PDB Short entry for 3S4Y HEADER TRANSFERASE 20-MAY-11 3S4Y TITLE CRYSTAL STRUCTURE OF HUMAN THIAMIN PYROPHOSPHOKINASE 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIAMIN PYROPHOSPHOKINASE 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HTPK1, PLACENTAL PROTEIN 20, PP20, THIAMINE COMPND 5 PYROPHOSPHOKINASE 1; COMPND 6 EC: 2.7.6.2; COMPND 7 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: TPK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28-MHL KEYWDS KINASE, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.SHEN,W.TEMPEL,Y.TONG,Y.LI,J.R.WALKER,C.H.ARROWSMITH,A.M.EDWARDS, AUTHOR 2 C.BOUNTRA,J.WEIGELT,H.PARK,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 2 11-OCT-17 3S4Y 1 REMARK REVDAT 1 08-JUN-11 3S4Y 0 JRNL AUTH L.SHEN,W.TEMPEL,Y.TONG,Y.LI,J.R.WALKER,C.H.ARROWSMITH, JRNL AUTH 2 A.M.EDWARDS,C.BOUNTRA,J.WEIGELT,H.PARK JRNL TITL CRYSTAL STRUCTURE OF HUMAN THIAMIN PYROPHOSPHOKINASE 1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 48583 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : THIN SHELLS (SFTOOLS) REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.322 REMARK 3 FREE R VALUE TEST SET COUNT : 2100 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3564 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE SET COUNT : 0 REMARK 3 BIN FREE R VALUE : 0.2230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3495 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 88 REMARK 3 SOLVENT ATOMS : 314 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.66200 REMARK 3 B22 (A**2) : -0.22100 REMARK 3 B33 (A**2) : 0.11800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.97600 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.109 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.056 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3774 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2442 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5178 ; 1.292 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5990 ; 0.869 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 480 ; 5.788 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 163 ;30.310 ;24.540 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 619 ;11.381 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;12.821 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 594 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4157 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 727 ; 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): 2297 ; 0.629 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 935 ; 0.140 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3746 ; 1.137 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1477 ; 1.762 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1419 ; 2.842 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 16 A 242 REMARK 3 ORIGIN FOR THE GROUP (A): -2.6042 71.3474 54.1739 REMARK 3 T TENSOR REMARK 3 T11: 0.0103 T22: 0.0748 REMARK 3 T33: 0.0732 T12: -0.0015 REMARK 