HEADER OXIDOREDUCTASE 08-JUN-04 1TKL TITLE YEAST OXYGEN-DEPENDENT COPROPORPHYRINOGEN OXIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPROPORPHYRINOGEN III OXIDASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: COPROPORPHYRINOGENASE, COPROGEN OXIDASE, COX; COMPND 5 EC: 1.3.3.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: HEM13, YDR044W, YD5112.02; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET16B KEYWDS COPROPORPHYRINOGEN OXIDASE, HEME BIOSYNTHESIS, ENZYME, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.D.PHILLIPS,F.G.WHITBY,C.A.WARBY,P.LABBE,C.YANG,J.W.PFLUGRATH, AUTHOR 2 J.D.FERRARA,H.ROBINSON,J.P.KUSHNER,C.P.HILL REVDAT 4 14-FEB-24 1TKL 1 REMARK REVDAT 3 24-FEB-09 1TKL 1 VERSN REVDAT 2 28-SEP-04 1TKL 1 JRNL REVDAT 1 20-JUL-04 1TKL 0 JRNL AUTH J.D.PHILLIPS,F.G.WHITBY,C.A.WARBY,P.LABBE,C.YANG, JRNL AUTH 2 J.W.PFLUGRATH,J.D.FERRARA,H.ROBINSON,J.P.KUSHNER,C.P.HILL JRNL TITL CRYSTAL STRUCTURE OF THE OXYGEN-DEPENDANT COPROPORPHYRINOGEN JRNL TITL 2 OXIDASE (HEM13P) OF SACCHAROMYCES CEREVISIAE JRNL REF J.BIOL.CHEM. V. 279 38960 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15194705 JRNL DOI 10.1074/JBC.M406050200 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0003 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 79.06 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 51064 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) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2732 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3676 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE SET COUNT : 186 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5286 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 418 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.50000 REMARK 3 B22 (A**2) : 1.50000 REMARK 3 B33 (A**2) : -2.99000 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): 0.184 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.173 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.130 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.636 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5190 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 4514 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7032 ; 1.507 ; 1.919 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10520 ; 0.898 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 616 ; 7.290 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 268 ;34.000 ;23.433 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 860 ;16.043 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;19.944 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 720 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5802 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1129 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1134 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4658 ; 0.197 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2462 ; 0.186 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2904 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 423 ; 0.164 ; 0.200 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): 6 ; 0.203 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 29 ; 0.260 