HEADER LYASE 28-MAR-03 1UB3 TITLE CRYSTAL STRUCTURE OF TETRAMERIC STRUCTURE OF ALDOLASE FROM THERMUS TITLE 2 THERMOPHILUS HB8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALDOLASE PROTEIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 EC: 4.1.2.4; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-11A KEYWDS SCHIFF BASE, DEOXYRIBOSE PHOSPHATE, CARBINOLAMINE, STRUCTURAL KEYWDS 2 GENOMICS, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, KEYWDS 3 LYASE EXPDTA X-RAY DIFFRACTION AUTHOR N.K.LOKANATH,M.MIYANO,S.YOKOYAMA,S.KURAMITSU,N.KUNISHIMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 5 06-NOV-24 1UB3 1 REMARK REVDAT 4 27-DEC-23 1UB3 1 REMARK LINK REVDAT 3 24-FEB-09 1UB3 1 VERSN REVDAT 2 07-DEC-04 1UB3 1 JRNL REVDAT 1 08-APR-03 1UB3 0 JRNL AUTH N.K.LOKANATH,I.SHIROMIZU,N.OHSHIMA,Y.NODAKE,M.SUGAHARA, JRNL AUTH 2 S.YOKOYAMA,S.KURAMITSU,M.MIYANO,N.KUNISHIMA JRNL TITL STRUCTURE OF ALDOLASE FROM THERMUS THERMOPHILUS HB8 SHOWING JRNL TITL 2 THE CONTRIBUTION OF OLIGOMERIC STATE TO THERMOSTABILITY. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 60 1816 2004 JRNL REFN ISSN 0907-4449 JRNL PMID 15388928 JRNL DOI 10.1107/S0907444904020190 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1106896.530 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 164987 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 SET) : 0.202 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 16428 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.002 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 24291 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 2754 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.005 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6322 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 442 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.96000 REMARK 3 B22 (A**2) : 1.23000 REMARK 3 B33 (A**2) : -4.19000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.15 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.270 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 57.99 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : HPD.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : HPD.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UB3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000005638. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.80 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 164987 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : 0.04600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, TRIS-HCL, MGCL2, DEOXYRIBOSE REMARK 280 PHOSPHATE , PH 7.9, MICROBATCH, TEMPERATURE 295.0K 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 31.91000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.96250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.44350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.96250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.91000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.44350 REMARK 290 SMTRY3 4 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 300 REMARK: MOLECULE IS IN THE TETRAMER FORM. THE BIOLOGICAL ASSEMPBLY REMARK 300 IS A TETRAMER GENERATED FROM THE MONOMER IN THE ASYMMETRIC UNIT. 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: 10190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 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 GLY A 213 REMARK 465 GLU A 214 REMARK 465 GLY A 215 REMARK 465 GLY A 216 REMARK 465 THR A 217 REMARK 465 LEU A 218 REMARK 465 GLY A 219 REMARK 465 TYR A 220 REMARK 465 ALA B 212 REMARK 465 GLY B 213 REMARK 465 GLU B 214 REMARK 465 GLY B 215 REMARK 465 GLY B 216 REMARK 465 THR B 217 REMARK 465 LEU B 218 REMARK 465 GLY B 219 REMARK 465 TYR B 220 REMARK 465 MET C 1 REMARK 465 ALA C 212 REMARK 465 GLY C 213 REMARK 465 GLU C 214 REMARK 465 GLY C 215 REMARK 465 GLY C 216 REMARK 465 THR C 217 REMARK 465 LEU C 218 REMARK 465 GLY C 219 REMARK 465 TYR C 220 REMARK 465 MET D 1 REMARK 465 GLY D 213 REMARK 465 GLU D 214 REMARK 465 GLY D 215 REMARK 465 GLY D 216 REMARK 465 THR D 217 REMARK 465 LEU D 218 REMARK 465 GLY D 219 REMARK 465 TYR D 220 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 ALA B 209 N LEU B 210 1.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LEU B 29 C GLU B 30 N -0.158 REMARK 500 GLN B 174 C GLY B 175 N -0.415 REMARK 500 GLY B 207 C VAL B 208 N -0.174 REMARK 500 ALA B 209 C LEU B 210 N -0.520 REMARK 500 LEU B 210 C VAL B 211 N -0.152 REMARK 500 ASP C 2 C LEU C 3 N -0.192 REMARK 500 GLN C 118 C ALA C 119 N -0.173 REMARK 500 GLU C 133 CD GLU C 133 OE1 -0.104 REMARK 500 ALA C 136 C ARG C 137 N -0.144 REMARK 500 ARG C 171 C VAL C 172 N -0.157 REMARK 500 GLU C 189 CD GLU C 189 OE2 -0.121 REMARK 500 LYS C 196 C ALA C 197 N -0.226 REMARK 500 ASP D 2 C LEU D 3 N -0.225 REMARK 500 HIS D 6 C ILE D 7 N -0.220 REMARK 500 GLU D 26 C GLU D 27 N -0.190 REMARK 500 LEU D 29 C GLU D 30 N -0.252 REMARK 500 ARG D 49 C TYR D 50 N -0.154 REMARK 500 HIS D 52 C ALA D 53 N -0.161 REMARK 500 ARG D 110 CZ ARG D 110 NH1 0.079 REMARK 500 ARG D 110 CZ ARG D 110 NH2 -0.087 REMARK 500 PRO D 117 C GLN D 118 N -0.223 