDUCT OF THE QUINOHEMOPROTEIN AMINE TITLE 2 DEHYDROGENASE FROM PARACOCCUS DENITRIFICANS AT 1.7 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: QUINOHEMOPROTEIN AMINE DEHYDROGENASE 60 KDA SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 EC: 1.4.99.3; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: QUINOHEMOPROTEIN AMINE DEHYDROGENASE 40 KDA SUBUNIT; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: QUINOHEMOPROTEIN AMINE DEHYDROGENASE 9 KDA SUBUNIT; COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARACOCCUS DENITRIFICANS; SOURCE 3 ORGANISM_TAXID: 266; SOURCE 4 EXPRESSION_SYSTEM: PARACOCCUS DENITRIFICANS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 266; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: IFO12442; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: PARACOCCUS DENITRIFICANS; SOURCE 9 ORGANISM_TAXID: 266; SOURCE 10 EXPRESSION_SYSTEM: PARACOCCUS DENITRIFICANS; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 266; SOURCE 12 MOL_ID: 3; SOURCE 13 ORGANISM_SCIENTIFIC: PARACOCCUS DENITRIFICANS; SOURCE 14 ORGANISM_TAXID: 266; SOURCE 15 EXPRESSION_SYSTEM: PARACOCCUS DENITRIFICANS; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 266 KEYWDS QUINOHEMOPROTEIN, AMINE DEHYDROGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.DATTA,T.IKEDA,K.KANO,F.S.MATHEWS REVDAT 6 16-AUG-23 1PBY 1 REMARK REVDAT 5 03-MAR-21 1PBY 1 COMPND REMARK SEQADV HET REVDAT 5 2 1 HETNAM HETSYN FORMUL LINK REVDAT 5 3 1 SITE ATOM REVDAT 4 11-OCT-17 1PBY 1 REMARK REVDAT 3 24-FEB-09 1PBY 1 VERSN REVDAT 2 09-SEP-03 1PBY 1 MODRES REVDAT 1 02-SEP-03 1PBY 0 JRNL AUTH S.DATTA,T.IKEDA,K.KANO,F.S.MATHEWS JRNL TITL STRUCTURE OF THE PHENYLHYDRAZINE ADDUCT OF THE JRNL TITL 2 QUINOHEMOPROTEIN AMINE DEHYDROGENASE FROM PARACOCCUS JRNL TITL 3 DENITRIFICANS AT 1.7 A RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 59 1551 2003 JRNL REFN ISSN 0907-4449 JRNL PMID 12925784 JRNL DOI 10.1107/S090744490301429X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 TITL STRUCTURE OF A QUINOHEMOPROTEIN AMINE DEHYDROGENASE WITH AN REMARK 1 TITL 2 UNCOMMON REDOX COFACTOR AND HIGHLY UNUSUAL CROSSLINKING REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 98 14268 2001 REMARK 1 REFN ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.2 REMARK 3 NUMBER OF REFLECTIONS : 105982 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) : 0.191 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 10633 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.002 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 68.