HEADER HYDROLASE 30-SEP-09 3K2I TITLE HUMAN ACYL-COENZYME A THIOESTERASE 4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACYL-COENZYME A THIOESTERASE 4; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ACYL-COA THIOESTERASE 4, PEROXISOMAL ACYL COENZYME A COMPND 5 THIOESTER HYDROLASE IB, PEROXISOMAL LONG-CHAIN ACYL-COA THIOESTERASE COMPND 6 IB, PTE-IB, PTE-2B; COMPND 7 EC: 3.1.2.2; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ACOT4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) GOLD PRARE2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC-BSA4 KEYWDS ALPHA/BETA HYDROLASE FOLD SEVEN-STRANDED BETA-SANDWICH, STRUCTURAL KEYWDS 2 GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, HYDROLASE, KEYWDS 3 PEROXISOME, POLYMORPHISM, SERINE ESTERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.I.SIPONEN,M.MOCHE,C.H.ARROWSMITH,H.BERGLUND,C.BOUNTRA,R.COLLINS, AUTHOR 2 A.M.EDWARDS,S.FLODIN,A.FLORES,S.GRASLUND,M.HAMMARSTROM,A.JOHANSSON, AUTHOR 3 I.JOHANSSON,A.KALLAS,T.KARLBERG,P.KRAULIS,T.KOTENYOVA,A.KOTZSCH, AUTHOR 4 N.MARKOVA,T.K.NIELSEN,P.NORDLUND,T.NYMAN,C.PERSSON,A.K.ROOS, AUTHOR 5 P.SCHUTZ,L.SVENSSON,A.G.THORSELL,L.TRESAUGUES,S.VAN DEN BERG, AUTHOR 6 E.WAHLBERG,J.WEIGELT,M.WELIN,M.WISNIEWSKA,H.SCHULER,STRUCTURAL AUTHOR 7 GENOMICS CONSORTIUM (SGC) REVDAT 3 01-NOV-23 3K2I 1 REMARK REVDAT 2 10-NOV-21 3K2I 1 REMARK SEQADV REVDAT 1 20-OCT-09 3K2I 0 JRNL AUTH M.I.SIPONEN,M.MOCHE,C.H.ARROWSMITH,H.BERGLUND,C.BOUNTRA, JRNL AUTH 2 R.COLLINS,A.M.EDWARDS,S.FLODIN,A.FLORES,S.GRASLUND, JRNL AUTH 3 M.HAMMARSTROM,A.JOHANSSON,I.JOHANSSON,A.KALLAS,T.KARLBERG, JRNL AUTH 4 P.KRAULIS,T.KOTENYOVA,A.KOTZSCH,N.MARKOVA,T.K.NIELSEN, JRNL AUTH 5 P.NORDLUND,T.NYMAN,C.PERSSON,A.K.ROOS,P.SCHUTZ,L.SVENSSON, JRNL AUTH 6 A.G.THORSELL,L.TRESAUGUES,S.VAN DEN BERG,E.WAHLBERG, JRNL AUTH 7 J.WEIGELT,M.WELIN,M.WISNIEWSKA,H.SCHULER JRNL TITL HUMAN ACYL-COENZYME A THIOESTERASE 4 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 34897 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1124 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2551 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2450 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6308 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 187 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.81000 REMARK 3 B22 (A**2) : 2.11000 REMARK 3 B33 (A**2) : -1.30000 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): 0.415 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.263 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.172 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.078 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6622 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4635 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9013 ; 1.579 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11239 ; 0.919 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 832 ; 6.407 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 294 ;34.327 ;22.721 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1063 ;16.225 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 56 ;16.207 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 956 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7474 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1392 ; 0.001 ; 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): 4112 ; 0.867 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1658 ; 0.176 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6613 ; 1.693 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2510 ; 2.606 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2400 ; 4.310 ; 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 : 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 3K2I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055463. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36079 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 66.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.122 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 13.20 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : 0.11700 REMARK 200 FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 13.50 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : 0.40000 REMARK 200 FOR SHELL : 7.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3HLK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2M NAI, 0.1M BTP, PH REMARK 280 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 36.23500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.86000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.86000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.23500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.50000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 SER A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 PRO A 10 REMARK 465 GLY A 11 REMARK 465 ARG A 12 REMARK 465 GLY A 411 REMARK 465 GLY A 412 REMARK 465 THR A 413 REMARK 465 GLN A 414 REMARK 465 LYS A 415 REMARK 465 THR A 416 REMARK 465 ALA A 417 REMARK 465 VAL A 418 REMARK 465 PRO A 419 REMARK 465 LYS A 420 REMARK 465 LEU A 421 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 PRO B 10 REMARK 465 GLY B 11 REMARK 465 ARG B 12 REMARK 465 GLY B 411 REMARK 465 GLY B 412 REMARK 465 THR B 413 REMARK 465 GLN B 414 REMARK 465 LYS B 415 REMARK 465 THR B 416 REMARK 465 ALA B 417 REMARK 465 VAL B 418 REMARK 465 PRO B 419 REMARK 465 LYS B 420 REMARK 465 LEU B 421 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LEU B 333 N CA C O CB CG CD1 REMARK 480 LEU B 333 CD2 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 ND2 ASN B 262 O HOH B 525 1.83 REMARK 500 ND2 ASN A 262 O HOH A 486 1.98 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 CYS B 121 CB CYS B 121 SG -0.160 REMARK 500 GLU B 387 CD GLU B 387 OE2 0.069 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 MET B 308 CG - SD - CE ANGL. DEV. = -10.3 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 ASP A 40 -163.99 -79.29 REMARK 500 ASP A 55 -169.00 -79.38 REMARK 500 PHE A 193 118.49 -160.87 REMARK 500 GLU A 194 -128.20 45.26 REMARK 500 PRO A 197 155.29 -49.80 REMARK 500 SER A 232 -130.35 70.72 REMARK 500 LYS A 268 -114.18 53.78 REMARK 500 CYS B 121 148.98 -175.82 REMARK 