REMARK 500 GLN D 174 C GLY D 175 N -0.200 REMARK 500 ARG D 193 C MET D 194 N -0.171 REMARK 500 VAL D 208 C ALA D 209 N -0.271 REMARK 500 LEU D 210 C VAL D 211 N -0.254 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 GLU A 140 O - C - N ANGL. DEV. = -12.6 DEGREES REMARK 500 ARG A 193 NE - CZ - NH1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 193 NE - CZ - NH2 ANGL. DEV. = -7.6 DEGREES REMARK 500 MET B 1 O - C - N ANGL. DEV. = 11.1 DEGREES REMARK 500 ASP B 2 O - C - N ANGL. DEV. = 10.7 DEGREES REMARK 500 ARG B 171 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG B 171 NE - CZ - NH2 ANGL. DEV. = -7.4 DEGREES REMARK 500 GLY B 175 C - N - CA ANGL. DEV. = 17.7 DEGREES REMARK 500 ASP C 2 CB - CG - OD1 ANGL. DEV. = -10.0 DEGREES REMARK 500 ASP C 2 CB - CG - OD2 ANGL. DEV. = 8.9 DEGREES REMARK 500 ARG C 171 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 GLN C 174 CG - CD - OE1 ANGL. DEV. = -13.1 DEGREES REMARK 500 ASP D 2 N - CA - CB ANGL. DEV. = -16.3 DEGREES REMARK 500 ASP D 2 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG D 49 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG D 49 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 HIS D 52 C - N - CA ANGL. DEV. = -16.1 DEGREES REMARK 500 CYS D 81 CA - CB - SG ANGL. DEV. = -12.7 DEGREES REMARK 500 ASP D 103 CB - CG - OD1 ANGL. DEV. = 11.5 DEGREES REMARK 500 ASP D 103 CB - CG - OD2 ANGL. DEV. = -11.6 DEGREES REMARK 500 ARG D 110 CG - CD - NE ANGL. DEV. = 13.6 DEGREES REMARK 500 ARG D 110 CD - NE - CZ ANGL. DEV. = -11.6 DEGREES REMARK 500 ARG D 110 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG D 193 CD - NE - CZ ANGL. DEV. = -11.3 DEGREES REMARK 500 ARG D 193 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 LEU D 210 O - C - N ANGL. DEV. = -13.1 DEGREES REMARK 500 VAL D 211 O - C - N ANGL. DEV. = -13.4 DEGREES REMARK 500 ALA D 212 C - N - CA ANGL. DEV. = 21.2 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 ALA A 5 1.14 -69.02 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 ARG B 171 0.14 SIDE CHAIN REMARK 500 ARG B 186 0.08 SIDE CHAIN REMARK 500 ARG C 171 0.08 SIDE CHAIN REMARK 500 ARG C 186 0.10 SIDE CHAIN REMARK 500 ARG D 49 0.24 SIDE CHAIN REMARK 500 ARG D 193 0.13 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 GLY B 175 -10.39 REMARK 500 GLU C 189 -11.84 REMARK 500 LEU D 210 12.30 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 HPD A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HPD B 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HPD C 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HPD