HEADER ISOMERASE 17-APR-15 4ZDF TITLE CRYSTAL STRUCTURE OF YEAST ENOYL-COA ISOMERASE HELIX-10 DELETION TITLE 2 (SCECI2-H10) MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3,2-TRANS-ENOYL-COA ISOMERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DELTA(3),DELTA(2)-ENOYL-COA ISOMERASE,D3,D2-ENOYL-COA COMPND 5 ISOMERASE,DODECENOYL-COA ISOMERASE; COMPND 6 EC: 5.3.3.8; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: CYS212 WAS OXIDIZED TO CME DUE TO THE PRESENCE OF BME COMPND 10 IN THE PURIFICATION BUFFERS 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: ECI1, YLR284C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CROTONASE, ISOMERASE, ENOYL-COA ISOMERASE, BETA-OXIDATION EXPDTA X-RAY DIFFRACTION AUTHOR G.U.ONWUKWE,M.K.KOSKI,R.K.WIERENGA REVDAT 3 10-JAN-24 4ZDF 1 REMARK REVDAT 2 18-NOV-15 4ZDF 1 JRNL REVDAT 1 11-NOV-15 4ZDF 0 JRNL AUTH G.U.ONWUKWE,M.K.KOSKI,P.PIHKO,W.SCHMITZ,R.K.WIERENGA JRNL TITL STRUCTURES OF YEAST PEROXISOMAL DELTA (3), DELTA JRNL TITL 2 (2)-ENOYL-COA ISOMERASE COMPLEXED WITH ACYL-COA SUBSTRATE JRNL TITL 3 ANALOGUES: THE IMPORTANCE OF HYDROGEN-BOND NETWORKS FOR THE JRNL TITL 4 REACTIVITY OF THE CATALYTIC BASE AND THE OXYANION HOLE. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 2178 2015 JRNL REFN ESSN 1399-0047 JRNL PMID 26527136 JRNL DOI 10.1107/S139900471501559X REMARK 2 REMARK 2 RESOLUTION. 1.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 60869 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3239 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) : 1.81 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4296 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.2990 REMARK 3 BIN FREE R VALUE SET COUNT : 247 REMARK 3 BIN FREE R VALUE : 0.3120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4072 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 305 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.66000 REMARK 3 B22 (A**2) : -0.66000 REMARK 3 B33 (A**2) : 2.15000 REMARK 3 B12 (A**2) : -0.33000 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): 0.095 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.094 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.071 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.428 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4271 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4080 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5782 ; 1.464 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9416 ; 0.992 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 529 ; 5.304 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 196 ;37.005 ;24.694 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 750 ;15.210 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;18.784 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 634 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4859 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 991 ; 0.003 ; 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): 2095 ; 2.497 ; 3.226 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2094 ; 2.497 ; 3.225 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2631 ; 3.698 ; 4.811 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2632 ; 3.697 ; 4.812 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2176 ; 3.674 ; 3.761 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2176 ; 3.656 ; 3.761 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3152 ; 5.771 ; 5.424 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5040 ; 9.300 ;26.997 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5041 ; 9.302 ;27.004 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 4 267 B 4 267 15394 0.10 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 4ZDF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208979. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 273 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64106 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.810 REMARK 200 RESOLUTION RANGE LOW (A) : 48.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 1.06400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1K39 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM IMIDAZOLE PH 6.5, 1 M REMARK 280 NAACETATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 22360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 53700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -141.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 118.12100 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 409.18315 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -295.30250 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 306.88736 REMARK 350 BIOMT3 3 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 HOH A 541 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 428 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 GLN A 3 REMARK 465 ALA A 78 REMARK 465 GLN A 79 REMARK 465 GLY A 80 REMARK 465 ASP A 81 REMARK 465 ASP A 82 REMARK 465 THR A 83 REMARK 465 ASN A 84 REMARK 465 PHE A 268 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 GLN B 3 REMARK 465 ILE B 75 REMARK 465 ALA B 76 REMARK 465 LYS B 77 REMARK 465 ALA B 78 REMARK 465 GLN B 79 REMARK 465 GLY B 80 REMARK 465 ASP B 81 REMARK 465 ASP B 82 REMARK 465 THR B 83 REMARK 465 ASN B 84 REMARK 465 PHE B 268 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 NH1 ARG B 14 OE1 GLU B 16 1.82 REMARK 500 O HOH B 360 O HOH B 414 2.06 REMARK 500 O HOH B 304 O HOH B 307 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH B 426 O HOH B 426 67612 0.86 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 6 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 VAL B 102 CB - CA - C ANGL. DEV. = -16.0 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 SER A 61 -157.74 -133.24 REMARK 500 SER A 67 130.76 -171.32 REMARK 500 ILE A 75 -61.75 8.35 REMARK 500 ALA A 76 -71.64 91.11 REMARK 500 PRO A 149 32.12 -87.40 REMARK 500 ILE A 156 -167.22 -126.72 REMARK 500 SER B 61 -156.35 -132.49 REMARK 500 SER B 67 129.21 -171.42 REMARK 500 PRO B 149 35.06 -88.49 REMARK 500 ILE B 156 -166.81 -126.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 301 DBREF 4ZDF A 1 268 UNP Q05871 ECI1_YEAST 1 268 DBREF 4ZDF B 1 268 UNP Q05871 ECI1_YEAST 1 268 SEQADV 4ZDF MET A -19 UNP Q05871 INITIATING METHIONINE SEQADV 4ZDF GLY A -18 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF SER A -17 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF SER A -16 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF HIS A -15 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF HIS A -14 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF HIS A -13 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF HIS A -12 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF HIS A -11 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF HIS A -10 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF SER A -9 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF SER A -8 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF GLY A -7 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF LEU A -6 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF VAL A -5 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF PRO A -4 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF ARG A -3 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF GLY A -2 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF SER A -1 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF HIS A 0 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF ILE A 25 UNP Q05871 MET 25 CONFLICT SEQADV 4ZDF MET B -19 UNP Q05871 INITIATING METHIONINE SEQADV 4ZDF GLY B -18 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF SER B -17 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF SER B -16 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF HIS B -15 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF HIS B -14 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF HIS B -13 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF HIS B -12 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF HIS B -11 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF HIS B -10 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF SER B -9 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF SER B -8 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF GLY B -7 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF LEU B -6 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF VAL B -5 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF PRO B -4 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF ARG B -3 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF GLY B -2 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF SER B -1 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF HIS B 0 UNP Q05871 EXPRESSION TAG SEQADV 4ZDF ILE B 25 UNP Q05871 MET 25 CONFLICT SEQRES 1 A 288 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 288 LEU VAL PRO ARG GLY SER HIS MET SER GLN GLU ILE ARG SEQRES 3 A 288 GLN ASN GLU LYS ILE SER TYR ARG ILE GLU GLY PRO PHE SEQRES 4 A 288 PHE ILE ILE HIS LEU ILE ASN PRO ASP ASN LEU ASN ALA SEQRES 5 A 288 LEU GLU GLY GLU ASP TYR ILE TYR LEU GLY GLU LEU LEU SEQRES 6 A 288 GLU LEU ALA ASP ARG ASN ARG ASP VAL TYR PHE THR ILE SEQRES 7 A 288 ILE GLN SER SER GLY ARG PHE PHE SER SER GLY ALA ASP SEQRES 8 A 288 PHE LYS GLY ILE ALA LYS ALA GLN GLY ASP ASP THR ASN SEQRES 9 A 288 LYS TYR PRO SER GLU THR SER LYS TRP VAL SER ASN PHE SEQRES 10 A 288 VAL ALA ARG ASN VAL TYR VAL THR ASP ALA PHE ILE LYS SEQRES 11 A 288 HIS SER LYS VAL LEU ILE CYS CYS LEU ASN GLY PRO ALA SEQRES 12 A 288 ILE GLY LEU SER ALA ALA LEU VAL ALA LEU CYS ASP ILE SEQRES 13 A 288 VAL TYR SER ILE ASN ASP LYS VAL TYR LEU LEU TYR PRO SEQRES 14 A 288 PHE ALA ASN LEU GLY LEU ILE THR GLU GLY GLY THR THR SEQRES 15 A 288 VAL SER LEU PRO LEU LYS PHE GLY THR ASN THR THR TYR SEQRES 16 A 288 GLU CYS LEU MET PHE ASN LYS PRO PHE LYS TYR ASP ILE SEQRES 17 A 288 MET CME GLU ASN GLY PHE ILE SER LYS ASN PHE ASN MET SEQRES 18 A 288 PRO SER SER ASN ALA GLU ALA PHE ASN ALA LYS VAL LEU SEQRES 19 A 288 GLU GLU LEU ARG GLU LYS VAL LYS GLY LEU TYR LEU PRO SEQRES 20 A 288 SER CYS LEU GLY MET LYS LYS LEU LEU LYS SER ASN HIS SEQRES 21 A 288 ILE ASP ALA PHE ASN LYS ALA ASN SER VAL GLU VAL ASN SEQRES 22 A 288 GLU SER LEU LYS TYR TRP VAL ASP GLY GLU PRO LEU LYS SEQRES 23 A 288 ARG PHE SEQRES 1 B 288 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 288 LEU VAL PRO ARG GLY SER HIS MET SER GLN GLU ILE ARG SEQRES 3 B 288 GLN ASN GLU LYS ILE SER TYR ARG ILE GLU GLY PRO PHE SEQRES 4 B 288 PHE ILE ILE HIS LEU ILE ASN PRO ASP ASN LEU ASN ALA SEQRES 5 B 288 LEU GLU GLY GLU ASP TYR ILE TYR LEU GLY GLU LEU LEU SEQRES 6 B 288 GLU LEU ALA ASP ARG ASN ARG ASP VAL TYR PHE THR ILE SEQRES 7 B 288 ILE GLN SER SER GLY ARG PHE PHE SER SER GLY ALA ASP SEQRES 8 B 288 PHE LYS GLY ILE ALA LYS ALA GLN GLY ASP ASP THR ASN SEQRES 