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.187 ; 0.200 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): 3951 ; 1.508 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1256 ; 0.238 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4965 ; 1.696 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2540 ; 2.242 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2066 ; 3.070 ; 4.500 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 : BABINET MODEL WITH MASK 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 1TKL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000022722. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.10 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51064 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : 0.05700 REMARK 200 FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 9.10 REMARK 200 R MERGE FOR SHELL (I) : 0.58300 REMARK 200 R SYM FOR SHELL (I) : 0.58300 REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: CHROMIUM SULFUR SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL 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): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 8000, 0.1 M HEPES, 2% REMARK 280 ISOPROPANOL, 0.2 M SODIUM ACETATE, PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K 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 103.91750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 43.41100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 43.41100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 155.87625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 43.41100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 43.41100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 51.95875 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 43.41100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.41100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 155.87625 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 43.41100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.41100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 51.95875 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 103.91750 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 3 REMARK 465 ALA B 3 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 ARG A 94 REMARK 475 LEU A 95 REMARK 475 PRO A 96 REMARK 475 GLU A 97 REMARK 475 ASP A 98 REMARK 475 PRO A 99 REMARK 475 LYS A 100 REMARK 475 THR A 101 REMARK 475 GLY A 102 REMARK 475 LEU A 103 REMARK 475 PRO A 104 REMARK 475 VAL A 105 REMARK 475 THR A 106 REMARK 475 PRO B 4 REMARK 475 GLN B 5 REMARK 475 ASP B 6 REMARK 475 PRO B 7 REMARK 475 ARG B 8 REMARK 475 ASN B 9 REMARK 475 ARG B 94 REMARK 475 LEU B 95 REMARK 475 PRO B 96 REMARK 475 GLU B 97 REMARK 475 ASP B 98 REMARK 475 PRO B 99 REMARK 475 LYS B 100 REMARK 475 THR B 101 REMARK 475 GLY B 102 REMARK 475 LEU B 103 REMARK 475 PRO B 104 REMARK 475 VAL B 105 REMARK 475 THR B 106 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O THR A 106 N ASP A 107 1.19 REMARK 500 O LEU A 93 N ARG A 94 1.29 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 LEU A 93 C ARG A 94 N -0.626 REMARK 500 ARG A 94 N ARG A 94 CA 0.169 REMARK 500 ARG A 94 CB ARG A 94 CG -0.635 REMARK 500 