3 T13: 0.0010 T23: -0.0274 REMARK 3 L TENSOR REMARK 3 L11: 0.6143 L22: 1.8778 REMARK 3 L33: 2.5227 L12: -0.6128 REMARK 3 L13: 0.7378 L23: -1.4345 REMARK 3 S TENSOR REMARK 3 S11: 0.0295 S12: -0.0858 S13: -0.0940 REMARK 3 S21: -0.0387 S22: 0.0134 S23: 0.2109 REMARK 3 S31: 0.0243 S32: -0.2605 S33: -0.0429 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 16 B 242 REMARK 3 ORIGIN FOR THE GROUP (A): 14.2718 73.9829 34.6665 REMARK 3 T TENSOR REMARK 3 T11: 0.0859 T22: 0.0576 REMARK 3 T33: 0.0141 T12: 0.0536 REMARK 3 T13: 0.0039 T23: -0.0035 REMARK 3 L TENSOR REMARK 3 L11: 3.1389 L22: 1.3808 REMARK 3 L33: 0.7894 L12: 0.9923 REMARK 3 L13: 0.3440 L23: 0.2669 REMARK 3 S TENSOR REMARK 3 S11: 0.0064 S12: 0.2451 S13: -0.0139 REMARK 3 S21: -0.1740 S22: -0.0012 S23: -0.0476 REMARK 3 S31: -0.0491 S32: 0.0479 S33: -0.0052 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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. U VALUES WITH TLS ADDED. THIAMINE PYROPHOSPHATE REMARK 3 RESTRAINTS WERE OBTAINED FROM THE PRODRG SERVER, USING REMARK 3 COORDINATES FROM PDB ENTRY 2PGN. PARROT WAS USED FOR DENSITY REMARK 3 MODIFICATION. ARP/WARP AND BUCCANEER WERE USED FOR AUTOMATED REMARK 3 TRACING. COOT WAS USED FOR INTERACTIVE MODEL REBUILDING AND REMARK 3 MOLPROBITY WAS USED FOR GEOMETRY VALIDATION. CAVEAT: DENSITY FOR REMARK 3 THE PYROPHOSPHATE MOIETIES OF THE THIAMINE PYROPHOSPHATE MODELS REMARK 3 IS POORER THAN FOR THE PROTEIN/LIGAND MODEL AS A WHOLE. GEOMETRY REMARK 3 OF THE MOIETY IS DISTORTED. ANOMALOUS DIFFERENCE FOURIER DENSITY REMARK 3 IS OBSERVED AT THE PYROPHOSPHATE SITES. ASSIGNMENT OF THE CATION REMARK 3 NEAR THE TPP BINDING SITE AS CALCIUM IS TENTATIVE, AS REMARK 3 COORDINATION GEOMETRY DEVIATES FROM EXPECTED IDEAL REMARK 3 CONFIGURATION. THE CATION POSITIONS ARE SUPPORTED BY ANOMALOUS REMARK 3 DIFFERENCE FOURIER DENSITY. REMARK 4 REMARK 4 3S4Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000065766. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT 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 RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48623 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 29.587 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 45.2300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.47900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG-3350, 0.2M AMMONIUM SULFATE, REMARK 280 0.1M SODIUM CACODYLATE. 0.02M ATP, 0.004M MAGNESIUM CHLORIDE REMARK 280 WERE ADDED TO THE PROTEIN STOCK SOLUTION, PH 5.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 46.85000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.69500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 46.85000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 48.69500 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: AUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 -24.95182 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 58.55535 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 UNK UNX B 249 