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 11945 REMARK 3 BIN R VALUE (WORKING SET) : 0.2652 REMARK 3 BIN FREE R VALUE : 0.2823 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 1292 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.008 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6931 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 106 REMARK 3 SOLVENT ATOMS : 1295 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.50 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) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.18 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.860 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 1PBY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAY-03. REMARK 100 THE DEPOSITION ID IS D_1000019220. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 110131 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 36.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 6.760 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.30 REMARK 200 R MERGE FOR SHELL (I) : 0.48100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: REFINED DIRECTLY REMARK 200 SOFTWARE USED: REFINED DIRECTLY REMARK 200 STARTING MODEL: PDB ENTRY 1JJU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM CITRATE, T-BUTYL REMARK 280 ALCOHOL, PH 5.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 106.52800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 49.61850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 49.61850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 53.26400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 49.61850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 49.61850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 159.79200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 49.61850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.61850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 53.26400 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 49.61850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.61850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 159.79200 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 106.52800 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -83.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 HIS A 15 CB - CG - CD2 ANGL. DEV. = -10.9 DEGREES REMARK 500 HIS A 15 ND1 - CG - CD2 ANGL. DEV. = 11.3 DEGREES REMARK 500 HIS A 104 CB - CG - CD2 ANGL. DEV. = -11.4 DEGREES REMARK 500 HIS A 104 ND1 - CG - CD2 ANGL. DEV. = 11.2 DEGREES REMARK 500 HIS A 126 CB - CG - CD2 ANGL. DEV. = -10.9 DEGREES REMARK 500 HIS A 126 ND1 - CG - CD2 ANGL. DEV. = 11.3 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 ALA A 10 -53.90 -123.50 REMARK 500 CYS A 14 -37.06 -130.05 REMARK 500 ARG A 25 -61.60 72.11 REMARK 500 GLU A 76 -3.91 77.83 REMARK 500 CYS A 103 -63.82 -106.01 REMARK 500 LEU A 138 1.04 82.22 REMARK 500 SER A 260 86.06 -157.51 REMARK 500 ILE A 288 129.17 -38.39 REMARK 500 PRO A 394 79.37 -33.17 REMARK 500 ASP A 398 -3.05 -164.89 REMARK 500 ASN A 453 42.55 -80.15 REMARK 500 ASP A 464 -155.39 -98.27 