ARG A 94 CG ARG A 94 CD -0.544 REMARK 500 ARG A 94 C LEU A 95 N -0.499 REMARK 500 THR A 106 C ASP A 107 N -0.609 REMARK 500 ASN B 9 C LEU B 10 N 0.232 REMARK 500 LEU B 93 C ARG B 94 N -0.255 REMARK 500 THR B 106 C ASP B 107 N 0.312 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 ASP A 35 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 GLY A 51 N - CA - C ANGL. DEV. = -16.8 DEGREES REMARK 500 LEU A 93 CA - C - N ANGL. DEV. = 37.8 DEGREES REMARK 500 LEU A 93 O - C - N ANGL. DEV. = -45.4 DEGREES REMARK 500 ARG A 94 C - N - CA ANGL. DEV. = 17.7 DEGREES REMARK 500 ARG A 94 CB - CA - C ANGL. DEV. = -18.1 DEGREES REMARK 500 ARG A 94 N - CA - CB ANGL. DEV. = 43.5 DEGREES REMARK 500 ARG A 94 CA - CB - CG ANGL. DEV. = 23.9 DEGREES REMARK 500 ARG A 94 CB - CG - CD ANGL. DEV. = 36.6 DEGREES REMARK 500 ARG A 94 CG - CD - NE ANGL. DEV. = 35.1 DEGREES REMARK 500 ARG A 94 CA - C - N ANGL. DEV. = 36.0 DEGREES REMARK 500 ARG A 94 O - C - N ANGL. DEV. = -56.1 DEGREES REMARK 500 LEU A 95 C - N - CA ANGL. DEV. = 42.0 DEGREES REMARK 500 THR A 106 CA - C - N ANGL. DEV. = 41.3 DEGREES REMARK 500 THR A 106 O - C - N ANGL. DEV. = -53.6 DEGREES REMARK 500 ASP A 182 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 194 CB - CG - OD2 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP A 215 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 217 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 LEU B 10 C - N - CA ANGL. DEV. = -19.6 DEGREES REMARK 500 ASP B 60 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP B 107 C - N - CA ANGL. DEV. = -21.1 DEGREES REMARK 500 ASP B 194 CB - CG - OD2 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP B 214 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP B 220 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 233 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG B 263 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG B 263 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ASP B 274 CB - CG - OD2 ANGL. DEV. = 5.8 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 PRO A 80 -27.82 -29.41 REMARK 500 ALA A 81 -26.73 -30.32 REMARK 500 ARG A 94 91.50 138.11 REMARK 500 LEU A 95 77.21 -151.41 REMARK 500 LYS A 100 -59.58 -158.28 REMARK 500 VAL A 105 -90.78 44.62 REMARK 500 THR A 106 -131.83 64.59 REMARK 500 ASP A 107 -54.28 111.95 REMARK 500 GLN A 147 -80.39 -98.67 REMARK 500 ASP A 182 122.59 -172.62 REMARK 500 ASP A 217 30.70 -142.85 REMARK 500 ASP B 6 72.52 66.14 REMARK 500 ARG B 8 -46.51 90.89 REMARK 500 ASN B 9 -14.08 -47.50 REMARK 500 ASN B 48 -52.55 39.58 REMARK 500 MET B 86 47.20 -88.57 REMARK 500 ASN B 92 -24.26 78.54 REMARK 500 ARG B 94 -152.14 -123.60 REMARK 500 LEU B 95 85.57 41.09 REMARK 500 PRO B 99 53.84 -51.22 REMARK 500 LYS B 100 2.55 101.74 REMARK 500 THR B 101 -99.42 -130.13 REMARK 500 VAL B 105 12.67 -69.02 REMARK 500 THR B 106 -128.15 53.10 REMARK 500 ASP B 107 -82.28 82.76 REMARK 500 GLN B 142 78.14 -17.36 REMARK 500 ASP B 143 20.25 136.38 REMARK 500 GLN B 147 -85.21 -75.45 REMARK 500 ASP B 182 120.49 171.02 REMARK 500 ARG B 282 178.99 -59.07 REMARK 500 THR B 283 91.61 72.21 REMARK 500 VAL B 327 126.23 -170.