D 804 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: TTK003000501.2 RELATED DB: TARGETDB DBREF 1UB3 A 1 220 UNP Q7SIC8 Q7SIC8_THETH 1 220 DBREF 1UB3 B 1 220 UNP Q7SIC8 Q7SIC8_THETH 1 220 DBREF 1UB3 C 1 220 UNP Q7SIC8 Q7SIC8_THETH 1 220 DBREF 1UB3 D 1 220 UNP Q7SIC8 Q7SIC8_THETH 1 220 SEQRES 1 A 220 MET ASP LEU ALA ALA HIS ILE ASP HIS THR LEU LEU LYS SEQRES 2 A 220 PRO THR ALA THR LEU GLU GLU VAL ALA LYS ALA ALA GLU SEQRES 3 A 220 GLU ALA LEU GLU TYR GLY PHE TYR GLY LEU CYS ILE PRO SEQRES 4 A 220 PRO SER TYR VAL ALA TRP VAL ARG ALA ARG TYR PRO HIS SEQRES 5 A 220 ALA PRO PHE ARG LEU VAL THR VAL VAL GLY PHE PRO LEU SEQRES 6 A 220 GLY TYR GLN GLU LYS GLU VAL LYS ALA LEU GLU ALA ALA SEQRES 7 A 220 LEU ALA CYS ALA ARG GLY ALA ASP GLU VAL ASP MET VAL SEQRES 8 A 220 LEU HIS LEU GLY ARG ALA LYS ALA GLY ASP LEU ASP TYR SEQRES 9 A 220 LEU GLU ALA GLU VAL ARG ALA VAL ARG GLU ALA VAL PRO SEQRES 10 A 220 GLN ALA VAL LEU LYS VAL ILE LEU GLU THR GLY TYR PHE SEQRES 11 A 220 SER PRO GLU GLU ILE ALA ARG LEU ALA GLU ALA ALA ILE SEQRES 12 A 220 ARG GLY GLY ALA ASP PHE LEU LYS THR SER THR GLY PHE SEQRES 13 A 220 GLY PRO ARG GLY ALA SER LEU GLU ASP VAL ALA LEU LEU SEQRES 14 A 220 VAL ARG VAL ALA GLN GLY ARG ALA GLN VAL LYS ALA ALA SEQRES 15 A 220 GLY GLY ILE ARG ASP ARG GLU THR ALA LEU ARG MET LEU SEQRES 16 A 220 LYS ALA GLY ALA SER ARG LEU GLY THR SER SER GLY VAL SEQRES 17 A 220 ALA LEU VAL ALA GLY GLU GLY GLY THR LEU GLY TYR SEQRES 1 B 220 MET ASP LEU ALA ALA HIS ILE ASP HIS THR LEU LEU LYS SEQRES 2 B 220 PRO THR ALA THR LEU GLU GLU VAL ALA LYS ALA ALA GLU SEQRES 3 B 220 GLU ALA LEU GLU TYR GLY PHE TYR GLY LEU CYS ILE PRO SEQRES 4 B 220 PRO SER TYR VAL ALA TRP VAL ARG ALA ARG TYR PRO HIS SEQRES 5 B 220 ALA PRO PHE ARG LEU VAL THR VAL VAL GLY PHE PRO LEU SEQRES 6 B 220 GLY TYR GLN GLU LYS GLU VAL LYS ALA LEU GLU ALA ALA SEQRES 7 B 220 LEU ALA CYS ALA ARG GLY ALA ASP GLU VAL ASP MET VAL SEQRES 8 B 220 LEU HIS LEU GLY ARG ALA LYS ALA GLY ASP LEU ASP TYR SEQRES 9 B 220 LEU GLU ALA GLU VAL ARG ALA VAL ARG GLU ALA VAL PRO SEQRES 10 B 220 GLN ALA VAL LEU LYS VAL ILE LEU GLU THR GLY TYR PHE SEQRES 11 B 220 SER PRO GLU GLU ILE ALA ARG LEU ALA GLU ALA ALA ILE SEQRES 12 B 220 ARG GLY GLY ALA ASP PHE LEU LYS THR SER THR GLY PHE SEQRES 13 B 220 GLY PRO ARG GLY ALA SER LEU GLU ASP VAL ALA LEU LEU SEQRES 14 B 220 VAL ARG VAL ALA GLN GLY ARG ALA GLN VAL LYS ALA ALA SEQRES 15 B 220 GLY GLY ILE ARG ASP ARG GLU THR ALA LEU ARG MET LEU SEQRES 16 B 220 LYS ALA GLY ALA SER ARG LEU GLY THR SER SER GLY VAL SEQRES 17 B 220 ALA LEU