500 TYR B 190 -12.21 -143.87 REMARK 500 GLU B 194 -124.70 43.62 REMARK 500 ASN B 198 -45.21 -25.92 REMARK 500 MET B 200 76.79 -106.66 REMARK 500 SER B 232 -132.27 64.40 REMARK 500 LYS B 268 -111.72 49.80 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 NI A 422 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 423 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 423 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS SEQUENCE IS FROM NATURAL VARIANT. REMARK 999 REFER TO REF. 3 IN UNP DATABASE Q8N9L9. DBREF 3K2I A 1 421 UNP Q8N9L9 ACOT4_HUMAN 1 421 DBREF 3K2I B 1 421 UNP Q8N9L9 ACOT4_HUMAN 1 421 SEQADV 3K2I SER A 0 UNP Q8N9L9 EXPRESSION TAG SEQADV 3K2I CYS A 57 UNP Q8N9L9 ARG 57 SEE REMARK 999 SEQADV 3K2I TRP A 135 UNP Q8N9L9 ARG 135 ENGINEERED MUTATION SEQADV 3K2I SER B 0 UNP Q8N9L9 EXPRESSION TAG SEQADV 3K2I CYS B 57 UNP Q8N9L9 ARG 57 SEE REMARK 999 SEQADV 3K2I TRP B 135 UNP Q8N9L9 ARG 135 ENGINEERED MUTATION SEQRES 1 A 422 SER MET SER ALA THR LEU ILE LEU GLU PRO PRO GLY ARG SEQRES 2 A 422 CYS CYS TRP ASN GLU PRO VAL ARG ILE ALA VAL ARG GLY SEQRES 3 A 422 LEU ALA PRO GLU GLN ARG VAL THR LEU ARG ALA SER LEU SEQRES 4 A 422 ARG ASP GLU LYS GLY ALA LEU PHE ARG ALA HIS ALA ARG SEQRES 5 A 422 TYR CYS ALA ASP ALA CYS GLY GLU LEU ASP LEU GLU ARG SEQRES 6 A 422 ALA PRO ALA LEU GLY GLY SER PHE ALA GLY LEU GLU PRO SEQRES 7 A 422 MET GLY LEU LEU TRP ALA LEU GLU PRO GLU LYS PRO PHE SEQRES 8 A 422 TRP ARG PHE LEU LYS ARG ASP VAL GLN ILE PRO PHE VAL SEQRES 9 A 422 VAL GLU LEU GLU VAL LEU ASP GLY HIS ASP PRO GLU PRO SEQRES 10 A 422 GLY ARG LEU LEU CYS GLN ALA GLN HIS GLU ARG HIS PHE SEQRES 11 A 422 LEU PRO PRO GLY VAL TRP ARG GLN SER VAL ARG ALA GLY SEQRES 12 A 422 ARG VAL ARG ALA THR LEU PHE LEU PRO PRO GLY PRO GLY SEQRES 13 A 422 PRO PHE PRO GLY ILE ILE ASP ILE PHE GLY ILE GLY GLY SEQRES 14 A 422 GLY LEU LEU GLU TYR ARG ALA SER LEU LEU ALA GLY HIS SEQRES 15 A 422 GLY PHE ALA THR LEU ALA LEU ALA TYR TYR ASN PHE GLU SEQRES 16 A 422 ASP LEU PRO ASN ASN MET ASP ASN ILE SER LEU GLU TYR SEQRES 17 A 422 PHE GLU GLU ALA VAL CYS TYR MET LEU GLN HIS PRO GLN SEQRES 18 A 422 VAL LYS GLY PRO GLY ILE GLY LEU LEU GLY ILE SER LEU SEQRES 19 A 422 GLY ALA ASP ILE CYS LEU SER MET ALA SER PHE LEU LYS SEQRES 20 A 422 ASN VAL SER ALA THR VAL SER ILE ASN GLY SER GLY ILE SEQRES 21 A 422 SER GLY ASN THR ALA ILE ASN TYR LYS HIS SER SER ILE SEQRES 22 A 422 PRO PRO LEU GLY TYR ASP LEU ARG ARG ILE LYS VAL ALA SEQRES 23 A 422 PHE SER GLY LEU VAL ASP ILE VAL ASP ILE ARG ASN ALA SEQRES 24 A 422 LEU VAL GLY GLY TYR LYS ASN PRO SER MET ILE PRO ILE SEQRES 25 A 422 GLU LYS ALA GLN GLY PRO ILE LEU LEU ILE VAL GLY GLN SEQRES 26 A 422 ASP ASP HIS ASN TRP ARG SER GLU LEU TYR ALA GLN THR SEQRES 27 A 422 VAL SER GLU ARG LEU GLN ALA HIS GLY LYS GLU LYS PRO SEQRES 28 A 422 GLN ILE ILE CYS TYR PRO GLY THR GLY HIS TYR ILE GLU SEQRES 29 A 422 PRO PRO TYR PHE PRO LEU CYS PRO ALA SER LEU HIS ARG SEQRES 30 A 422 LEU LEU ASN LYS HIS VAL ILE TRP GLY GLY GLU PRO ARG SEQRES 31 A 422 ALA HIS SER LYS ALA GLN GLU ASP ALA TRP LYS GLN ILE SEQRES 32 A 422 LEU ALA PHE PHE CYS LYS HIS LEU GLY GLY THR GLN LYS SEQRES 