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 93 ARG A 94 -45.76 REMARK 500 ARG A 94 LEU A 95 115.34 REMARK 500 GLU A 97 ASP A 98 -145.76 REMARK 500 PRO A 104 VAL A 105 137.69 REMARK 500 THR A 106 ASP A 107 92.45 REMARK 500 THR B 45 ARG B 46 145.35 REMARK 500 THR B 106 ASP B 107 146.65 REMARK 500 VAL B 327 LYS B 328 144.59 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 ANGLE, 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 LEU A 93 -38.02 REMARK 500 ARG A 94 -67.33 REMARK 500 THR A 106 55.45 REMARK 500 ASN B 9 -11.39 REMARK 500 LEU B 93 -10.48 REMARK 500 THR B 106 10.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TK1 RELATED DB: PDB REMARK 900 RELATED ID: 1TLB RELATED DB: PDB DBREF 1TKL A 3 328 UNP P11353 HEM6_YEAST 3 328 DBREF 1TKL B 3 328 UNP P11353 HEM6_YEAST 3 328 SEQRES 1 A 326 ALA PRO GLN ASP PRO ARG ASN LEU PRO ILE ARG GLN GLN SEQRES 2 A 326 MET GLU ALA LEU ILE ARG ARG LYS GLN ALA GLU ILE THR SEQRES 3 A 326 GLN GLY LEU GLU SER ILE ASP THR VAL LYS PHE HIS ALA SEQRES 4 A 326 ASP THR TRP THR ARG GLY ASN ASP GLY GLY GLY GLY THR SEQRES 5 A 326 SER MET VAL ILE GLN ASP GLY THR THR PHE GLU LYS GLY SEQRES 6 A 326 GLY VAL ASN VAL SER VAL VAL TYR GLY GLN LEU SER PRO SEQRES 7 A 326 ALA ALA VAL SER ALA MET LYS ALA ASP HIS LYS ASN LEU SEQRES 8 A 326 ARG LEU PRO GLU ASP PRO LYS THR GLY LEU PRO VAL THR SEQRES 9 A 326 ASP GLY VAL LYS PHE PHE ALA CYS GLY LEU SER MET VAL SEQRES 10 A 326 ILE HIS PRO VAL ASN PRO HIS ALA PRO THR THR HIS LEU SEQRES 11 A 326 ASN TYR ARG TYR PHE GLU THR TRP ASN GLN ASP GLY THR SEQRES 12 A 326 PRO GLN THR TRP TRP PHE GLY GLY GLY ALA ASP LEU THR SEQRES 13 A 326 PRO SER TYR LEU TYR GLU GLU ASP GLY GLN LEU PHE HIS SEQRES 14 A 326 GLN LEU HIS LYS ASP ALA LEU ASP LYS HIS ASP THR ALA SEQRES 15 A 326 LEU TYR PRO ARG PHE LYS LYS TRP CYS ASP GLU TYR PHE SEQRES 16 A 326 TYR ILE THR HIS ARG LYS GLU THR ARG GLY ILE GLY GLY SEQRES 17 A 326 ILE PHE PHE ASP ASP TYR ASP GLU ARG ASP PRO GLN GLU SEQRES 18 A 326 ILE LEU LYS MET VAL GLU ASP CYS PHE ASP ALA PHE LEU SEQRES 19 A 326 PRO SER TYR LEU THR ILE VAL LYS ARG ARG LYS ASP MET SEQRES 20 A 326 PRO TYR THR LYS GLU GLU GLN GLN TRP GLN ALA ILE ARG SEQRES 21 A 326 ARG GLY ARG TYR VAL GLU PHE ASN LEU ILE TYR ASP ARG SEQRES 22 A 326 GLY THR GLN PHE GLY LEU ARG THR PRO GLY SER ARG VAL SEQRES 23 A 326 GLU SER ILE LEU MET SER LEU PRO GLU HIS ALA SER TRP SEQRES 24 A 326 LEU TYR ASN HIS HIS PRO ALA PRO GLY SER ARG GLU ALA SEQRES 25 A 326 LYS LEU LEU GLU VAL THR THR LYS PRO ARG GLU TRP VAL SEQRES 26 A 326 LYS SEQRES 1 B 326 ALA PRO GLN ASP PRO ARG ASN LEU PRO ILE ARG GLN GLN SEQRES 2 B 326 MET GLU ALA LEU ILE ARG ARG LYS GLN ALA GLU ILE THR SEQRES 3 B 326 GLN GLY LEU GLU SER ILE ASP THR VAL LYS PHE HIS ALA SEQRES 4 B 326 ASP THR TRP THR ARG GLY ASN ASP GLY GLY GLY GLY THR SEQRES 5 B 326 SER MET VAL ILE GLN ASP GLY THR THR PHE GLU LYS GLY SEQRES 6 B 326 GLY VAL ASN VAL SER VAL VAL TYR GLY GLN LEU SER PRO SEQRES 7 B 326 ALA ALA VAL SER ALA MET LYS ALA ASP HIS LYS ASN LEU SEQRES 8 B 326 ARG LEU PRO GLU ASP PRO LYS THR GLY LEU PRO VAL THR SEQRES 9 B 326 ASP GLY VAL LYS PHE PHE ALA CYS GLY LEU SER MET VAL SEQRES 10 B 326 ILE HIS PRO VAL ASN PRO HIS ALA PRO THR THR HIS LEU SEQRES 11 B 326 ASN TYR ARG TYR PHE GLU THR TRP ASN GLN ASP GLY THR SEQRES 12 B 326 PRO GLN THR TRP TRP PHE GLY GLY