HEADER METHYLTRANSFERASE 18-SEP-96 1VZA TITLE THYMIDYLATE SYNTHASE E60D MUTANT BINARY COMPLEX WITH 2'-DEOXYURIDINE TITLE 2 5'-MONOPHOSPHATE (DUMP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: THYMIDYLATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TS, LCTS; COMPND 5 EC: 2.1.1.45; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOBACILLUS CASEI; SOURCE 3 ORGANISM_TAXID: 1582; SOURCE 4 GENE: THYMIDYLATE SYNTHASE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: X(CHI)2913 THY-; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PSCTS13; SOURCE 9 EXPRESSION_SYSTEM_GENE: THYMIDYLATE SYNTHASE KEYWDS METHYLTRANSFERASE, NUCLEOTIDE SYNTHASE EXPDTA X-RAY DIFFRACTION AUTHOR D.L.BIRDSALL,J.FINER-MOORE,R.M.STROUD REVDAT 4 14-FEB-24 1VZA 1 REMARK REVDAT 3 03-NOV-21 1VZA 1 REMARK SEQADV REVDAT 2 24-FEB-09 1VZA 1 VERSN REVDAT 1 12-MAR-97 1VZA 0 JRNL AUTH D.L.BIRDSALL,W.HUANG,D.V.SANTI,R.M.STROUD,J.FINER-MOORE JRNL TITL THE SEPARATE EFFECTS OF E60Q IN LACTOBACILLUS CASEI JRNL TITL 2 THYMIDYLATE SYNTHASE DELINEATE BETWEEN MECHANISMS FOR JRNL TITL 3 FORMATION OF INTERMEDIATES IN CATALYSIS. JRNL REF PROTEIN ENG. V. 11 171 1998 JRNL REFN ISSN 0269-2139 JRNL PMID 9613841 JRNL DOI 10.1093/PROTEIN/11.3.171 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.FINER-MOORE,E.B.FAUMAN,P.G.FOSTER,K.M.PERRY,D.V.SANTI, REMARK 1 AUTH 2 R.M.STROUD REMARK 1 TITL REFINED STRUCTURES OF SUBSTRATE-BOUND AND PHOSPHATE-BOUND REMARK 1 TITL 2 THYMIDYLATE SYNTHASE FROM LACTOBACILLUS CASEI REMARK 1 REF J.MOL.BIOL. V. 232 1101 1993 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 11228 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2589 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 29 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.023 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.94 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.870 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARAM19X.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1VZA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177153. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-93 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROCESS REMARK 200 DATA SCALING SOFTWARE : PROCESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13861 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 60.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07990 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 76.76667 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 153.53333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 115.15000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 191.91667 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 38.38333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 76.76667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 153.53333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 191.91667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 115.15000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 38.38333 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 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -115.15000 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 ILE A 310 H1 HOH A 342 1.50 REMARK 500 O LYS A 51 H2 HOH A 343 1.55 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 HIS A 25 NE2 HIS A 25 CD2 -0.073 REMARK 500 HIS A 80 NE2 HIS A 80 CD2 -0.071 REMARK 500 TRP A 153 CG TRP A 153 CD2 -0.107 REMARK 500 TRP A 185 CG TRP A 185 CD2 -0.103 REMARK 500 HIS A 199 NE2 HIS A 199 CD2 -0.092 REMARK 500 HIS A 242 NE2 HIS A 242 CD2 -0.069 REMARK 500 HIS A 253 NE2 HIS A 253 CD2 -0.074 REMARK 500 HIS A 259 NE2 HIS A 259 CD2 -0.088 REMARK 500 HIS A 264 NE2 HIS A 264 CD2 -0.068 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 LEU A 2 N - CA - CB ANGL. DEV. = -12.3 DEGREES REMARK 500 TYR A 6 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 23 CA - CB - CG