VAL ALA GLY GLU GLY GLY THR LEU GLY TYR SEQRES 1 C 220 MET ASP LEU ALA ALA HIS ILE ASP HIS THR LEU LEU LYS SEQRES 2 C 220 PRO THR ALA THR LEU GLU GLU VAL ALA LYS ALA ALA GLU SEQRES 3 C 220 GLU ALA LEU GLU TYR GLY PHE TYR GLY LEU CYS ILE PRO SEQRES 4 C 220 PRO SER TYR VAL ALA TRP VAL ARG ALA ARG TYR PRO HIS SEQRES 5 C 220 ALA PRO PHE ARG LEU VAL THR VAL VAL GLY PHE PRO LEU SEQRES 6 C 220 GLY TYR GLN GLU LYS GLU VAL LYS ALA LEU GLU ALA ALA SEQRES 7 C 220 LEU ALA CYS ALA ARG GLY ALA ASP GLU VAL ASP MET VAL SEQRES 8 C 220 LEU HIS LEU GLY ARG ALA LYS ALA GLY ASP LEU ASP TYR SEQRES 9 C 220 LEU GLU ALA GLU VAL ARG ALA VAL ARG GLU ALA VAL PRO SEQRES 10 C 220 GLN ALA VAL LEU LYS VAL ILE LEU GLU THR GLY TYR PHE SEQRES 11 C 220 SER PRO GLU GLU ILE ALA ARG LEU ALA GLU ALA ALA ILE SEQRES 12 C 220 ARG GLY GLY ALA ASP PHE LEU LYS THR SER THR GLY PHE SEQRES 13 C 220 GLY PRO ARG GLY ALA SER LEU GLU ASP VAL ALA LEU LEU SEQRES 14 C 220 VAL ARG VAL ALA GLN GLY ARG ALA GLN VAL LYS ALA ALA SEQRES 15 C 220 GLY GLY ILE ARG ASP ARG GLU THR ALA LEU ARG MET LEU SEQRES 16 C 220 LYS ALA GLY ALA SER ARG LEU GLY THR SER SER GLY VAL SEQRES 17 C 220 ALA LEU VAL ALA GLY GLU GLY GLY THR LEU GLY TYR SEQRES 1 D 220 MET ASP LEU ALA ALA HIS ILE ASP HIS THR LEU LEU LYS SEQRES 2 D 220 PRO THR ALA THR LEU GLU GLU VAL ALA LYS ALA ALA GLU SEQRES 3 D 220 GLU ALA LEU GLU TYR GLY PHE TYR GLY LEU CYS ILE PRO SEQRES 4 D 220 PRO SER TYR VAL ALA TRP VAL ARG ALA ARG TYR PRO HIS SEQRES 5 D 220 ALA PRO PHE ARG LEU VAL THR VAL VAL GLY PHE PRO LEU SEQRES 6 D 220 GLY TYR GLN GLU LYS GLU VAL LYS ALA LEU GLU ALA ALA SEQRES 7 D 220 LEU ALA CYS ALA ARG GLY ALA ASP GLU VAL ASP MET VAL SEQRES 8 D 220 LEU HIS LEU GLY ARG ALA LYS ALA GLY ASP LEU ASP TYR SEQRES 9 D 220 LEU GLU ALA GLU VAL ARG ALA VAL ARG GLU ALA VAL PRO SEQRES 10 D 220 GLN ALA VAL LEU LYS VAL ILE LEU GLU THR GLY TYR PHE SEQRES 11 D 220 SER PRO GLU GLU ILE ALA ARG LEU ALA GLU ALA ALA ILE SEQRES 12 D 220 ARG GLY GLY ALA ASP PHE LEU LYS THR SER THR GLY PHE SEQRES 13 D 220 GLY PRO ARG GLY ALA SER LEU GLU ASP VAL ALA LEU LEU SEQRES 14 D 220 VAL ARG VAL ALA GLN GLY ARG ALA GLN VAL LYS ALA ALA SEQRES 15 D 220 GLY GLY ILE ARG ASP ARG GLU THR ALA LEU ARG MET LEU SEQRES 16 D 220 LYS ALA GLY ALA SER ARG LEU GLY THR SER SER GLY VAL SEQRES 17 D 220 ALA LEU VAL ALA GLY GLU GLY GLY THR LEU GLY TYR HET HPD A 801 13 HET HPD B 802 13 HET HPD C 803 13 HET HPD D 804 13 HETNAM HPD 1-HYDROXY-PENTANE-3,4-DIOL-5-PHOSPHATE HETSYN HPD OPEN FORM OF 2'-DEOXY-RIBOFURANOSE-5'-PHOSPHATE FORMUL 5 HPD 4(C5 H13 O7 P) FORMUL 9 HOH *442(H2 O) HELIX 