GLY ALA ASP LEU THR SEQRES 13 B 326 PRO SER TYR LEU TYR GLU GLU ASP GLY GLN LEU PHE HIS SEQRES 14 B 326 GLN LEU HIS LYS ASP ALA LEU ASP LYS HIS ASP THR ALA SEQRES 15 B 326 LEU TYR PRO ARG PHE LYS LYS TRP CYS ASP GLU TYR PHE SEQRES 16 B 326 TYR ILE THR HIS ARG LYS GLU THR ARG GLY ILE GLY GLY SEQRES 17 B 326 ILE PHE PHE ASP ASP TYR ASP GLU ARG ASP PRO GLN GLU SEQRES 18 B 326 ILE LEU LYS MET VAL GLU ASP CYS PHE ASP ALA PHE LEU SEQRES 19 B 326 PRO SER TYR LEU THR ILE VAL LYS ARG ARG LYS ASP MET SEQRES 20 B 326 PRO TYR THR LYS GLU GLU GLN GLN TRP GLN ALA ILE ARG SEQRES 21 B 326 ARG GLY ARG TYR VAL GLU PHE ASN LEU ILE TYR ASP ARG SEQRES 22 B 326 GLY THR GLN PHE GLY LEU ARG THR PRO GLY SER ARG VAL SEQRES 23 B 326 GLU SER ILE LEU MET SER LEU PRO GLU HIS ALA SER TRP SEQRES 24 B 326 LEU TYR ASN HIS HIS PRO ALA PRO GLY SER ARG GLU ALA SEQRES 25 B 326 LYS LEU LEU GLU VAL THR THR LYS PRO ARG GLU TRP VAL SEQRES 26 B 326 LYS FORMUL 3 HOH *418(H2 O) HELIX 1 1 ASP A 6 LEU A 10 5 5 HELIX 2 2 PRO A 11 SER A 33 1 23 HELIX 3 3 GLY A 47 ASP A 49 5 3 HELIX 4 4 SER A 79 SER A 84 1 6 HELIX 5 5 MET A 86 HIS A 90 5 5 HELIX 6 6 TYR A 163 LYS A 180 1 18 HELIX 7 7 ALA A 184 PHE A 197 1 14 HELIX 8 8 THR A 200 LYS A 203 5 4 HELIX 9 9 ASP A 220 ASP A 233 1 14 HELIX 10 10 ALA A 234 ARG A 245 1 12 HELIX 11 11 THR A 252 TYR A 273 1 22 HELIX 12 12 ASP A 274 THR A 283 1 10 HELIX 13 13 ARG A 287 LEU A 292 1 6 HELIX 14 14 MET A 293 LEU A 295 5 3 HELIX 15 15 SER A 311 LYS A 322 1 12 HELIX 16 16 PRO B 11 SER B 33 1 23 HELIX 17 17 SER B 79 MET B 86 1 8 HELIX 18 18 TYR B 163 LYS B 180 1 18 HELIX 19 19 ALA B 184 PHE B 197 1 14 HELIX 20 20 THR B 200 LYS B 203 5 4 HELIX 21 21 ASP B 220 ASP B 233 1 14 HELIX 22 22 ALA B 234 LYS B 247 1 14 HELIX 23 23 THR B 252 TYR B 273 1 22 HELIX 24 24 ASP B 274 ARG B 282 1 9 HELIX 25 25 ARG B 287 LEU B 292 1 6 HELIX 26 26 MET B 293 LEU B 295 5 3 HELIX 27 27 SER B 311 LYS B 322 1 12 SHEET 1 A 7 HIS A 40 THR A 45 0 SHEET 2 A 7 GLY A 51 GLN A 59 -1 O VAL A 57 N HIS A 40 SHEET 3 A 7 PHE A 64 LEU A 78 -1 O VAL A 71 N THR A 54 SHEET 4 A 7 VAL A 109 PRO A 122 -1 O ALA A 113 N VAL A 74 SHEET 5 A 7 THR A 129 TRP A 140 -1 O TYR A 136 N CYS A 114 SHEET 6 A 7 PRO A 146 THR A 158 -1 O THR A 158 N THR A 129 SHEET 7 A 7 GLY A 210 TYR A 216 -1 O TYR A 216 N PHE A 151 SHEET 1 B 2 TYR A 198 ILE A 199 0 SHEET 2 B 2 GLU A 204 THR A 205 -1 O GLU A 204 N ILE A 199 SHEET 1 C 2 HIS A 298 SER A 300 0 SHEET 2 C 2 HIS B 298 SER B 300 -1 O ALA B 299 N ALA A 299 SHEET 1 D 7 HIS B 40 ARG B 46 0 SHEET 2 D 7 GLY B 51 GLN B 59 -1 O SER B 55 N ASP B 42 SHEET 3 D 7 PHE B 64 LEU B 78 -1 O VAL B 71 N THR B 54 SHEET 4 D 7 VAL B 109 PRO B 122 -1 O ALA B 113 N VAL B 74 SHEET 5 D 7 THR B 129 ASN B 141 -1 O LEU B 132 N MET B 118 SHEET 6 D 7 THR B 145 THR B 158 -1 O THR B 158 N THR B 129 SHEET 7 D 7 GLY B 210 TYR B 216 -1 O PHE B 213 N GLY B 153 SHEET 1 E 2 TYR B 198 ILE B 199 0 SHEET 2 E 2 GLU B 204 THR B 205 -1 O GLU B 204 N ILE B 199 CISPEP 1 GLY A 50 GLY A 51 0 -14.62 CRYST1 86.822 86.822 207.835 90.00 90.00 90.00 P 43 21 2 16 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 0.011518 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011518 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004812 0.00000