ANGL. DEV. = 15.1 DEGREES REMARK 500 TYR A 29 N - CA - C ANGL. DEV. = -17.9 DEGREES REMARK 500 MET A 36 CG - SD - CE ANGL. DEV. = 11.6 DEGREES REMARK 500 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 37 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 TRP A 63 CD1 - CG - CD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 TRP A 63 CE2 - CD2 - CG ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 HIS A 77 CA - CB - CG ANGL. DEV. = -13.4 DEGREES REMARK 500 ARG A 78 CB - CG - CD ANGL. DEV. = 17.2 DEGREES REMARK 500 ARG A 78 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 TRP A 82 CD1 - CG - CD2 ANGL. DEV. = 7.4 DEGREES REMARK 500 TRP A 82 CE2 - CD2 - CG ANGL. DEV. = -5.8 DEGREES REMARK 500 TRP A 85 CD1 - CG - CD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 TRP A 85 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 TRP A 90 CD1 - CG - CD2 ANGL. DEV. = 7.7 DEGREES REMARK 500 TRP A 90 CG - CD1 - NE1 ANGL. DEV. = -6.3 DEGREES REMARK 500 TRP A 90 CE2 - CD2 - CG ANGL. DEV. = -6.0 DEGREES REMARK 500 TRP A 90 O - C - N ANGL. DEV. = 10.3 DEGREES REMARK 500 TYR A 96 CB - CG - CD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 TYR A 96 CB - CG - CD1 ANGL. DEV. = 3.6 DEGREES REMARK 500 HIS A 97 CA - C - N ANGL. DEV. = -14.6 DEGREES REMARK 500 PRO A 99 N - CA - C ANGL. DEV. = 19.0 DEGREES REMARK 500 MET A 101 CG - SD - CE ANGL. DEV. = -10.6 DEGREES REMARK 500 HIS A 106 CA - CB - CG ANGL. DEV. = -13.2 DEGREES REMARK 500 ARG A 107 N - CA - C ANGL. DEV. = -18.5 DEGREES REMARK 500 MET A 122 CG - SD - CE ANGL. DEV. = -13.1 DEGREES REMARK 500 ASP A 126 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 128 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 128 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP A 141 N - CA - C ANGL. DEV. = -18.4 DEGREES REMARK 500 TRP A 150 CD1 - CG - CD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 TRP A 150 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 151 NE - CZ - NH1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG A 151 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 TRP A 153 CD1 - CG - CD2 ANGL. DEV. = 7.6 DEGREES REMARK 500 TRP A 153 CE2 - CD2 - CG ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP A 159 N - CA - CB ANGL. DEV. = -12.8 DEGREES REMARK 500 ASP A 166 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 GLU A 169 CA - CB - CG ANGL. DEV. = -18.4 DEGREES REMARK 500 TYR A 176 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 178 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 LEU A 180 CA - CB - CG ANGL. DEV. = 13.8 DEGREES REMARK 500 TRP A 185 CD1 - CG - CD2 ANGL. DEV. = 6.8 DEGREES REMARK 500 TRP A 185 CE2 - CD2 - CG ANGL. DEV. = -6.1 DEGREES REMARK 500 LEU A 195 N - CA - C ANGL. DEV. = -16.3 DEGREES REMARK 500 LEU A 201 CA - CB - CG ANGL. DEV. = 16.7 DEGREES REMARK 500 TYR A 202 CB - CG - CD1 ANGL. DEV. = -5.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 56 ANGLE DEVIATIONS. 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 LYS A 11 -70.92 -55.39 REMARK 500 GLU A 16 27.41 -146.13 REMARK 500 HIS A 25 41.62 36.45 REMARK 500 THR A 26 -167.91 -112.43 REMARK 500 LEU A 40 -6.91 -59.92 REMARK 500 LYS A 50 114.70 -164.07 REMARK 500 HIS A 80 19.45 -143.18 REMARK 500 ASP A 94 -60.21 5.16 REMARK 500 PRO A 99 -101.69 -101.11 REMARK 500 ASP A 100 -83.42 -92.58 REMARK 500 MET A 101 -44.41 36.08 REMARK 500 THR A 102 109.90 -48.48 REMARK 500 ASP A 103 -47.41 119.79 REMARK 500 PHE A 104 -128.81 30.61 REMARK 500 SER A 108 -93.52 160.62 REMARK 500 ALA A 111 -167.87 92.87 REMARK 500 PRO A 112 -120.22 -76.32 REMARK 500 ALA A 116 -116.94 -82.71 REMARK 500 VAL A 117 -67.17 10.98 REMARK 500 HIS A 131 -61.47 -151.94 REMARK 500 ALA A 152 69.38 -173.25 REMARK 500 ASP A 162 70.21 -114.88 REMARK 500 HIS A 174 93.95 -166.21 REMARK 500 ALA A 194 -81.59 -67.34 REMARK 500 HIS A 242 -14.30 -46.80 REMARK 500 PRO A 276 131.30 -32.50 REMARK 500 HIS A 289 -35.71 -137.71 REMARK 500 MET A 296 -9.91 -35.74 REMARK 500 ASN A 303 79.66 58.48 REMARK 500 PRO A 308 157.48 -26.92 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 ALA A 111 PRO A 112 -35.63 REMARK 500 ALA A 312 PRO A 313 148.