HEADER HYDROLASE 20-MAY-04 1TBU TITLE CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF YEAST PEROXISOMAL TITLE 2 THIOESTERASE-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXISOMAL ACYL-COENZYME A THIOESTER HYDROLASE 1; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN; COMPND 5 SYNONYM: PEROXISOMAL LONG-CHAIN ACYL-COA THIOESTERASE 1; COMPND 6 EC: 3.1.2.2; COMPND 7 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: PTE1, TES1, YJR019C, J1456; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS YEAST PEROXISOMAL THIOESTERASE; X-RAY STRUCTURE; DOMAIN SWAPPING; KEYWDS 2 IODINE SOAK; SIRAS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.D.DEVEDJIEV,J.LI,U.DEREWENDA,Z.S.DEREWENDA REVDAT 3 14-FEB-24 1TBU 1 REMARK REVDAT 2 24-FEB-09 1TBU 1 VERSN REVDAT 1 04-OCT-05 1TBU 0 JRNL AUTH Y.D.DEVEDJIEV,J.LI,U.DEREWENDA,Z.S.DEREWENDA JRNL TITL CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF YEAST PEROXISOMAL JRNL TITL 2 THIOESTERASE-1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 25524 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) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.200 REMARK 3 FREE R VALUE TEST SET COUNT : 852 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1813 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3101 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 106 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.21000 REMARK 3 B22 (A**2) : -0.21000 REMARK 3 B33 (A**2) : 0.32000 REMARK 3 B12 (A**2) : -0.11000 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): 0.234 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.203 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.138 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.449 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3093 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2796 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4203 ; 1.835 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6483 ; 0.946 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 377 ; 9.510 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 493 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3361 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 652 ; 0.010 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 590 ; 0.271 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3186 ; 0.260 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1883 ; 0.096 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 112 ; 0.206 ; 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 ; 0.169 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 44 ; 0.201 ; 0.200 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): 1917 ; 1.243 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3110 ; 2.282 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1176 ; 2.568 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1093 ; 4.260 ; 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 : 1.40 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 1TBU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000022533. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-AUG-01 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9149 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26378 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.22500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SHELXD, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M SODIUM FORMATE, 0.1 M SODIUM REMARK 280 CITRATE BUFFER, PH 5.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 45.69300 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 91.38600 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 91.38600 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 45.69300 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 300 REMARK: PRESENT STRUCTURE PRESENTS ONLY N-TERMINAL DOMAIN OF THE REMARK 300 ENZYME 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 MET A 1 REMARK 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 SER A 4 REMARK 465 LYS A 5 REMARK 465 MET A 6 REMARK 465 ALA A 7 REMARK 465 MET A 8 REMARK 465 SER A 9 REMARK 465 ASN A 10 REMARK 465 LEU A 11 REMARK 465 GLU A 12 REMARK 465 ALA A 32 REMARK 465 ALA A 33 REMARK 465 PRO A 34 REMARK 465 VAL A 35 REMARK 465 GLY A 36 REMARK 465 SER A 37 REMARK 465 LYS A 38 REMARK 465 GLY A 39 REMARK 465 GLN A 117 REMARK 465 ARG A 118 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 ALA B 3 REMARK 465 SER B 4 REMARK 465 LYS B 5 REMARK 465 MET B 6 REMARK 465 ALA B 7 REMARK 465 MET B 8 REMARK 465 SER B 9 REMARK 465 ASN B 10 REMARK 465 LEU B 11 REMARK 465 GLU B 12 REMARK 465 PRO B 31 REMARK 465 ALA B 32 REMARK 465 ALA B 33 REMARK 465 PRO B 34 REMARK 465 VAL B 35 REMARK 465 GLY B 36 REMARK 465 SER B 37 REMARK 465 LYS B 38 REMARK 465 MET C 1 REMARK 465 SER C 2 REMARK 465 ALA C 3 REMARK 465 SER C 4 REMARK 465 LYS C 5 REMARK 465 MET C 6 REMARK 465 ALA C 7 REMARK 465 MET C 8 REMARK 465 SER C 9 REMARK 465 ASN C 10 REMARK 465 LEU C 11 REMARK 465 GLU C 12 REMARK 465 LYS C 13 REMARK 465 ALA C 32 REMARK 465 ALA C 33 REMARK 465 PRO C 34 REMARK 465 VAL C 35 REMARK 465 GLY C 36 REMARK 465 SER C 37 REMARK 465 LYS C 38 REMARK 465 GLY C 39 REMARK 465 ARG C 118 REMARK 465 MET D 1 REMARK 465 SER D 2 REMARK 465 ALA D 3 REMARK 465 SER D 4 REMARK 465 LYS D 5 REMARK 465 MET D 6 REMARK 465 ALA D 7 REMARK 465 MET D 8 REMARK 465 SER D 9 REMARK 465 ASN D 10 REMARK 465 LEU D 11 REMARK 465 GLU D 12 REMARK 465 LYS D 13 REMARK 465 PRO D 31 REMARK 465 ALA D 32 REMARK 465 ALA D 33 REMARK 465 PRO D 34 REMARK 465 VAL D 35 REMARK 465 GLY D 36 REMARK 465 SER D 37 REMARK 465 LYS D 38 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 LYS A 13 CB CG CD CE NZ REMARK 480 ILE A 14 CB CG1 CG2 CD1 REMARK 480 LYS A 28 CG CD CE NZ REMARK 480 TYR A 29 CB CG CD1 CD2 CE1 CE2 CZ REMARK 480 TYR A 29 OH REMARK 480 ARG A 77 CG CD NE CZ NH1 NH2 REMARK 480 ARG A 91 CG CD NE CZ NH1 NH2 REMARK 480 LYS B 13 CB CG CD CE NZ REMARK 480 ILE B 14 CB CG1 CG2 CD1 REMARK 480 LEU B 59 CG CD1 CD2 REMARK 480 ARG B 77 CB CG CD NE CZ NH1 NH2 REMARK 480 ARG B 88 NE CZ NH1 NH2 REMARK 480 LYS B 105 CE NZ REMARK 480 GLN B 117 CD OE1 NE2 REMARK 480 ILE C 14 CB CG1 CG2 CD1 REMARK 480 LYS C 72 CD CE NZ REMARK 480 LYS C 79 CG CD CE NZ REMARK 480 LYS D 72 CG CD CE NZ REMARK 480 ARG D 77 CA CB CG CD NE CZ NH1 REMARK 480 ARG D 77 NH2 REMARK 480 LYS D 79 CG CD CE NZ 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 CA ARG D 77 N THR D 78 1.71 REMARK 500 CB VAL B 26 O HOH B 208 2.15 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 LYS A 13 CA LYS A 13 CB -0.141 REMARK 500 ILE A 14 CA ILE A 14 CB 0.279 REMARK 500 LYS A 28 CB LYS A 28 CG -0.404 REMARK 500 ARG A 91 CB ARG A 91 CG -0.298 REMARK 500 ARG A 91 CZ ARG A 91 NH2 0.084 REMARK 500 LYS B 13 CA LYS B 13 CB -0.403 REMARK 500 ILE B 14 CA ILE B 14 CB -0.299 REMARK 500 ARG B 77 CA ARG B 77 CB 0.435 REMARK 500 ARG B 88 CD ARG B 88 NE -0.175 REMARK 500 ILE C 14 CA ILE C 14 CB -0.262 REMARK 500 LYS C 72 CG LYS C 72 CD 0.350 REMARK 500 LYS D 72 CB LYS D 72 CG -0.484 REMARK 500 ARG D 77 N ARG D 77 CA 0.393 REMARK 500 ARG D 77 CA ARG D 77 C -0.239 REMARK 500 LYS D 79 CB LYS D 79 CG -0.172 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 LYS A 13 N - CA - CB ANGL. DEV. = 27.7 DEGREES REMARK 500 ILE A 14 CB - CA - C ANGL. DEV. = -20.3 DEGREES REMARK 500 LYS A 28 CA - CB - CG ANGL. DEV. = 27.8 DEGREES REMARK 500 LYS A 28 CB - CG - CD ANGL. DEV. = 21.2 DEGREES REMARK 500 LEU A 66 CA - CB - CG ANGL. DEV. = 14.2 DEGREES REMARK 500 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 13.1 DEGREES REMARK 500 ARG A 77 NE - CZ - NH2 ANGL. DEV. = -16.4 DEGREES REMARK 500 ARG A 91 CA - CB - CG ANGL. DEV. = 47.3 DEGREES REMARK 500 ARG A 91 CB - CG - CD ANGL. DEV. = 33.5 DEGREES REMARK 500 ARG A 91 CD - NE - CZ ANGL. DEV. = 16.4 DEGREES REMARK 500 ARG A 91 NE - CZ - NH1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG A 91 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 LEU B 66 CA - CB - CG ANGL. DEV. = 14.5 DEGREES REMARK 500 ARG B 77 CB - CA - C ANGL. DEV. = -35.0 DEGREES REMARK 500 ARG B 88 CD - NE - CZ ANGL. DEV. = -10.9 DEGREES REMARK 500 GLN B 117 CB - CG - CD ANGL. DEV. = -20.0 DEGREES REMARK 500 ILE C 14 CB - CA - C ANGL. DEV. = 15.9 DEGREES REMARK 500 ILE C 14 CA - CB - CG1 ANGL. DEV. = -15.0 DEGREES REMARK 500 VAL C 26 CB - CA - C ANGL. DEV. = -13.4 DEGREES REMARK 500 LEU C 66 CA - CB - CG ANGL. DEV. = 14.6 DEGREES REMARK 500 LYS C 72 CB - CG - CD ANGL. DEV. = -20.9 DEGREES REMARK 500 LYS D 72 CA - CB - CG ANGL. DEV. = 29.7 DEGREES REMARK 500 ARG D 77 C - N - CA ANGL. DEV. = -47.9 DEGREES REMARK 500 ARG D 77 CB - CA - C ANGL. DEV. = -20.7 DEGREES REMARK 500 ARG D 77 N - CA - CB ANGL. DEV. = -50.9 DEGREES REMARK 500 ARG D 77 N - CA - C ANGL. DEV. = 32.9 DEGREES REMARK 500 ARG D 77 