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 HIS A 2 REMARK 465 HIS A 3 REMARK 465 SER A 4 REMARK 465 SER A 5 REMARK 465 GLY A 6 REMARK 465 ARG A 7 REMARK 465 GLU A 8 REMARK 465 ASN A 9 REMARK 465 LEU A 10 REMARK 465 TYR A 11 REMARK 465 PHE A 12 REMARK 465 GLN A 13 REMARK 465 GLY A 14 REMARK 465 GLY A 15 REMARK 465 ASP A 175 REMARK 465 THR A 176 REMARK 465 GLY A 177 REMARK 465 SER A 243 REMARK 465 MET B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 HIS B 0 REMARK 465 HIS B 1 REMARK 465 HIS B 2 REMARK 465 HIS B 3 REMARK 465 SER B 4 REMARK 465 SER B 5 REMARK 465 GLY B 6 REMARK 465 ARG B 7 REMARK 465 GLU B 8 REMARK 465 ASN B 9 REMARK 465 LEU B 10 REMARK 465 TYR B 11 REMARK 465 PHE B 12 REMARK 465 GLN B 13 REMARK 465 GLY B 14 REMARK 465 GLY B 15 REMARK 465 ASP B 175 REMARK 465 THR B 176 REMARK 465 GLY B 177 REMARK 465 SER B 243 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 16 CG OD1 ND2 REMARK 470 LEU A 17 CG CD1 CD2 REMARK 470 LYS A 18 CD CE NZ REMARK 470 LYS A 38 CE NZ REMARK 470 LYS A 118 CG CD CE NZ REMARK 470 LYS A 169 NZ REMARK 470 MET A 178 CG SD CE REMARK 470 ASP A 181 OD1 OD2 REMARK 470 LYS A 242 CG CD CE NZ REMARK 470 ASN B 16 CG OD1 ND2 REMARK 470 LYS B 38 CG CD CE NZ REMARK 470 ASP B 95 OD1 OD2 REMARK 470 LYS B 110 CG CD CE NZ REMARK 470 LYS B 118 CE NZ REMARK 470 LYS B 169 CD CE NZ REMARK 470 ARG B 171 CD NE CZ NH1 NH2 REMARK 470 MET B 178 CG SD CE REMARK 470 ASP B 181 OD1 OD2 REMARK 470 LYS B 242 CG CD CE NZ 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 46 -108.90 46.39 REMARK 500 GLU A 59 30.49 -151.86 REMARK 500 GLU A 158 -113.67 58.71 REMARK 500 THR A 213 -61.81 -122.36 REMARK 500 ASP B 46 -104.99 40.81 REMARK 500 GLU B 59 27.83 -148.40 REMARK 500 ASP B 116 52.68 39.43 REMARK 500 GLU B 158 -112.77 57.84 REMARK 500 THR B 213 -65.25 -122.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TPP A1301 O2A REMARK 620 2 ASP A 46 OD2 176.8 REMARK 620 3 ASP A 73 OD1 97.9 84.0 REMARK 620 4 ASP A 100 OD2 93.0 85.9 160.3 REMARK 620 5 ASP A 71 OD1 96.7 86.1 81.3 81.2 REMARK 620 6 SO4 A1302 O3 83.6 93.8 92.4 105.1 173.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TPP B1301 O2A REMARK 620 2 ASP B 100 OD2 84.9 REMARK 620 3 ASP B 46 OD2 170.2 92.6 REMARK 620 4 ASP B 71 OD1 101.1 87.4 88.2 REMARK 620 5 SO4 B1302 O3 78.4 94.7 92.4 177.8 REMARK 620 6 ASP B 73 OD1 102.1 166.0 82.5 79.4 98.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TPP A 1301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TPP B 1301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 1303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 244 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 244 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 245 DBREF 3S4Y A 15 243 UNP Q9H3S4 TPK1_HUMAN 15 243 DBREF 3S4Y B 15 243 UNP Q9H3S4 TPK1_HUMAN 15 243 SEQADV 3S4Y MET A -3 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y HIS A -2 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y HIS A -1 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y