33 A 422 THR ALA VAL PRO LYS LEU SEQRES 1 B 422 SER MET SER ALA THR LEU ILE LEU GLU PRO PRO GLY ARG SEQRES 2 B 422 CYS CYS TRP ASN GLU PRO VAL ARG ILE ALA VAL ARG GLY SEQRES 3 B 422 LEU ALA PRO GLU GLN ARG VAL THR LEU ARG ALA SER LEU SEQRES 4 B 422 ARG ASP GLU LYS GLY ALA LEU PHE ARG ALA HIS ALA ARG SEQRES 5 B 422 TYR CYS ALA ASP ALA CYS GLY GLU LEU ASP LEU GLU ARG SEQRES 6 B 422 ALA PRO ALA LEU GLY GLY SER PHE ALA GLY LEU GLU PRO SEQRES 7 B 422 MET GLY LEU LEU TRP ALA LEU GLU PRO GLU LYS PRO PHE SEQRES 8 B 422 TRP ARG PHE LEU LYS ARG ASP VAL GLN ILE PRO PHE VAL SEQRES 9 B 422 VAL GLU LEU GLU VAL LEU ASP GLY HIS ASP PRO GLU PRO SEQRES 10 B 422 GLY ARG LEU LEU CYS GLN ALA GLN HIS GLU ARG HIS PHE SEQRES 11 B 422 LEU PRO PRO GLY VAL TRP ARG GLN SER VAL ARG ALA GLY SEQRES 12 B 422 ARG VAL ARG ALA THR LEU PHE LEU PRO PRO GLY PRO GLY SEQRES 13 B 422 PRO PHE PRO GLY ILE ILE ASP ILE PHE GLY ILE GLY GLY SEQRES 14 B 422 GLY LEU LEU GLU TYR ARG ALA SER LEU LEU ALA GLY HIS SEQRES 15 B 422 GLY PHE ALA THR LEU ALA LEU ALA TYR TYR ASN PHE GLU SEQRES 16 B 422 ASP LEU PRO ASN ASN MET ASP ASN ILE SER LEU GLU TYR SEQRES 17 B 422 PHE GLU GLU ALA VAL CYS TYR MET LEU GLN HIS PRO GLN SEQRES 18 B 422 VAL LYS GLY PRO GLY ILE GLY LEU LEU GLY ILE SER LEU SEQRES 19 B 422 GLY ALA ASP ILE CYS LEU SER MET ALA SER PHE LEU LYS SEQRES 20 B 422 ASN VAL SER ALA THR VAL SER ILE ASN GLY SER GLY ILE SEQRES 21 B 422 SER GLY ASN THR ALA ILE ASN TYR LYS HIS SER SER ILE SEQRES 22 B 422 PRO PRO LEU GLY TYR ASP LEU ARG ARG ILE LYS VAL ALA SEQRES 23 B 422 PHE SER GLY LEU VAL ASP ILE VAL ASP ILE ARG ASN ALA SEQRES 24 B 422 LEU VAL GLY GLY TYR LYS ASN PRO SER MET ILE PRO ILE SEQRES 25 B 422 GLU LYS ALA GLN GLY PRO ILE LEU LEU ILE VAL GLY GLN SEQRES 26 B 422 ASP ASP HIS ASN TRP ARG SER GLU LEU TYR ALA GLN THR SEQRES 27 B 422 VAL SER GLU ARG LEU GLN ALA HIS GLY LYS GLU LYS PRO SEQRES 28 B 422 GLN ILE ILE CYS TYR PRO GLY THR GLY HIS TYR ILE GLU SEQRES 29 B 422 PRO PRO TYR PHE PRO LEU CYS PRO ALA SER LEU HIS ARG SEQRES 30 B 422 LEU LEU ASN LYS HIS VAL ILE TRP GLY GLY GLU PRO ARG SEQRES 31 B 422 ALA HIS SER LYS ALA GLN GLU ASP ALA TRP LYS GLN ILE SEQRES 32 B 422 LEU ALA PHE PHE CYS LYS HIS LEU GLY GLY THR GLN LYS SEQRES 33 B 422 THR ALA VAL PRO LYS LEU HET NI A 422 1 HET CL A 423 1 HET CL A 424 1 HET NI B 422 1 HET CL B 423 1 HETNAM NI NICKEL (II) ION HETNAM CL CHLORIDE ION FORMUL 3 NI 2(NI 2+) FORMUL 4 CL 3(CL 1-) FORMUL 8 HOH *187(H2 O) HELIX 1 1 MET A 78 ALA A 83 1 6 HELIX 2 2 GLU A 172 GLY A 180 1 9 HELIX 3 3 LEU A 205 GLN A 217 1 13 HELIX 4 4 SER A 232 LEU A 245 1 14 HELIX 5 5 ASP A 278 ILE A 282 5 5 HELIX 6 6 GLY A 301 ASN A 305 5 5 HELIX 7 7 PRO A 310 ALA A 314 5 5 HELIX 8 8 ARG A 330 HIS A 345 1 16 HELIX 9 9 GLU A 387 LEU A 410 1 24 HELIX 10 10 MET B 78 ALA B 83 1 6 HELIX 11 11 GLU B 172 GLY B 180 1 9 HELIX 12 12 LEU B 205 HIS B 218 1 14 HELIX 13 13 SER B 232 LEU B 245 1 14 HELIX 14 14 ASP B 278 ILE B 282 5 5 HELIX 15 15 GLY B 301 ASN B 305 5 5 HELIX 16 16 PRO B 310 ALA B 314 5 5 HELIX 17 17 ARG B 330 HIS B 345 1 16 HELIX 18 18 GLU B 387 LEU B 410 1 24 SHEET 1 A 3 THR A 4 GLU A 8 0 SHEET 2 A 3 ARG A 20 