CA - C - O ANGL. DEV. = -60.9 DEGREES REMARK 500 ARG D 77 CA - C - N ANGL. DEV. = -35.5 DEGREES REMARK 500 LYS D 79 CA - CB - CG ANGL. DEV. = 16.3 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 ILE A 14 -38.11 156.40 REMARK 500 LEU A 15 46.71 -94.09 REMARK 500 SER A 21 -176.14 -170.32 REMARK 500 PHE A 108 138.25 -172.27 REMARK 500 ILE B 14 -32.07 106.03 REMARK 500 PRO B 76 26.73 -8.24 REMARK 500 LYS B 79 135.74 -13.46 REMARK 500 PHE B 108 138.86 -174.56 REMARK 500 SER C 21 -179.66 -173.50 REMARK 500 ASP C 75 132.25 -26.72 REMARK 500 PHE C 108 138.31 -170.84 REMARK 500 LEU D 15 26.81 30.60 REMARK 500 ARG D 77 113.47 -167.29 REMARK 500 ARG D 88 112.68 152.90 REMARK 500 ARG D 91 -79.54 1.86 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 LYS A 13 ILE A 14 -147.53 REMARK 500 THR B 40 PHE B 41 139.41 REMARK 500 GLY C 73 GLY C 74 127.26 REMARK 500 GLY C 74 ASP C 75 -119.09 REMARK 500 PRO D 76 ARG D 77 137.92 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 ARG D 77 37.08 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 FMT B 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT D 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1C8U RELATED DB: PDB REMARK 900 BACTERIAL ISOFORM OF THE SAME ENZYME DBREF 1TBU A 1 118 UNP P41903 PTE1_YEAST 1 118 DBREF 1TBU B 1 118 UNP P41903 PTE1_YEAST 1 118 DBREF 1TBU C 1 118 UNP P41903 PTE1_YEAST 1 118 DBREF 1TBU D 1 118 UNP P41903 PTE1_YEAST 1 118 SEQRES 1 A 118 MET SER ALA SER LYS MET ALA MET SER ASN LEU GLU LYS SEQRES 2 A 118 ILE LEU GLU LEU VAL PRO LEU SER PRO THR SER PHE VAL SEQRES 3 A 118 THR LYS TYR LEU PRO ALA ALA PRO VAL GLY SER LYS GLY SEQRES 4 A 118 THR PHE GLY GLY THR LEU VAL SER GLN SER LEU LEU ALA SEQRES 5 A 118 SER LEU HIS THR VAL PRO LEU ASN PHE PHE PRO THR SER SEQRES 6 A 118 LEU HIS SER TYR PHE ILE LYS GLY GLY ASP PRO ARG THR SEQRES 7 A 118 LYS ILE THR TYR HIS VAL GLN ASN LEU ARG ASN GLY ARG SEQRES 8 A 118 ASN PHE ILE HIS LYS GLN VAL SER ALA TYR GLN HIS ASP SEQRES 9 A 118 LYS LEU ILE PHE THR SER MET ILE LEU PHE ALA VAL GLN SEQRES 10 A 118 ARG SEQRES 1 B 118 MET SER ALA SER LYS MET ALA MET SER ASN LEU GLU LYS SEQRES 2 B 118 ILE LEU GLU LEU VAL PRO LEU SER PRO THR SER PHE VAL SEQRES 3 B 118 THR LYS TYR LEU PRO ALA ALA PRO VAL GLY SER LYS GLY SEQRES 4 B 118 THR PHE GLY GLY THR LEU VAL SER GLN SER LEU LEU ALA SEQRES 5 B 118 SER LEU HIS THR VAL PRO LEU ASN PHE PHE PRO THR SER SEQRES 6 B 118 LEU HIS SER TYR PHE ILE LYS GLY GLY ASP PRO ARG THR SEQRES 7 B 118 LYS ILE THR TYR HIS VAL GLN ASN LEU ARG ASN GLY ARG SEQRES 8 B 118 ASN PHE ILE HIS LYS GLN VAL SER ALA TYR GLN HIS ASP SEQRES 9 B 118 LYS LEU ILE PHE THR SER MET ILE LEU PHE ALA VAL GLN SEQRES 10 B 118 ARG SEQRES 1 C 118 MET SER ALA SER LYS MET ALA MET SER ASN LEU GLU LYS SEQRES 2 C 118 ILE LEU GLU LEU VAL PRO LEU SER PRO THR SER PHE VAL SEQRES 3 C 118 THR LYS TYR LEU PRO ALA ALA PRO VAL GLY SER LYS GLY SEQRES 4 C 118 THR PHE GLY GLY THR LEU VAL SER GLN SER LEU LEU