1 1 ASP A 2 ALA A 5 5 4 HELIX 2 2 THR A 17 GLY A 32 1 16 HELIX 3 3 PRO A 39 SER A 41 5 3 HELIX 4 4 TYR A 42 TYR A 50 1 9 HELIX 5 5 GLU A 69 ARG A 83 1 15 HELIX 6 6 HIS A 93 ALA A 99 1 7 HELIX 7 7 ASP A 101 VAL A 116 1 16 HELIX 8 8 GLU A 126 PHE A 130 5 5 HELIX 9 9 SER A 131 GLY A 146 1 16 HELIX 10 10 SER A 162 GLN A 174 1 13 HELIX 11 11 ASP A 187 ALA A 197 1 11 HELIX 12 12 SER A 206 ALA A 212 1 7 HELIX 13 13 LEU B 3 ALA B 5 5 3 HELIX 14 14 THR B 17 GLY B 32 1 16 HELIX 15 15 PRO B 39 SER B 41 5 3 HELIX 16 16 TYR B 42 TYR B 50 1 9 HELIX 17 17 GLU B 69 ARG B 83 1 15 HELIX 18 18 HIS B 93 ALA B 99 1 7 HELIX 19 19 ASP B 101 VAL B 116 1 16 HELIX 20 20 GLU B 126 PHE B 130 5 5 HELIX 21 21 SER B 131 GLY B 145 1 15 HELIX 22 22 SER B 162 GLN B 174 1 13 HELIX 23 23 ASP B 187 ALA B 197 1 11 HELIX 24 24 SER B 206 VAL B 211 1 6 HELIX 25 25 ASP C 2 ALA C 5 5 4 HELIX 26 26 THR C 17 GLY C 32 1 16 HELIX 27 27 PRO C 39 SER C 41 5 3 HELIX 28 28 TYR C 42 TYR C 50 1 9 HELIX 29 29 GLU C 69 ARG C 83 1 15 HELIX 30 30 HIS C 93 ALA C 99 1 7 HELIX 31 31 ASP C 101 VAL C 116 1 16 HELIX 32 32 GLU C 126 PHE C 130 5 5 HELIX 33 33 SER C 131 GLY C 145 1 15 HELIX 34 34 SER C 162 GLN C 174 1 13 HELIX 35 35 ASP C 187 ALA C 197 1 11 HELIX 36 36 SER C 206 VAL C 211 1 6 HELIX 37 37 ASP D 2 ALA D 5 5 4 HELIX 38 38 THR D 17 GLY D 32 1 16 HELIX 39 39 PRO D 39 SER D 41 5 3 HELIX 40 40 TYR D 42 TYR D 50 1 9 HELIX 41 41 GLU D 69 ARG D 83 1 15 HELIX 42 42 HIS D 93 ALA D 99 1 7 HELIX 43 43 ASP D 101 VAL D 116 1 16 HELIX 44 44 GLU D 126 PHE D 130 5 5 HELIX 45 45 SER D 131 GLY D 145 1 15 HELIX 46 46 SER D 162 GLN D 174 1 13 HELIX 47 47 ASP D 187 ALA D 197 1 11 HELIX 48 48 SER D 206 ALA D 212 1 7 SHEET 1 A 9 ILE A 7 THR A 10 0 SHEET 2 A 9 GLY A 35 CYS A 37 1 O CYS A 37 N HIS A 9 SHEET 3 A 9 ARG A 56 VAL A 61 1 O VAL A 58 N LEU A 36 SHEET 4 A 9 GLU A 87 VAL A 91 1 O ASP A 89 N THR A 59 SHEET 5 A 9 VAL A 120 ILE A 124 1 O ILE A 124 N MET A 90 SHEET 6 A 9 PHE A 149 LYS A 151 1 O LYS A 151 N VAL A 123 SHEET 7 A 9 GLN A 178 ALA A 182 1 O LYS A 180 N LEU A 150 SHEET 8 A 9 ARG A 201 THR A 204 1 O GLY A 203 N ALA A 181 SHEET 9 A 9 ILE A 7 THR A 10 1 N ASP A 8 O LEU A 202 SHEET 1 B 9 ILE B 7 THR B 10 0 SHEET 2 B 9 GLY B 35 CYS B 37 1 O CYS B 37 N HIS B 9 SHEET 3 B 9 ARG B 56 VAL B 61 1 O VAL B 58 N LEU B 36 SHEET 4 B 9 GLU B 87 VAL B 91 1 O ASP B 89 N THR B 59 SHEET 5 B 9 VAL B 120 ILE B 124 1 O ILE B 124 N MET B 90 SHEET 6 B 9 PHE B 149 LYS B 151 1 O LYS B 151 N VAL B 123 SHEET 7 B 9 GLN B 178 ALA B 182 1 O LYS B 180 N LEU B 150 SHEET 8 B 9 ARG B 201 THR B 204 1 O GLY