ARG A 24 -1 O ALA A 22 N ILE A 6 SHEET 3 A 3 LEU A 60 ASP A 61 -1 O LEU A 60 N VAL A 23 SHEET 1 B 3 GLY A 69 GLY A 70 0 SHEET 2 B 3 LEU A 45 CYS A 53 -1 N ARG A 51 O GLY A 69 SHEET 3 B 3 GLU A 85 PRO A 86 -1 O GLU A 85 N ARG A 47 SHEET 1 C 5 GLY A 69 GLY A 70 0 SHEET 2 C 5 LEU A 45 CYS A 53 -1 N ARG A 51 O GLY A 69 SHEET 3 C 5 ARG A 31 ARG A 39 -1 N VAL A 32 O TYR A 52 SHEET 4 C 5 PHE A 102 ASP A 110 -1 O LEU A 109 N THR A 33 SHEET 5 C 5 LEU A 119 ARG A 127 -1 O HIS A 125 N VAL A 104 SHEET 1 D 8 TRP A 135 ALA A 141 0 SHEET 2 D 8 VAL A 144 LEU A 150 -1 O LEU A 148 N GLN A 137 SHEET 3 D 8 ALA A 184 ALA A 189 -1 O ALA A 187 N THR A 147 SHEET 4 D 8 GLY A 159 ILE A 163 1 N ASP A 162 O LEU A 186 SHEET 5 D 8 ILE A 226 ILE A 231 1 O GLY A 227 N GLY A 159 SHEET 6 D 8 VAL A 248 ILE A 254 1 O VAL A 252 N LEU A 228 SHEET 7 D 8 ILE A 318 GLY A 323 1 O ILE A 321 N SER A 253 SHEET 8 D 8 GLN A 351 TYR A 355 1 O TYR A 355 N VAL A 322 SHEET 1 E 3 ILE A 203 SER A 204 0 SHEET 2 E 3 ILE A 265 TYR A 267 1 O ASN A 266 N ILE A 203 SHEET 3 E 3 SER A 270 ILE A 272 -1 O SER A 270 N TYR A 267 SHEET 1 F 2 LYS A 283 VAL A 284 0 SHEET 2 F 2 VAL A 290 ASP A 291 -1 O ASP A 291 N LYS A 283 SHEET 1 G 2 ALA A 372 HIS A 375 0 SHEET 2 G 2 LYS A 380 ILE A 383 -1 O VAL A 382 N SER A 373 SHEET 1 H 3 THR B 4 GLU B 8 0 SHEET 2 H 3 ARG B 20 ARG B 24 -1 O ARG B 24 N THR B 4 SHEET 3 H 3 LEU B 60 ASP B 61 -1 O LEU B 60 N VAL B 23 SHEET 1 I 3 GLY B 69 GLY B 70 0 SHEET 2 I 3 LEU B 45 CYS B 53 -1 N ARG B 51 O GLY B 69 SHEET 3 I 3 GLU B 85 PRO B 86 -1 O GLU B 85 N ARG B 47 SHEET 1 J 5 GLY B 69 GLY B 70 0 SHEET 2 J 5 LEU B 45 CYS B 53 -1 N ARG B 51 O GLY B 69 SHEET 3 J 5 ARG B 31 ARG B 39 -1 N LEU B 38 O PHE B 46 SHEET 4 J 5 PHE B 102 ASP B 110 -1 O LEU B 109 N THR B 33 SHEET 5 J 5 LEU B 119 ARG B 127 -1 O HIS B 125 N VAL B 104 SHEET 1 K 8 TRP B 135 ALA B 141 0 SHEET 2 K 8 VAL B 144 LEU B 150 -1 O LEU B 148 N GLN B 137 SHEET 3 K 8 ALA B 184 LEU B 188 -1 O ALA B 187 N THR B 147 SHEET 4 K 8 GLY B 159 ILE B 163 1 N ASP B 162 O LEU B 186 SHEET 5 K 8 ILE B 226 ILE B 231 1 O LEU B 229 N ILE B 161 SHEET 6 K 8 VAL B 248 ILE B 254 1 O VAL B 252 N LEU B 228 SHEET 7 K 8 ILE B 318 GLY B 323 1 O ILE B 321 N SER B 253 SHEET 8 K 8 GLN B 351 TYR B 355 1 O GLN B 351 N LEU B 320 SHEET 1 L 3 ILE B 203 SER B 204 0 SHEET 2 L 3 ILE B 265 TYR B 267 1 O ASN B 266 N ILE B 203 SHEET 3 L 3 SER B 270 ILE B 272 -1 O SER B 270 N TYR B 267 SHEET 1 M 2 LYS B 283 VAL B 284 0 SHEET 2 M 2 VAL B 290 ASP B 291 -1 O ASP B 291 N LYS B 283 SHEET 1 N 2 ALA B 372 HIS B 375 0 SHEET 2 N 2 LYS B 380 ILE B 383 -1 O VAL B 382 N SER B 373 CISPEP 1 GLU A 8 PRO A 9 0 -3.98 CISPEP 2 GLY A 155 PRO A 156 0 -10.03 CISPEP 3 GLY A 223 PRO A 224 0 10.52 CISPEP 4 GLU B 8 PRO B 9 0 -25.44 CISPEP 5 GLY B 155 PRO B 156 0 4.13 CISPEP 6 GLY B 223 PRO B 224 0 8.11 SITE 1 AC1 1 LEU B 289 SITE 1 AC2 1 HOH A 492 SITE 1 AC3 1 HOH B 526 CRYST1 72.470 93.000 133.720 90.00 90.00 90.00 P 21 21 21 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 0.013799 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010753 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007478 0.00000