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 6 0.09 SIDE CHAIN 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 THR A 102 10.98 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 UMP A 317 DBREF 1VZA A 1 316 UNP P00469 TYSY_LACCA 1 316 SEQADV 1VZA ASP A 60 UNP P00469 GLU 60 ENGINEERED MUTATION SEQADV 1VZA ALA A 111 UNP P00469 ASP 111 CONFLICT SEQRES 1 A 316 MET LEU GLU GLN PRO TYR LEU ASP LEU ALA LYS LYS VAL SEQRES 2 A 316 LEU ASP GLU GLY HIS PHE LYS PRO ASP ARG THR HIS THR SEQRES 3 A 316 GLY THR TYR SER ILE PHE GLY HIS GLN MET ARG PHE ASP SEQRES 4 A 316 LEU SER LYS GLY PHE PRO LEU LEU THR THR LYS LYS VAL SEQRES 5 A 316 PRO PHE GLY LEU ILE LYS SER ASP LEU LEU TRP PHE LEU SEQRES 6 A 316 HIS GLY ASP THR ASN ILE ARG PHE LEU LEU GLN HIS ARG SEQRES 7 A 316 ASN HIS ILE TRP ASP GLU TRP ALA PHE GLU LYS TRP VAL SEQRES 8 A 316 LYS SER ASP GLU TYR HIS GLY PRO ASP MET THR ASP PHE SEQRES 9 A 316 GLY HIS ARG SER GLN LYS ALA PRO GLU PHE ALA ALA VAL SEQRES 10 A 316 TYR HIS GLU GLU MET ALA LYS PHE ASP ASP ARG VAL LEU SEQRES 11 A 316 HIS ASP ASP ALA PHE ALA ALA LYS TYR GLY ASP LEU GLY SEQRES 12 A 316 LEU VAL TYR GLY SER GLN TRP ARG ALA TRP HIS THR SER SEQRES 13 A 316 LYS GLY ASP THR ILE ASP GLN LEU GLY ASP VAL ILE GLU SEQRES 14 A 316 GLN ILE LYS THR HIS PRO TYR SER ARG ARG LEU ILE VAL SEQRES 15 A 316 SER ALA TRP ASN PRO GLU ASP VAL PRO THR MET ALA LEU SEQRES 16 A 316 PRO PRO CYS HIS THR LEU TYR GLN PHE TYR VAL ASN ASP SEQRES 17 A 316 GLY LYS LEU SER LEU GLN LEU TYR GLN ARG SER ALA ASP SEQRES 18 A 316 ILE PHE LEU GLY VAL PRO PHE ASN ILE ALA SER TYR ALA SEQRES 19 A 316 LEU LEU THR HIS LEU VAL ALA HIS GLU CYS GLY LEU GLU SEQRES 20 A 316 VAL GLY GLU PHE ILE HIS THR PHE GLY ASP ALA HIS LEU SEQRES 21 A 316 TYR VAL ASN HIS LEU ASP GLN ILE LYS GLU GLN LEU SER SEQRES 22 A 316 ARG THR PRO ARG PRO ALA PRO THR LEU GLN LEU ASN PRO SEQRES 23 A 316 ASP LYS HIS ASP ILE PHE ASP PHE ASP MET LYS ASP ILE SEQRES 24 A 316 LYS LEU LEU ASN TYR ASP PRO TYR PRO ALA ILE LYS ALA SEQRES 25 A 316 PRO VAL ALA VAL HET UMP A 317 21 HETNAM UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE HETSYN UMP DUMP FORMUL 2 UMP C9 H13 N2 O8 P FORMUL 3 HOH *29(H2 O) HELIX 1 1 GLN A 4 GLU A 16 1 13 HELIX 2 2 LEU A 40 LYS A 42 5 3 HELIX 3 3 PHE A 54 HIS A 66 1 13 HELIX 4 4 ILE A 71 HIS A 77 1 7 HELIX 5 5 ILE A 81 TRP A 90 5 10 HELIX 6 6 GLU A 113 ALA A 115 5 3 HELIX 7 7 TYR A 118 VAL A 129 1 12 HELIX 8 8 ASP A 133 TYR A 139 1 7 HELIX 9 9 TYR A 146 ARG A 151 1 6 HELIX 10 10 GLN A 163 THR A 173 1 11 HELIX 11 11 VAL A 190 THR A 192 5 3 HELIX 12 12 VAL A 226 CYS A 244 1 19 HELIX 13 13 VAL A 262 SER A 273 5 12 HELIX 14 14 ILE A 291 ASP A 293 5 3 SHEET 1 A 4 HIS A 18 LYS A 20 0 SHEET 2 A 4 THR A 28 PHE A 32 -1 N SER A 30 O HIS A 18 SHEET 3 A 4 ASP A 257 TYR A 261 -1 N LEU A 260 O TYR A 29 SHEET 4 A 4 SER A 219 ASP A 221 1 N ALA A 220 O ASP A 257 SHEET 1 B 5 HIS A 34 ASP A 39 0 SHEET 2 B 5 GLU A 250 PHE A 255 -1 N PHE A 255 O HIS A 34 SHEET 3 B 5 LYS A 210 GLN A 217 1 N LEU A 213 O ILE A 252 SHEET 4 B 5 HIS A 199 ASN A 207 -1 N ASN A 207 O LYS A 210 SHEET 5 B 5 LEU A 180 SER A 183 -1 N VAL A 182 O TYR A 202 SHEET 1 C 2 THR A 281 LEU A 284 0 SHEET 2 C 2 ILE A 299 LEU A 302 -1 N LEU A 302 O THR A 281 SITE 1 AC1 15 ARG A 23 ARG A 178 ARG A 179 LEU A 195 SITE 2 AC1 15 HIS A 199 GLN A 217 ARG A 218 SER A 219 SITE 3 AC1 15 ALA A 220 ASP A 221 GLY A 225 ASN A 229 SITE 4 AC1 15 HIS A 259 TYR A 261 HOH A 334 CRYST1 79.100 79.100 230.300 90.00 90.00 120.00 P 61 2 2 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 0.012642 0.007299 0.000000 0.00000 SCALE2 0.000000 0.014598 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004342 0.00000