B 203 N ALA B 181 SHEET 9 B 9 ILE B 7 THR B 10 1 N ASP B 8 O LEU B 202 SHEET 1 C 9 ILE C 7 THR C 10 0 SHEET 2 C 9 GLY C 35 CYS C 37 1 O CYS C 37 N HIS C 9 SHEET 3 C 9 ARG C 56 VAL C 61 1 O VAL C 58 N LEU C 36 SHEET 4 C 9 GLU C 87 VAL C 91 1 O ASP C 89 N THR C 59 SHEET 5 C 9 VAL C 120 ILE C 124 1 O ILE C 124 N MET C 90 SHEET 6 C 9 PHE C 149 LYS C 151 1 O LYS C 151 N VAL C 123 SHEET 7 C 9 GLN C 178 ALA C 182 1 O LYS C 180 N LEU C 150 SHEET 8 C 9 ARG C 201 THR C 204 1 O GLY C 203 N ALA C 181 SHEET 9 C 9 ILE C 7 THR C 10 1 N ASP C 8 O LEU C 202 SHEET 1 D 9 ILE D 7 THR D 10 0 SHEET 2 D 9 GLY D 35 CYS D 37 1 O CYS D 37 N HIS D 9 SHEET 3 D 9 ARG D 56 VAL D 61 1 O VAL D 58 N LEU D 36 SHEET 4 D 9 GLU D 87 VAL D 91 1 O ASP D 89 N THR D 59 SHEET 5 D 9 VAL D 120 ILE D 124 1 O ILE D 124 N MET D 90 SHEET 6 D 9 PHE D 149 LYS D 151 1 O LYS D 151 N VAL D 123 SHEET 7 D 9 GLN D 178 ALA D 182 1 O LYS D 180 N LEU D 150 SHEET 8 D 9 ARG D 201 THR D 204 1 O GLY D 203 N ALA D 181 SHEET 9 D 9 ILE D 7 THR D 10 1 N ASP D 8 O LEU D 202 LINK NZ LYS A 151 C1' HPD A 801 1555 1555 1.38 LINK NZ LYS B 151 C1' HPD B 802 1555 1555 1.38 LINK NZ LYS C 151 C1' HPD C 803 1555 1555 1.38 LINK NZ LYS D 151 C1' HPD D 804 1555 1555 1.38 CISPEP 1 PHE A 63 PRO A 64 0 0.19 CISPEP 2 PHE B 63 PRO B 64 0 0.02 CISPEP 3 PHE C 63 PRO C 64 0 0.13 CISPEP 4 PHE D 63 PRO D 64 0 0.14 SITE 1 AC1 18 LEU A 12 CYS A 37 VAL A 60 LYS A 151 SITE 2 AC1 18 THR A 154 GLY A 155 ALA A 182 GLY A 183 SITE 3 AC1 18 GLY A 184 ARG A 186 GLY A 203 THR A 204 SITE 4 AC1 18 SER A 205 HOH A 810 HOH A 815 HOH A 834 SITE 5 AC1 18 HOH A 853 HOH A 895 SITE 1 AC2 17 LEU B 12 CYS B 37 VAL B 60 ASP B 89 SITE 2 AC2 17 LYS B 151 THR B 154 ALA B 182 GLY B 183 SITE 3 AC2 17 GLY B 184 ARG B 186 GLY B 203 THR B 204 SITE 4 AC2 17 SER B 205 HOH B 815 HOH B 828 HOH B 838 SITE 5 AC2 17 HOH B 881 SITE 1 AC3 18 LEU C 12 CYS C 37 VAL C 60 LYS C 151 SITE 2 AC3 18 THR C 154 GLY C 155 ALA C 182 GLY C 183 SITE 3 AC3 18 GLY C 184 ARG C 186 GLY C 203 THR C 204 SITE 4 AC3 18 SER C 205 HOH C 812 HOH C 814 HOH C 837 SITE 5 AC3 18 HOH C 858 HOH C 898 SITE 1 AC4 17 LEU D 12 CYS D 37 VAL D 60 ASP D 89 SITE 2 AC4 17 LYS D 151 THR D 154 ALA D 182 GLY D 183 SITE 3 AC4 17 GLY D 184 ARG D 186 GLY D 203 THR D 204 SITE 4 AC4 17 SER D 205 HOH D 812 HOH D 824 HOH D 832 SITE 5 AC4 17 HOH D 840 CRYST1 63.820 96.887 137.925 90.00 90.00 90.00 P 21 21 21 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015669 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010321 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007250 0.00000