REMARK 500 ALA A 465 169.31 -10.84 REMARK 500 GLU A 466 110.63 45.45 REMARK 500 GLU A 468 51.49 32.87 REMARK 500 PRO A 469 57.60 -115.68 REMARK 500 THR A 479 -163.95 -112.42 REMARK 500 ASP B 11 32.46 -143.52 REMARK 500 THR B 35 144.14 -178.46 REMARK 500 LEU B 84 -105.36 52.80 REMARK 500 THR B 138 -80.54 -95.98 REMARK 500 THR B 138 -79.77 -95.98 REMARK 500 ILE B 172 -59.28 -126.11 REMARK 500 GLN B 191 39.60 -159.63 REMARK 500 TYR B 259 -91.97 -170.83 REMARK 500 ALA B 299 -72.17 68.36 REMARK 500 LEU B 300 -147.20 -106.25 REMARK 500 SER B 326 -139.80 48.84 REMARK 500 ASP B 336 92.27 -61.32 REMARK 500 TRP C 15 -60.41 -129.37 REMARK 500 ASN C 52 -63.30 -143.02 REMARK 500 PRO C 76 5.39 -43.66 REMARK 500 GLU C 77 91.72 65.83 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 A2245 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH A2264 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH A2511 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A2541 DISTANCE = 7.21 ANGSTROMS REMARK 525 HOH A2549 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A2571 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH A2593 DISTANCE = 6.64 ANGSTROMS REMARK 525 HOH A2609 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A2610 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A2616 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A2632 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A2636 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH A2647 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH B2088 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH B2211 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH B2385 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH B2414 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH B2462 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH B2499 DISTANCE = 6.18 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 A 991 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 15 NE2 REMARK 620 2 HEC A 991 NA 88.7 REMARK 620 3 HEC A 991 NB 83.5 90.1 REMARK 620 4 HEC A 991 NC 89.6 178.2 89.3 REMARK 620 5 HEC A 991 ND 97.7 90.9 178.4 89.7 REMARK 620 6 MET A 43 SD 177.2 90.2 93.9 91.5 84.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 992 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 104 NE2 REMARK 620 2 HEC A 992 NA 92.9 REMARK 620 3 HEC A 992 NB 96.1 89.9 REMARK 620 4 HEC A 992 NC 87.5 179.2 89.4 REMARK 620 5 HEC A 992 ND 86.4 90.6 177.4 90.1 REMARK 620 6 HIS A 126 NE2 175.9 90.1 81.0 89.5 96.