HEADER OXIDOREDUCTASE 06-SEP-16 5LTH TITLE CRYSTAL STRUCTURE OF THE ALPHA SUBUNIT OF HEME DEPENDENT OXIDATIVE N- TITLE 2 DEMETHYLASE (HODM) IN COMPLEX WITH THE DIMETHYLAMINE SUBSTRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEME DEPENDENT OXIDATIVE N-DEMETHYLASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS MENDOCINA; SOURCE 3 ORGANISM_TAXID: 300; SOURCE 4 GENE: PMEN_3455; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HEME BINDING, PAS DOMAIN, AMINE OXIDASE, DIMETHYLAMINE, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.ORTMAYER,D.LEYS REVDAT 5 17-JAN-24 5LTH 1 LINK REVDAT 4 21-DEC-16 5LTH 1 JRNL REVDAT 3 07-DEC-16 5LTH 1 JRNL REVDAT 2 23-NOV-16 5LTH 1 JRNL REVDAT 1 09-NOV-16 5LTH 0 JRNL AUTH M.ORTMAYER,P.LAFITE,B.R.MENON,T.TRALAU,K.FISHER,L.DENKHAUS, JRNL AUTH 2 N.S.SCRUTTON,S.E.RIGBY,A.W.MUNRO,S.HAY,D.LEYS JRNL TITL AN OXIDATIVE N-DEMETHYLASE REVEALS PAS TRANSITION FROM JRNL TITL 2 UBIQUITOUS SENSOR TO ENZYME. JRNL REF NATURE V. 539 593 2016 JRNL REFN ESSN 1476-4687 JRNL PMID 27851736 JRNL DOI 10.1038/NATURE20159 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 45286 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2412 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3261 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.2410 REMARK 3 BIN FREE R VALUE SET COUNT : 178 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2738 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 267 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.090 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.088 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.622 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2896 ; 0.027 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2672 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3952 ; 2.318 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6107 ; 1.069 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 337 ; 6.505 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 152 ;32.640 ;22.566 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 453 ;12.646 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;19.484 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 401 ; 0.174 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3314 ; 0.015 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 744 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5LTH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1200001328. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.917 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45331 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 33.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.30 REMARK 200 R MERGE FOR SHELL (I) : 0.75200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 5LTE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE HODM-HEME SUBUNIT WAS CRYSTALLISED REMARK 280 AT 3 MG ML-1 IN 50 MM KPI, 100 MM KCL, PH 7.5. INITIAL REMARK 280 CRYSTALLISATION CONDITIONS WERE IDENTIFIED USING THE JCSG+ REMARK 280 MATRIX SCREEN (MOLECULAR DIMENSIONS). CRYSTALS SUITABLE FOR REMARK 280 DIFFRACTION EXPERIMENTS WERE OBTAINED BY SITTING DROP VAPOUR REMARK 280 DIFFUSION AT 277 K IN 400 NL DROPS CONTAINING EQUAL VOLUMES OF REMARK 280 PROTEIN AND A SOLUTION CONTAINING 30% PEG 2K MME AND 0.1 M REMARK 280 POTASSIUM THIOCYANATE., VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 72.39500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 40.19000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.19000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 108.59250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.19000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 40.19000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.19750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 