9 B 288 LYS TYR PRO SER GLU THR SER LYS TRP VAL SER ASN PHE SEQRES 10 B 288 VAL ALA ARG ASN VAL TYR VAL THR ASP ALA PHE ILE LYS SEQRES 11 B 288 HIS SER LYS VAL LEU ILE CYS CYS LEU ASN GLY PRO ALA SEQRES 12 B 288 ILE GLY LEU SER ALA ALA LEU VAL ALA LEU CYS ASP ILE SEQRES 13 B 288 VAL TYR SER ILE ASN ASP LYS VAL TYR LEU LEU TYR PRO SEQRES 14 B 288 PHE ALA ASN LEU GLY LEU ILE THR GLU GLY GLY THR THR SEQRES 15 B 288 VAL SER LEU PRO LEU LYS PHE GLY THR ASN THR THR TYR SEQRES 16 B 288 GLU CYS LEU MET PHE ASN LYS PRO PHE LYS TYR ASP ILE SEQRES 17 B 288 MET CME GLU ASN GLY PHE ILE SER LYS ASN PHE ASN MET SEQRES 18 B 288 PRO SER SER ASN ALA GLU ALA PHE ASN ALA LYS VAL LEU SEQRES 19 B 288 GLU GLU LEU ARG GLU LYS VAL LYS GLY LEU TYR LEU PRO SEQRES 20 B 288 SER CYS LEU GLY MET LYS LYS LEU LEU LYS SER ASN HIS SEQRES 21 B 288 ILE ASP ALA PHE ASN LYS ALA ASN SER VAL GLU VAL ASN SEQRES 22 B 288 GLU SER LEU LYS TYR TRP VAL ASP GLY GLU PRO LEU LYS SEQRES 23 B 288 ARG PHE MODRES 4ZDF CME A 190 CYS MODIFIED RESIDUE MODRES 4ZDF CME B 190 CYS MODIFIED RESIDUE HET CME A 190 10 HET CME B 190 10 HET GOL A 301 6 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 CME 2(C5 H11 N O3 S2) FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *305(H2 O) HELIX 1 AA1 ASN A 26 LEU A 30 5 5 HELIX 2 AA2 GLU A 34 ASN A 51 1 18 HELIX 3 AA3 PHE A 72 ALA A 76 5 5 HELIX 4 AA4 SER A 88 PHE A 97 1 10 HELIX 5 AA5 PHE A 97 HIS A 111 1 15 HELIX 6 AA6 GLY A 125 CYS A 134 1 10 HELIX 7 AA7 PRO A 149 GLY A 154 1 6 HELIX 8 AA8 GLY A 160 GLY A 170 1 11 HELIX 9 AA9 GLY A 170 PHE A 180 1 11 HELIX 10 AB1 TYR A 186 ASN A 192 1 7 HELIX 11 AB2 ASN A 205 VAL A 221 1 17 HELIX 12 AB3 TYR A 225 SER A 238 1 14 HELIX 13 AB4 HIS A 240 GLY A 262 1 23 HELIX 14 AB5 ASN B 26 LEU B 30 5 5 HELIX 15 AB6 GLU B 34 ASN B 51 1 18 HELIX 16 AB7 SER B 88 PHE B 97 1 10 HELIX 17 AB8 PHE B 97 HIS B 111 1 15 HELIX 18 AB9 GLY B 125 CYS B 134 1 10 HELIX 19 AC1 PRO B 149 GLY B 154 1 6 HELIX 20 AC2 GLY B 160 GLY B 170 1 11 HELIX 21 AC3 GLY B 170 PHE B 180 1 11 HELIX 22 AC4 TYR B 186 ASN B 192 1 7 HELIX 23 AC5 ASN B 205 VAL B 221 1 17 HELIX 24 AC6 TYR B 225 SER B 238 1 14 HELIX 25 AC7 HIS B 240 GLY B 262 1 23 SHEET 1 AA1 6 ILE A 11 GLU A 16 0 SHEET 2 AA1 6 PHE A 19 LEU A 24 -1 O ILE A 21 N ARG A 14 SHEET 3 AA1 6 PHE A 56 GLN A 60 1 O ILE A 58 N PHE A 20 SHEET 4 AA1 6 VAL A 114 LEU A 119 1 O ILE A 116 N ILE A 59 SHEET 5 AA1 6 ILE A 136 SER A 139 1 O TYR A 138 N LEU A 119 SHEET 6 AA1 6 LYS A 197 ASN A 198 1 O LYS A 197 N SER A 139 SHEET 1 AA2 3 ALA A 123 ILE A 124 0 SHEET 2 AA2 3 TYR A 145 LEU A 147 1 O LEU A 147 N ALA A 123 SHEET 3 AA2 3 PHE A 184 LYS A 185 -1 O PHE A 184 N LEU A 146 SHEET 1 AA3 6 ILE B 11 GLU B 16 0 SHEET 2 AA3 6 PHE B 19 LEU B 24 -1 O ILE B 21 N ARG B 14 SHEET 3 AA3 6 PHE B 56 GLN B 60 1 O ILE B 58 N ILE B 22 SHEET 4 AA3 6 VAL B 114 LEU B 119 1 O ILE B 116 N ILE B 59 SHEET 5 AA3 6 ILE B 136 SER B 139 1 O TYR B 138 N LEU B 119 SHEET 6 AA3 6 LYS B 197 ASN B 198 1 O LYS B 197 N SER B 139 SHEET 1 AA4 3 ALA B 123 ILE B 124 0 SHEET 2 AA4 3 TYR B 145 LEU B 147 1 O LEU B 147 N ALA B 123 SHEET 3 AA4 3 PHE B 184 LYS B 185 -1 O PHE B 184 N LEU B 146 LINK C MET A 189 N CME A 190 1555 1555 1.32 LINK C CME A 190 N GLU A 191 1555 1555 1.32 LINK C MET B 189 N CME B 190 1555 1555 1.33 LINK C CME B 190 N GLU B 191 1555 1555 1.32 SITE 1 AC1 7 GLY A 69 ALA A 70 ARG A 100 GLY A 125 SITE 2 AC1 7 LEU A 126 LEU A 155 GLU A 158 CRYST1 118.121 118.121 87.417 90.00 90.00 120.00 P 3 2 1 12 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 0.008466 0.004888 0.000000 0.00000 SCALE2 0.000000 0.009776 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011439 0.00000