HIS A 0 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y HIS A 1 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y HIS A 2 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y HIS A 3 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y SER A 4 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y SER A 5 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y GLY A 6 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y ARG A 7 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y GLU A 8 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y ASN A 9 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y LEU A 10 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y TYR A 11 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y PHE A 12 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y GLN A 13 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y GLY A 14 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y MET B -3 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y HIS B -2 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y HIS B -1 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y HIS B 0 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y HIS B 1 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y HIS B 2 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y HIS B 3 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y SER B 4 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y SER B 5 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y GLY B 6 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y ARG B 7 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y GLU B 8 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y ASN B 9 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y LEU B 10 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y TYR B 11 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y PHE B 12 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y GLN B 13 UNP Q9H3S4 EXPRESSION TAG SEQADV 3S4Y GLY B 14 UNP Q9H3S4 EXPRESSION TAG SEQRES 1 A 247 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 A 247 LEU TYR PHE GLN GLY GLY ASN LEU LYS TYR CYS LEU VAL SEQRES 3 A 247 ILE LEU ASN GLN PRO LEU ASP ASN TYR PHE ARG HIS LEU SEQRES 4 A 247 TRP ASN LYS ALA LEU LEU ARG ALA CYS ALA ASP GLY GLY SEQRES 5 A 247 ALA ASN ARG LEU TYR ASP ILE THR GLU GLY GLU ARG GLU SEQRES 6 A 247 SER PHE LEU PRO GLU PHE ILE ASN GLY ASP PHE ASP SER SEQRES 7 A 247 ILE ARG PRO GLU VAL ARG GLU TYR TYR ALA THR LYS GLY SEQRES 8 A 247 CYS GLU LEU ILE SER THR PRO ASP GLN ASP HIS THR ASP SEQRES 9 A 247 PHE THR LYS CYS LEU LYS MET LEU GLN LYS LYS ILE GLU SEQRES 10 A 247 GLU LYS ASP LEU LYS VAL ASP VAL ILE VAL THR LEU GLY SEQRES 11 A 247 GLY LEU ALA GLY ARG PHE ASP GLN ILE MET ALA SER VAL SEQRES 12 A 247 ASN THR LEU PHE GLN ALA THR HIS ILE THR PRO PHE PRO SEQRES 13 A 247 ILE ILE ILE ILE GLN GLU GLU SER LEU ILE TYR LEU LEU SEQRES 14 A 247 GLN PRO GLY LYS HIS ARG LEU HIS VAL ASP THR GLY MET SEQRES 15 A 247 