40.19000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.19000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 108.59250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 40.19000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.19000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 36.19750 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 72.39500 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 TOTAL BURIED SURFACE AREA: 1880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 NA NA A 404 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 762 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 LEU A 3 REMARK 465 THR A 4 REMARK 465 HIS A 339 REMARK 465 HIS A 340 REMARK 465 HIS A 341 REMARK 465 HIS A 342 REMARK 465 HIS A 343 REMARK 465 HIS A 344 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 C2 PEG A 403 C2 PEG A 403 7556 1.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 38 CZ TYR A 38 CE2 0.102 REMARK 500 GLU A 292 CG GLU A 292 CD 0.101 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 ARG A 12 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 34 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 81 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 GLU A 144 OE1 - CD - OE2 ANGL. DEV. = 7.4 DEGREES REMARK 500 ARG A 183 NE - CZ - NH1 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 183 NE - CZ - NH2 ANGL. DEV. = 4.8 DEGREES REMARK 500 PHE A 184 CB - CG - CD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 223 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 223 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 284 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 LEU A 290 CB - CG - CD2 ANGL. DEV. = 12.0 DEGREES REMARK 500 ASP A 291 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 316 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 332 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 332 NE - CZ - NH2 ANGL. DEV. = -5.3 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 GLU A 13 -101.72 62.37 REMARK 500 ASN A 41 43.54 -94.57 REMARK 500 ASP A 49 81.59 58.71 REMARK 500 MET A 199 -45.47 72.92 REMARK 500 ASN A 232 160.56 67.32 REMARK 500 THR A 237 59.71 -90.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 284 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PEG A 403 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 HEM A 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 194 NE2 REMARK 620 2 HEM A 401 NA 87.8 REMARK 620 3 HEM A 401 NB 90.9 91.8 REMARK 620 4 HEM A 401 NC 95.0 177.2 88.1 REMARK 620 5 HEM A 401 ND 90.9 88.4 178.1 91.6 REMARK 620 6 HOH A 705 O 169.2 83.2 95.4 94.0 82.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PEG A 403 O2 REMARK 620 2 PEG A 403 O4 66.1 REMARK 620 3 PEG A 403 O2 0.0 66.1 REMARK 620 4 PEG A 403 O4 66.1 0.0 66.1 REMARK 620 5 HOH A 649 O 91.2 97.3 91.2 97.3 REMARK 620 6 HOH A 649 O 66.7 85.6 66.7 85.6 154.6 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 HEM A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 404 DBREF 5LTH A 1 338 UNP A4XXY9 A4XXY9_PSEMY 1 338 SEQADV 5LTH HIS A 339 UNP A4XXY9 EXPRESSION TAG SEQADV 5LTH HIS A 340 UNP A4XXY9 EXPRESSION TAG SEQADV 5LTH HIS A 341 UNP A4XXY9 EXPRESSION TAG SEQADV 5LTH HIS A 342 UNP A4XXY9 EXPRESSION TAG SEQADV 5LTH HIS A 343 UNP A4XXY9 EXPRESSION TAG SEQADV 5LTH HIS A 344 UNP A4XXY9 EXPRESSION TAG SEQRES 1 A 344 MET THR LEU THR PHE LYS PRO LEU GLU SER TYR ARG GLU SEQRES 2 A 344 ASP PHE SER PHE ARG ASN SER PRO ALA ALA ILE ALA ARG SEQRES 3 A 344 PHE PRO PHE PRO PHE PRO GLU ASP GLN TYR MET TYR SER SEQRES 4 A 344 VAL ASN LEU GLU PRO ALA VAL SER ARG ASP PRO GLY SER SEQRES 5 A 344 VAL PHE GLU HIS GLN PHE ASP VAL ASP GLU HIS TYR VAL SEQRES 6 A 344 SER GLU MET ALA GLU ARG ALA ARG VAL LEU GLU LEU ASP SEQRES 7 A 344 PRO GLY ARG CYS LEU VAL MET PRO HIS MET ALA GLN ALA SEQRES 8 A 344 ALA TRP ASP THR LEU ALA MET LEU MET GLU HIS LEU ALA SEQRES 9 A 344 ARG ASP TYR PRO GLN HIS PHE ARG LEU THR ARG GLN GLY SEQRES 10 A 344 ASP ALA TRP HIS TRP GLN ASN LEU ALA LEU GLY ILE ASP SEQRES 11 A 344 GLN ARG PHE THR PHE GLY ASP PRO ALA SER LEU PRO CYS SEQRES 12 A 344 GLU PRO LEU GLU TYR ILE THR ARG GLN MET GLN GLY ASP SEQRES 13 A 344 PHE ALA VAL LEU ASP GLN ARG ASP GLY ASP LEU PHE MET SEQRES 14 A 344 ASP ALA GLY MET VAL THR CYS PRO ALA ASP TRP SER LEU SEQRES 15 A 344 ARG PHE ASP ALA GLY MET SER PHE LYS GLN TRP HIS SER SEQRES 16 A 344 PRO VAL PRO MET ALA HIS GLN MET GLY VAL PHE ASP ARG SEQRES 17 A 344 ALA LEU LYS TYR LEU LEU ASN ILE GLN VAL GLY ALA PRO SEQRES 18 A 344 VAL ARG ARG LEU ASN TRP THR LEU THR ILE ASN PRO ARG SEQRES 19 A 344 LEU ASP THR SER PRO GLU THR TYR HIS GLU TRP GLY ASN SEQRES 20 A 344 ASP ARG GLY LYS VAL THR PRO ASP ASN VAL GLY ARG LEU SEQRES 21 A 344 VAL HIS LEU ARG VAL GLU LEU GLN LEU MET ALA ARG LEU SEQRES 22 A 344 PRO ARG SER ASN ALA LEU LEU PHE GLY ILE ARG THR TYR SEQRES 23 A 344 LEU ILE SER LEU ASP GLU LEU VAL SER ASN PRO ALA TRP SEQRES 24 A 344 ALA GLN ARG LEU HIS ARG VAL MET ARG ASP LEU PRO ASP SEQRES 25 A 344 PRO ILE ALA ASP TYR LYS GLY ILE THR ARG TYR ARG GLN SEQRES 26 A 344 THR LEU VAL ASP TRP LEU ARG ARG PHE ASP PRO GLU ALA SEQRES 27 A 344 HIS HIS HIS HIS HIS HIS HET HEM A 401 43 HET DMN A 402 3 HET PEG A 403 5 HET NA A 404 1 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM DMN DIMETHYLAMINE HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM NA SODIUM ION HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 DMN C2 H7 N FORMUL 4 PEG C4 H10 O3 FORMUL 5 NA NA 1+ FORMUL 6 HOH *267(H2 O) HELIX 1 AA1 SER A 20 PHE A 27 1 8 HELIX 2 AA2 HIS A 63 ASP A 78 1 16 HELIX 3 AA3 MET A 88 TYR A 107 1 20 HELIX 4 AA4 ASP A 137 LEU A 141 5 5 HELIX 5 AA5 GLU A 144 ARG A 151 1 8 HELIX 6 AA6 SER A 181 ALA A 186 1 6 HELIX 7 AA7 SER A 189 HIS A 194 1 6 HELIX 8 AA8 GLY A 204 ASN A 215 1 12 HELIX 9 AA9 SER A 238 GLU A 240 5 3 HELIX 10 AB1 THR A 241 GLY A 246 1 6 HELIX 11 AB2 ASN A 247 LYS A 251 5 5 HELIX 12 AB3 ASN A 256 LEU A 260 1 5 HELIX 13 AB4 LEU A 290 VAL A 294 1 5 HELIX 14 AB5 ASN A 296 LEU A 310 1 15 HELIX 15 AB6 PRO A 311 GLY A 319 1 9 HELIX 16 AB7 ILE A 320 ARG A 322 5 3 HELIX 17 AB8 TYR A 323 ARG A 333 1 11 SHEET 1 AA1 7 GLU A 43 PRO A 44 0 SHEET 2 AA1 7 VAL A 222 ILE A 231 -1 O ARG A 223 N GLU A 43 SHEET 3 AA1 7 VAL A 261 ARG A 272 -1 O GLN A 268 N ARG A 224 SHEET 4 AA1 7 LEU A 279 SER A 289 -1 O TYR A 286 N VAL A 265 SHEET 5 AA1 7 ASP A 156 ARG A 163 -1 N ASP A 156 O ILE A 283 SHEET 6 AA1 7 ASP A 166 MET A 173 -1 O ALA A 171 N VAL A 159 SHEET 7 AA1 7 CYS A 82 VAL A 84 -1 N LEU A 83 O GLY A 172 SHEET 1 AA2 3 PHE A 111 GLN A 116 0 SHEET 2 AA2 3 ALA A 119 ASN A 124 -1 O GLN A 123 N ARG A 112 SHEET 3 AA2 3 ILE A 129 THR A 134 -1 O GLN A 131 N TRP A 122 LINK NE2 HIS A 194 FE HEM A 401 1555 1555 2.16 LINK FE HEM A 401 O AHOH A 705 1555 1555 2.53 LINK O2 PEG A 403 NA NA A 404 1555 1555 2.83 LINK O4 PEG A 403 NA NA A 404 1555 1555 2.82 LINK O2 PEG A 403 NA NA A 404 1555 7556 2.83 LINK O4 PEG A 403 NA NA A 404 1555 7556 2.83 LINK NA NA A 404 O HOH A 649 1555 1555 3.13 LINK NA NA A 404 O HOH A 649 1555 7556 3.13 SITE 1 AC1 22 TYR A 38 SER A 39 LEU A 160 TRP A 180 SITE 2 AC1 22 TRP A 193 HIS A 194 VAL A 197 VAL A 205 SITE 3 AC1 22 PHE A 206 ARG A 224 ASN A 226 TRP A 227 SITE 4 AC1 22 PHE A 281 TYR A 317 LYS A 318 DMN A 402 SITE 5 AC1 22 HOH A 519 HOH A 538 HOH A 589 HOH A 681 SITE 6 AC1 22 HOH A 685 HOH A 705 SITE 1 AC2 4 GLU A 266 GLN A 268 HEM A 401 HOH A 705 SITE 1 AC3 2 MET A 37 NA A 404 SITE 1 AC4 1 PEG A 403 CRYST1 80.380 80.380 144.790 90.00 90.00 90.00 P 43 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 0.012441 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012441 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006907 0.00000