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 991 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 992 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TBU A 1993 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TBU A 1994 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TBU B 1995 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TBU B 1996 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JJU RELATED DB: PDB REMARK 900 STRUCTURE OF A QUINOHEMOPROTEIN AMINE DEHYDROGENASE WITH AN REMARK 900 UNCOMMON REDOX COFACTOR AND HIGHLY UNUSUAL CROSSLINKING DBREF 1PBY A 1 489 UNP Q8VUT0 Q8VUT0_PARDE 24 512 DBREF 1PBY B 1 337 GB 17402571 BAB78729 22 358 DBREF 1PBY C 1 79 GB 17402570 BAB78728 29 107 SEQADV 1PBY TRW C 43 GB 17402570 TRP 71 MODIFIED RESIDUE SEQRES 1 A 489 VAL THR GLY GLU GLU VAL LEU GLN ASN ALA CYS ALA ALA SEQRES 2 A 489 CYS HIS VAL GLN HIS GLU ASP GLY ARG TRP GLU ARG ILE SEQRES 3 A 489 ASP ALA ALA ARG LYS THR PRO GLU GLY TRP ASP MET THR SEQRES 4 A 489 VAL THR ARG MET MET ARG ASN HIS GLY VAL ALA LEU GLU SEQRES 5 A 489 PRO GLU GLU ARG ALA ALA ILE VAL ARG HIS LEU SER ASP SEQRES 6 A 489 THR ARG GLY LEU SER LEU ALA GLU THR GLU GLU ARG ARG SEQRES 7 A 489 TYR ILE LEU GLU ARG GLU PRO VAL ALA TRP ASP GLU GLY SEQRES 8 A 489 PRO ASP THR SER MET THR GLN THR CYS GLY ARG CYS HIS SEQRES 9 A 489 SER TYR ALA ARG VAL ALA LEU GLN ARG ARG THR PRO GLU SEQRES 10 A 489 ASP TRP LYS HIS LEU VAL ASN PHE HIS LEU GLY GLN PHE SEQRES 11 A 489 PRO THR LEU GLU TYR GLN ALA LEU ALA ARG ASP ARG ASP SEQRES 12 A 489 TRP TRP GLY ILE ALA GLN ALA GLU ILE ILE PRO PHE LEU SEQRES 13 A 489 ALA ARG THR TYR PRO LEU GLY GLU ALA PRO ASP ALA TYR SEQRES 14 A 489 ALA ASP ASP ALA SER GLY ALA TYR VAL LEU ALA GLY ARG SEQRES 15 A 489 GLN PRO GLY ARG GLY ASP TYR THR GLY ARG LEU VAL LEU SEQRES 16 A 489 LYS LYS ALA GLY GLU ASP TYR GLU VAL THR MET THR LEU SEQRES 17 A 489 ASP PHE ALA ASP GLY SER ARG SER PHE SER GLY THR GLY SEQRES 18 A 489 ARG ILE LEU GLY ALA GLY GLU TRP ARG ALA THR LEU SER SEQRES 19 A 489 ASP GLY THR VAL THR ILE ARG GLN ILE PHE ALA LEU GLN SEQRES 20 A 489 ASP GLY ARG PHE SER GLY ARG TRP HIS ASP ALA ASP SER SEQRES 21 A 489 ASP VAL ILE GLY GLY ARG LEU ALA ALA VAL LYS ALA ASP SEQRES 22 A 489 ALA ALA PRO GLN VAL LEU ALA VAL ALA PRO ALA ARG LEU SEQRES 23 A 489 LYS ILE GLY GLU GLU THR GLN LEU ARG VAL ALA GLY THR SEQRES 24 A 489 GLY LEU GLY SER ASP LEU THR LEU PRO GLU GLY VAL ALA SEQRES 25 A 489 GLY SER VAL GLU SER ALA GLY ASN GLY VAL THR VAL LEU SEQRES 26 A 489 LYS LEU THR ALA THR GLY THR PRO GLY PRO VAL SER LEU SEQRES 27 A 489 GLU LEU GLY GLY GLN LYS VAL ASP LEU VAL ALA TYR ASP SEQRES 28 A 489 ARG PRO ASP ARG ILE SER ILE VAL PRO ASP LEU THR ILE SEQRES 29 A 489 ALA ARG ILE GLY GLY ASN GLY GLY PRO ILE PRO LYS VAL SEQRES 30 A 489 PRO ALA GLN PHE GLU ALA MET GLY TRP LEU ASN GLY PRO SEQRES 31 A 489 ASP GLY GLN PRO GLY THR GLY ASP ASP ILE ALA LEU GLY SEQRES 32 A 489 ALA PHE PRO ALA SER TRP ALA THR ASP ASN PHE ASP GLU SEQRES 33 A 489 GLU ALA GLU LYS MET GLN ASP ALA LYS TYR ALA GLY SER SEQRES 34 A 489 ILE ASP ASP THR GLY LEU PHE THR PRO ALA GLU ALA GLY SEQRES 35 A 489 PRO ASN PRO GLU ARG PRO MET GLN THR ASN