GLU GLY ASP TRP CYS GLY LEU ILE PRO VAL GLY GLN PRO SEQRES 16 A 247 CYS MET GLN VAL THR THR THR GLY LEU LYS TRP ASN LEU SEQRES 17 A 247 THR ASN ASP VAL LEU ALA PHE GLY THR LEU VAL SER THR SEQRES 18 A 247 SER ASN THR TYR ASP GLY SER GLY VAL VAL THR VAL GLU SEQRES 19 A 247 THR ASP HIS PRO LEU LEU TRP THR MET ALA ILE LYS SER SEQRES 1 B 247 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 B 247 LEU TYR PHE GLN GLY GLY ASN LEU LYS TYR CYS LEU VAL SEQRES 3 B 247 ILE LEU ASN GLN PRO LEU ASP ASN TYR PHE ARG HIS LEU SEQRES 4 B 247 TRP ASN LYS ALA LEU LEU ARG ALA CYS ALA ASP GLY GLY SEQRES 5 B 247 ALA ASN ARG LEU TYR ASP ILE THR GLU GLY GLU ARG GLU SEQRES 6 B 247 SER PHE LEU PRO GLU PHE ILE ASN GLY ASP PHE ASP SER SEQRES 7 B 247 ILE ARG PRO GLU VAL ARG GLU TYR TYR ALA THR LYS GLY SEQRES 8 B 247 CYS GLU LEU ILE SER THR PRO ASP GLN ASP HIS THR ASP SEQRES 9 B 247 PHE THR LYS CYS LEU LYS MET LEU GLN LYS LYS ILE GLU SEQRES 10 B 247 GLU LYS ASP LEU LYS VAL ASP VAL ILE VAL THR LEU GLY SEQRES 11 B 247 GLY LEU ALA GLY ARG PHE ASP GLN ILE MET ALA SER VAL SEQRES 12 B 247 ASN THR LEU PHE GLN ALA THR HIS ILE THR PRO PHE PRO SEQRES 13 B 247 ILE ILE ILE ILE GLN GLU GLU SER LEU ILE TYR LEU LEU SEQRES 14 B 247 GLN PRO GLY LYS HIS ARG LEU HIS VAL ASP THR GLY MET SEQRES 15 B 247 GLU GLY ASP TRP CYS GLY LEU ILE PRO VAL GLY GLN PRO SEQRES 16 B 247 CYS MET GLN VAL THR THR THR GLY LEU LYS TRP ASN LEU SEQRES 17 B 247 THR ASN ASP VAL LEU ALA PHE GLY THR LEU VAL SER THR SEQRES 18 B 247 SER ASN THR TYR ASP GLY SER GLY VAL VAL THR VAL GLU SEQRES 19 B 247 THR ASP HIS PRO LEU LEU TRP THR MET ALA ILE LYS SER HET TPP A1301 26 HET SO4 A1302 5 HET CA A1303 1 HET SO4 A 244 5 HET UNX A 245 1 HET UNX A 246 1 HET UNX A 247 1 HET UNX A 248 1 HET UNX A 249 1 HET TPP B1301 26 HET SO4 B1302 5 HET CA B1303 1 HET SO4 B 244 5 HET SO4 B 245 5 HET UNX B 246 1 HET UNX B 247 1 HET UNX B 248 1 HET UNX B 249 1 HETNAM TPP THIAMINE DIPHOSPHATE HETNAM SO4 SULFATE ION HETNAM CA CALCIUM ION HETNAM UNX UNKNOWN ATOM OR ION FORMUL 3 TPP 2(C12 H19 N4 O7 P2 S 1+) FORMUL 4 SO4 5(O4 S 2-) FORMUL 5 CA 2(CA 2+) FORMUL 7 UNX 9(X) FORMUL 21 HOH *314(H2 O) HELIX 1 1 TYR A 31 ALA A 39 1 9 HELIX 2 2 GLY A 47 THR A 56 1 10 HELIX 3 3 GLU A 59 PHE A 63 5 5 HELIX 4 4 ARG A 76 LYS A 86 1 11 HELIX 5 5 THR A 99 LYS A 115 1 17 HELIX 6 6 ARG A 131 ALA A 145 1 15 HELIX 7 7 THR A 146 ILE A 148 5 3 HELIX 8 8 TYR B 31 ALA B 39 1 9 HELIX 9 9 GLY B 47 THR B 56 1 10 HELIX 10 10 GLU B 59 PHE B 63 5 5 HELIX 11 11 ARG B 76 LYS B 86 1 11 HELIX 12 12 THR B 99 LYS B 115 1 17 HELIX 13 13 ARG B 131 THR B 146 1 16 SHEET 1 A10 GLU A 89 SER A 92 0 SHEET 2 A10 PHE A 67 GLY A 70 1 N ILE A 68 O ILE A 91 SHEET 3 A10 ARG A 42 ALA A 45 1 N CYS A 44 O PHE A 67 SHEET 4 A10 TYR A 19 ILE A 23 1 N ILE A 23 O ALA A 45 SHEET 5 A10 VAL A 121 LEU A 125 1 O LEU A 125 N VAL A 22 SHEET 6 A10 ILE A 153 GLN A 157 1 O ILE A 154 N THR A 124 SHEET 7 A10 SER A 160 LEU A 165 -1 O SER A 160 N GLN A 157 SHEET 8 A10 LEU A 235 ILE A 241 -1 O LEU A 235 N LEU A 165 SHEET 9 A10 GLU