ALA SEQRES 5 C 118 SER LEU HIS THR VAL PRO LEU ASN PHE PHE PRO THR SER SEQRES 6 C 118 LEU HIS SER TYR PHE ILE LYS GLY GLY ASP PRO ARG THR SEQRES 7 C 118 LYS ILE THR TYR HIS VAL GLN ASN LEU ARG ASN GLY ARG SEQRES 8 C 118 ASN PHE ILE HIS LYS GLN VAL SER ALA TYR GLN HIS ASP SEQRES 9 C 118 LYS LEU ILE PHE THR SER MET ILE LEU PHE ALA VAL GLN SEQRES 10 C 118 ARG SEQRES 1 D 118 MET SER ALA SER LYS MET ALA MET SER ASN LEU GLU LYS SEQRES 2 D 118 ILE LEU GLU LEU VAL PRO LEU SER PRO THR SER PHE VAL SEQRES 3 D 118 THR LYS TYR LEU PRO ALA ALA PRO VAL GLY SER LYS GLY SEQRES 4 D 118 THR PHE GLY GLY THR LEU VAL SER GLN SER LEU LEU ALA SEQRES 5 D 118 SER LEU HIS THR VAL PRO LEU ASN PHE PHE PRO THR SER SEQRES 6 D 118 LEU HIS SER TYR PHE ILE LYS GLY GLY ASP PRO ARG THR SEQRES 7 D 118 LYS ILE THR TYR HIS VAL GLN ASN LEU ARG ASN GLY ARG SEQRES 8 D 118 ASN PHE ILE HIS LYS GLN VAL SER ALA TYR GLN HIS ASP SEQRES 9 D 118 LYS LEU ILE PHE THR SER MET ILE LEU PHE ALA VAL GLN SEQRES 10 D 118 ARG HET FMT B 200 3 HET FMT D 201 3 HETNAM FMT FORMIC ACID FORMUL 5 FMT 2(C H2 O2) FORMUL 7 HOH *106(H2 O) HELIX 1 1 PHE A 41 HIS A 55 1 15 HELIX 2 2 THR B 40 HIS B 55 1 16 HELIX 3 3 PHE C 41 HIS C 55 1 15 HELIX 4 4 GLY D 39 HIS D 55 1 17 SHEET 1 A12 LEU A 17 PRO A 19 0 SHEET 2 A12 SER A 24 THR A 27 -1 O VAL A 26 N VAL A 18 SHEET 3 A12 THR A 81 ASN A 89 -1 O TYR A 82 N PHE A 25 SHEET 4 A12 PHE A 93 GLN A 102 -1 O HIS A 95 N ARG A 88 SHEET 5 A12 LYS A 105 ALA A 115 -1 O SER A 110 N VAL A 98 SHEET 6 A12 PHE A 62 PHE A 70 -1 N TYR A 69 O THR A 109 SHEET 7 A12 PHE B 61 PHE B 70 -1 O SER B 68 N LEU A 66 SHEET 8 A12 LYS B 105 VAL B 116 -1 O LEU B 113 N THR B 64 SHEET 9 A12 PHE B 93 GLN B 102 -1 N VAL B 98 O SER B 110 SHEET 10 A12 THR B 81 ASN B 89 -1 N GLN B 85 O GLN B 97 SHEET 11 A12 SER B 24 THR B 27 -1 N PHE B 25 O TYR B 82 SHEET 12 A12 LEU B 17 SER B 21 -1 N VAL B 18 O VAL B 26 SHEET 1 B12 LEU C 17 PRO C 19 0 SHEET 2 B12 SER C 24 THR C 27 -1 O VAL C 26 N VAL C 18 SHEET 3 B12 THR C 81 ASN C 89 -1 O TYR C 82 N PHE C 25 SHEET 4 B12 PHE C 93 GLN C 102 -1 O GLN C 97 N GLN C 85 SHEET 5 B12 LYS C 105 VAL C 116 -1 O PHE C 108 N ALA C 100 SHEET 6 B12 PHE C 61 PHE C 70 -1 N TYR C 69 O THR C 109 SHEET 7 B12 PHE D 61 PHE D 70 -1 O LEU D 66 N SER C 68 SHEET 8 B12 LYS D 105 VAL D 116 -1 O THR D 109 N TYR D 69 SHEET 9 B12 PHE D 93 GLN D 102 -1 N ALA D 100 O PHE D 108 SHEET 10 B12 THR D 81 ASN D 86 -1 N GLN D 85 O GLN D 97 SHEET 11 B12 SER D 24 THR D 27 -1 N PHE D 25 O TYR D 82 SHEET 12 B12 LEU D 17 PRO D 19 -1 N VAL D 18 O VAL D 26 SITE 1 AC1 6 THR B 64 SER B 65 LEU B 113 GLN C 85 SITE 2 AC1 6 SER C 99 THR C 109 SITE 1 AC2 7 GLN A 97 LEU A 106 THR A 109 THR D 64 SITE 2 AC2 7 SER D 65 LEU D 113 HOH D 214 CRYST1 80.261 80.261 137.079 90.00 90.00 120.00 P 31 2 1 24 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 0.012459 0.007193 0.000000 0.00000 SCALE2 0.000000 0.014387 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007295 0.00000