ASN ALA GLY SEQRES 36 A 489 ASN LEU LYS VAL ILE ALA THR VAL ASP ALA GLU GLY GLU SEQRES 37 A 489 PRO LEU SER ALA GLU ALA HIS LEU TYR ALA THR VAL GLN SEQRES 38 A 489 ARG PHE VAL ASP ALA PRO ILE ARG SEQRES 1 B 337 ARG ASP TYR ILE LEU ALA PRO ALA ARG PRO ASP LYS LEU SEQRES 2 B 337 VAL VAL ILE ASP THR GLU LYS MET ALA VAL ASP LYS VAL SEQRES 3 B 337 ILE THR ILE ALA ASP ALA GLY PRO THR PRO MET VAL PRO SEQRES 4 B 337 MET VAL ALA PRO GLY GLY ARG ILE ALA TYR ALA THR VAL SEQRES 5 B 337 ASN LYS SER GLU SER LEU VAL LYS ILE ASP LEU VAL THR SEQRES 6 B 337 GLY GLU THR LEU GLY ARG ILE ASP LEU SER THR PRO GLU SEQRES 7 B 337 GLU ARG VAL LYS SER LEU PHE GLY ALA ALA LEU SER PRO SEQRES 8 B 337 ASP GLY LYS THR LEU ALA ILE TYR GLU SER PRO VAL ARG SEQRES 9 B 337 LEU GLU LEU THR HIS PHE GLU VAL GLN PRO THR ARG VAL SEQRES 10 B 337 ALA LEU TYR ASP ALA GLU THR LEU SER ARG ARG LYS ALA SEQRES 11 B 337 PHE GLU ALA PRO ARG GLN ILE THR MET LEU ALA TRP ALA SEQRES 12 B 337 ARG ASP GLY SER LYS LEU TYR GLY LEU GLY ARG ASP LEU SEQRES 13 B 337 HIS VAL MET ASP PRO GLU ALA GLY THR LEU VAL GLU ASP SEQRES 14 B 337 LYS PRO ILE GLN SER TRP GLU ALA GLU THR TYR ALA GLN SEQRES 15 B 337 PRO ASP VAL LEU ALA VAL TRP ASN GLN HIS GLU SER SER SEQRES 16 B 337 GLY VAL MET ALA THR PRO PHE TYR THR ALA ARG LYS ASP SEQRES 17 B 337 ILE ASP PRO ALA ASP PRO THR ALA TYR ARG THR GLY LEU SEQRES 18 B 337 LEU THR MET ASP LEU GLU THR GLY GLU MET ALA MET ARG SEQRES 19 B 337 GLU VAL ARG ILE MET ASP VAL PHE TYR PHE SER THR ALA SEQRES 20 B 337 VAL ASN PRO ALA LYS THR ARG ALA PHE GLY ALA TYR ASN SEQRES 21 B 337 VAL LEU GLU SER PHE ASP LEU GLU LYS ASN ALA SER ILE SEQRES 22 B 337 LYS ARG VAL PRO LEU PRO HIS SER TYR TYR SER VAL ASN SEQRES 23 B 337 VAL SER THR ASP GLY SER THR VAL TRP LEU GLY GLY ALA SEQRES 24 B 337 LEU GLY ASP LEU ALA ALA TYR ASP ALA GLU THR LEU GLU SEQRES 25 B 337 LYS LYS GLY GLN VAL ASP LEU PRO GLY ASN ALA SER MET SEQRES 26 B 337 SER LEU ALA SER VAL ARG LEU PHE THR ARG ASP GLU SEQRES 1 C 79 MET ASN ALA LEU VAL GLY CYS THR THR SER PHE ASP PRO SEQRES 2 C 79 GLY TRP GLU VAL ASP ALA PHE GLY ALA VAL SER ASN LEU SEQRES 3 C 79 CYS GLN PRO MET GLU ALA ASP LEU TYR GLY CYS ALA ASP SEQRES 4 C 79 PRO CYS TRP TRW PRO ALA GLN VAL ALA ASP THR LEU ASN SEQRES 5 C 79 THR TYR PRO ASN TRP SER ALA GLY ALA ASP ASP VAL MET SEQRES 6 C 79 GLN ASP TRP ARG LYS LEU GLN SER VAL PHE PRO GLU THR SEQRES 7 C 79 LYS MODRES 1PBY TRW C 43 TRP HET TRW C 43 23 HET HEC A 991 43 HET HEC A 992 43 HET TBU A1993 5 HET TBU A1994 5 HET TBU B1995 5 HET TBU B1996 5 HETNAM TRW TRW3-(2-AMINO-3-HYDROXY-PROPYL)-6-(N'-CYCLOHEXYL- HETNAM 2 TRW HYDRAZINO)OCTAHYDRO-INDOL-7-OL HETNAM HEC HEME C HETNAM TBU TERTIARY-BUTYL ALCOHOL HETSYN TRW PHENYLHYDRAZINE ADDUCT HETSYN TBU 2-METHYL-2-PROPANOL FORMUL 3 TRW C17 H18 N4 O2 FORMUL 4 HEC 2(C34 H34 FE N4 O4) FORMUL 6 TBU 4(C4 H10 O) FORMUL 10 HOH *1295(H2 