A 179 ILE A 186 -1 N ILE A 186 O LEU A 236 SHEET 10 A10 SER A 216 ASN A 219 -1 O ASN A 219 N CYS A 183 SHEET 1 B 4 GLY A 168 HIS A 173 0 SHEET 2 B 4 VAL A 226 THR A 231 -1 O VAL A 227 N LEU A 172 SHEET 3 B 4 CYS A 192 THR A 198 -1 N THR A 196 O GLU A 230 SHEET 4 B 4 ASP A 207 LEU A 209 -1 O LEU A 209 N CYS A 192 SHEET 1 C10 GLU B 89 SER B 92 0 SHEET 2 C10 PHE B 67 GLY B 70 1 N ILE B 68 O ILE B 91 SHEET 3 C10 ARG B 42 ALA B 45 1 N CYS B 44 O ASN B 69 SHEET 4 C10 TYR B 19 ILE B 23 1 N ILE B 23 O ALA B 43 SHEET 5 C10 VAL B 121 LEU B 125 1 O LEU B 125 N VAL B 22 SHEET 6 C10 ILE B 153 GLN B 157 1 O ILE B 154 N THR B 124 SHEET 7 C10 SER B 160 LEU B 165 -1 O SER B 160 N GLN B 157 SHEET 8 C10 LEU B 235 ILE B 241 -1 O TRP B 237 N TYR B 163 SHEET 9 C10 GLU B 179 ILE B 186 -1 N ILE B 186 O LEU B 236 SHEET 10 C10 SER B 216 ASN B 219 -1 O ASN B 219 N CYS B 183 SHEET 1 D 4 GLY B 168 HIS B 173 0 SHEET 2 D 4 VAL B 226 THR B 231 -1 O VAL B 227 N LEU B 172 SHEET 3 D 4 CYS B 192 THR B 198 -1 N THR B 196 O GLU B 230 SHEET 4 D 4 ASP B 207 LEU B 209 -1 O LEU B 209 N CYS B 192 LINK O2AATPP A1301 CA CA A1303 1555 1555 1.99 LINK O2AATPP B1301 CA CA B1303 1555 1555 2.04 LINK OD2 ASP A 46 CA CA A1303 1555 1555 2.22 LINK OD1 ASP A 73 CA CA A1303 1555 1555 2.24 LINK OD2 ASP B 100 CA CA B1303 1555 1555 2.24 LINK OD2 ASP A 100 CA CA A1303 1555 1555 2.26 LINK OD2 ASP B 46 CA CA B1303 1555 1555 2.26 LINK OD1 ASP A 71 CA CA A1303 1555 1555 2.27 LINK OD1 ASP B 71 CA CA B1303 1555 1555 2.27 LINK O3 SO4 B1302 CA CA B1303 1555 1555 2.29 LINK O3 SO4 A1302 CA CA A1303 1555 1555 2.36 LINK OD1 ASP B 73 CA CA B1303 1555 1555 2.48 SITE 1 AC1 17 ASP A 71 ASP A 73 GLN A 96 ASP A 97 SITE 2 AC1 17 HIS A 98 THR A 99 ASP A 100 ARG A 131 SITE 3 AC1 17 GLN A 134 HOH A 327 SO4 A1302 CA A1303 SITE 4 AC1 17 TRP B 202 SER B 216 THR B 217 SER B 218 SITE 5 AC1 17 ASN B 219 SITE 1 AC2 12 ASN A 25 ALA A 45 ASP A 46 GLY A 47 SITE 2 AC2 12 ASP A 73 SER A 74 ASP A 100 GLN A 134 SITE 3 AC2 12 HOH A 308 HOH A 317 TPP A1301 CA A1303 SITE 1 AC3 6 ASP A 46 ASP A 71 ASP A 73 ASP A 100 SITE 2 AC3 6 TPP A1301 SO4 A1302 SITE 1 AC4 18 TRP A 202 SER A 216 THR A 217 SER A 218 SITE 2 AC4 18 ASN A 219 ASP B 71 ASP B 73 GLN B 96 SITE 3 AC4 18 ASP B 97 HIS B 98 THR B 99 ASP B 100 SITE 4 AC4 18 ARG B 131 GLN B 134 HOH B 347 HOH B 362 SITE 5 AC4 18 SO4 B1302 CA B1303 SITE 1 AC5 9 ASN B 25 ASP B 46 GLY B 47 ASP B 73 SITE 2 AC5 9 SER B 74 ASP B 100 HOH B 339 TPP B1301 SITE 3 AC5 9 CA B1303 SITE 1 AC6 6 ASP B 46 ASP B 71 ASP B 73 ASP B 100 SITE 2 AC6 6 TPP B1301 SO4 B1302 SITE 1 AC7 7 GLY A 58 GLU A 59 ARG A 60 HOH A 384 SITE 2 AC7 7 HOH A 385 HOH A 386 HIS B 34 SITE 1 AC8 7 HIS A 34 GLY B 58 GLU B 59 ARG B 60 SITE 2 AC8 7 HOH B 297 HOH B 299 HOH B 320 SITE 1 AC9 4 HOH A 387 HIS B 34 ASN B 37 HOH B 351 CRYST1 93.700 97.390 63.650 90.00 113.08 90.00 C 1 2 1 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 0.010672 0.000000 0.004548 0.00000 SCALE2 0.000000 0.010268 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017078 0.00000