O) HELIX 1 1 THR A 2 ALA A 10 1 9 HELIX 2 2 CYS A 11 CYS A 14 5 4 HELIX 3 3 ARG A 25 ASP A 27 5 3 HELIX 4 4 THR A 32 HIS A 47 1 16 HELIX 5 5 GLU A 52 ARG A 67 1 16 HELIX 6 6 LEU A 71 GLU A 75 5 5 HELIX 7 7 ARG A 77 ARG A 83 1 7 HELIX 8 8 ASP A 93 GLY A 101 1 9 HELIX 9 9 TYR A 106 LEU A 111 1 6 HELIX 10 10 THR A 115 PHE A 130 1 16 HELIX 11 11 PRO A 131 GLN A 136 5 6 HELIX 12 12 ASP A 143 GLU A 151 1 9 HELIX 13 13 GLU A 151 TYR A 160 1 10 HELIX 14 14 ASP A 415 GLN A 422 1 8 HELIX 15 15 GLN A 422 ALA A 427 1 6 HELIX 16 16 ARG A 447 THR A 451 5 5 HELIX 17 17 ASP B 213 THR B 215 5 3 HELIX 18 18 PRO B 320 ALA B 323 5 4 HELIX 19 19 MET C 30 ASP C 39 1 10 HELIX 20 20 ASP C 63 TRP C 68 1 6 HELIX 21 21 ARG C 69 LEU C 71 5 3 SHEET 1 A 2 ALA A 29 LYS A 31 0 SHEET 2 A 2 GLN A 112 ARG A 114 -1 O ARG A 113 N ARG A 30 SHEET 1 B 9 GLY A 175 GLN A 183 0 SHEET 2 B 9 GLY A 187 ALA A 198 -1 O LEU A 195 N GLY A 175 SHEET 3 B 9 ASP A 201 ASP A 209 -1 O GLU A 203 N LYS A 196 SHEET 4 B 9 SER A 214 LEU A 224 -1 O GLY A 219 N VAL A 204 SHEET 5 B 9 GLU A 228 ASP A 235 -1 O GLU A 228 N LEU A 224 SHEET 6 B 9 VAL A 238 GLN A 247 -1 O ILE A 240 N LEU A 233 SHEET 7 B 9 ARG A 250 ASP A 257 -1 O SER A 252 N ALA A 245 SHEET 8 B 9 SER A 260 LYS A 271 -1 O ILE A 263 N ASP A 257 SHEET 9 B 9 GLY A 175 GLN A 183 -1 N VAL A 178 O VAL A 270 SHEET 1 C 4 GLN A 277 ALA A 282 0 SHEET 2 C 4 THR A 292 THR A 299 -1 O ALA A 297 N ALA A 280 SHEET 3 C 4 VAL A 322 ALA A 329 -1 O LEU A 325 N LEU A 294 SHEET 4 C 4 VAL A 311 SER A 317 -1 N SER A 314 O LYS A 326 SHEET 1 D 4 ARG A 285 LYS A 287 0 SHEET 2 D 4 GLN A 343 TYR A 350 1 O VAL A 348 N LEU A 286 SHEET 3 D 4 GLY A 334 LEU A 340 -1 N VAL A 336 O LEU A 347 SHEET 4 D 4 LEU A 305 THR A 306 -1 N THR A 306 O GLU A 339 SHEET 1 E 3 ARG A 355 VAL A 359 0 SHEET 2 E 3 GLU A 382 LEU A 387 -1 O MET A 384 N SER A 357 SHEET 3 E 3 ILE A 400 PHE A 405 -1 O PHE A 405 N ALA A 383 SHEET 1 F 4 LEU A 362 ARG A 366 0 SHEET 2 F 4 SER A 471 THR A 479 1 O THR A 479 N ALA A 365 SHEET 3 F 4 GLY A 455 THR A 462 -1 N VAL A 459 O ALA A 474 SHEET 4 F 4 SER A 408 ASN A 413 -1 N ALA A 410 O ILE A 460 SHEET 1 G 3 ALA A 379 GLN A 380 0 SHEET 2 G 3 LEU A 435 PRO A 438 -1 O PHE A 436 N ALA A 379 SHEET 3 G 3 GLY A 428 ILE A 430 -1 N SER A 429 O THR A 437 SHEET 1 H 4 ALA B 22 THR B 28 0 SHEET 2 H 4 LYS B 12 ASP B 17 -1 N VAL B 15 O ASP B 24 SHEET 3 H 4 ASP B 2 ALA B 8 -1 N ALA B 6 O VAL B 14 SHEET 4 H 4 ARG B 331 THR B 334 -1 O PHE B 333 N TYR B 3 SHEET 1 I 4 PRO B 39 VAL B 41 0 SHEET 2 I 4 ILE B 47 VAL B 52 -1 O TYR B 49 N MET B 40 SHEET 3 I 4 SER B 57 ASP B 62 -1 O ILE B 61 N ALA B 48 SHEET 4 I 4 THR B 68 ASP B 73 -1 O ILE B 72 N LEU B 58 SHEET 1 J 3 GLU B 79 LYS B 82 0 SHEET 2 J 3 THR B 95 LEU B 105 -1 O SER B 101 N LYS B 82 SHEET 3 J 3 PHE B 110 VAL B 112 -1 O GLU B 111 N ARG B 104 SHEET 1 K 4 ALA B 87 LEU B 89 0 SHEET 2 K 4 THR B 95 LEU B 105 -1 O ALA B 97 N ALA B 88 SHEET 3 K 4 ARG B 116 ASP B 121 -1 O ALA B 118 N ILE B 98 SHEET 4 K 4 SER B 126 GLU B 132 -1 O LYS B 129 N LEU B 119 SHEET 1 L 4 LEU B 140 TRP B 142 0 SHEET 2 L 4 LEU B 149 LEU B 152 -1 O TYR B 150 N ALA B 141 SHEET 3 L 4 LEU B 156 ASP B 160 -1 O MET B 159 N LEU B 149 SHEET 4 L 4 THR B 165 LYS B 170 -1 O GLU B 168 N VAL B 158 SHEET 1 M 3 VAL B 197 ALA B 205 0 SHEET 2 M 3 TYR B 217 ASP B 225 -1 O GLY B 220 N PHE B 202 SHEET 3 M 3 MET B 231 ILE B 238 -1 O VAL B 236 N THR B 219 SHEET 1 N 4 SER B 245 VAL B 248 0 SHEET 2 N 4 ARG B 254 ALA B 258 -1 O PHE B 256 N ALA B 247 SHEET 3 N 4 VAL B 261 ASP B 266 -1 O PHE B 265 N ALA B 255 SHEET 4 N 4 ALA B 271 PRO B 277 -1 O ALA B 271 N ASP B 266 SHEET 1 O 4 SER B 284 VAL B 287 0 SHEET 2 O 4 THR B 293 GLY B 297 -1 O TRP B 295 N ASN B 286 SHEET 3 O 4 ASP B 302 ASP B 307 -1 O TYR B 306 N VAL B 294 SHEET 4 O 4 LYS B 313 ASP B 318 -1 O LYS B 314 N ALA B 305 LINK SG CYS A 11 CAB HEC A 991 1555 1555 1.80 LINK SG CYS A 14 CAC HEC A 991 1555 1555 1.87 LINK SG CYS A 100 CAB HEC A 992 1555 1555 1.78 LINK SG CYS A 103 CAC HEC A 992 1555 1555 1.84 LINK SG CYS C 7 CG GLU C 16 1555 1555 1.81 LINK SG CYS C 27 CB ASP C 33 1555 1555 1.80 LINK SG CYS C 37 CE3 TRW C 43 1555 1555 1.81 LINK SG CYS C 41 CB ASP C 49 1555 1555 1.81 LINK C TRP C 42 N TRW C 43 1555 1555 1.35 LINK C TRW C 43 N PRO C 44 1555 1555 1.34 LINK NE2 HIS A 15 FE HEC A 991 1555 1555 2.08 LINK SD MET A 43 FE HEC A 991 1555 1555 2.36 LINK NE2 HIS A 104 FE HEC A 992 1555 1555 2.05 LINK NE2 HIS A 126 FE HEC A 992 1555 1555 2.03 CISPEP 1 ALA A 282 PRO A 283 0 -0.51 CISPEP 2 VAL A 359 PRO A 360 0 -0.17 CISPEP 3 ARG B 9 PRO B 10 0 0.15 CISPEP 4 GLY B 33 PRO B 34 0 0.19 CISPEP 5 ASP C 12 PRO C 13 0 0.48 CISPEP 6 GLN C 28 PRO C 29 0 -0.39 SITE 1 AC1 20 ALA A 10 CYS A 11 CYS A 14 HIS A 15 SITE 2 AC1 20 ARG A 25 ILE A 26 TRP A 36 THR A 39 SITE 3 AC1 20 ARG A 42 MET A 43 HIS A 47 VAL A 49 SITE 4 AC1 20 ARG A 114 PHE A 125 HEC A 992 HOH A2001 SITE 5 AC1 20 HOH A2007 LEU B 107 THR B 108 HIS B 109 SITE 1 AC2 25 LYS A 31 THR A 39 ARG A 42 ARG A 45 SITE 2 AC2 25 THR A 99 CYS A 100 ARG A 102 CYS A 103 SITE 3 AC2 25 HIS A 104 ARG A 108 VAL A 109 GLN A 112 SITE 4 AC2 25 ARG A 114 LEU A 122 HIS A 126 PHE A 130 SITE 5 AC2 25 LEU A 133 GLN A 136 HEC A 991 HOH A1999 SITE 6 AC2 25 HOH A2008 HOH A2030 HOH A2176 PRO C 44 SITE 7 AC2 25 HOH C 80 SITE 1 AC3 2 GLY A 236 GLU B 162 SITE 1 AC4 2 HOH A2412 ARG B 128 SITE 1 AC5 5 SER A 303 GLU A 316 ALA A 318 ILE B 209 SITE 2 AC5 5 ASP B 213 SITE 1 AC6 3 GLU B 132 HOH B2247 HOH B2456 CRYST1 99.237 99.237 213.056 90.00 90.00 90.00 P 41 21 2 8 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 0.010077 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010077 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004694 0.00000