HEADER TRANSFERASE 28-MAY-13 4KXW TITLE HUMAN TRANSKETOLASE IN COVALENT COMPLEX WITH DONOR KETOSE D-XYLULOSE- TITLE 2 5-PHOSPHATE, CRYSTAL 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSKETOLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TK; COMPND 5 EC: 2.2.1.1; COMPND 6 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: TKT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; 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: PET-28A KEYWDS THIAMIN DIPHOSPHATE, ENZYME CATALYSIS, PENTOSE PHOSPHATE PATHWAY, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.NEUMANN,S.LUEDTKE,R.FICNER,K.TITTMANN REVDAT 6 20-SEP-23 4KXW 1 REMARK REVDAT 5 04-AUG-21 4KXW 1 COMPND REMARK SEQADV HET REVDAT 5 2 1 HETNAM FORMUL LINK SITE REVDAT 5 3 1 ATOM REVDAT 4 04-SEP-19 4KXW 1 REMARK LINK REVDAT 3 15-NOV-17 4KXW 1 REMARK REVDAT 2 04-SEP-13 4KXW 1 JRNL REVDAT 1 21-AUG-13 4KXW 0 JRNL AUTH S.LUDTKE,P.NEUMANN,K.M.ERIXON,F.LEEPER,R.KLUGER,R.FICNER, JRNL AUTH 2 K.TITTMANN JRNL TITL SUB-ANGSTROM-RESOLUTION CRYSTALLOGRAPHY REVEALS PHYSICAL JRNL TITL 2 DISTORTIONS THAT ENHANCE REACTIVITY OF A COVALENT ENZYMATIC JRNL TITL 3 INTERMEDIATE. JRNL REF NAT CHEM V. 5 762 2013 JRNL REFN ISSN 1755-4330 JRNL PMID 23965678 JRNL DOI 10.1038/NCHEM.1728 REMARK 2 REMARK 2 RESOLUTION. 0.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.099 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.095 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.121 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 2.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 6241 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 305775 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.083 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.079 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.104 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 2.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 5113 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4752 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 100 REMARK 3 SOLVENT ATOMS : 963 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 58206 REMARK 3 NUMBER OF RESTRAINTS : 62846 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 311.0 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.000 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 6.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 6.000 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.110 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.022 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.000 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.132 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4KXW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000079932. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93939 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 305775 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.970 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.2300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.43700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.740 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 3MOS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR MIXTURE OF 13.5-15 % PEG REMARK 280 6000 (W/V), 4% PEG 400 (V/V), 2 % GLYCEROL (V/V) , PH 7.9, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 279.0K 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 56.87800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.00850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.87800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 43.00850 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL 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 0.00000 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 HOH A7281 LIES ON A SPECIAL POSITION. REMARK 375 HOH A7332 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 1 REMARK 465 ALA A 623 REMARK 465 LEU A 624 REMARK 465 VAL A 625 REMARK 465 PRO A 626 REMARK 465 ARG A 627 REMARK 465 GLY A 628 REMARK 465 SER A 629 REMARK 465 LEU A 630 REMARK 465 GLU A 631 REMARK 465 HIS A 632 REMARK 465 HIS A 633 REMARK 465 HIS A 634 REMARK 465 HIS A 635 REMARK 465 HIS A 636 REMARK 465 HIS A 637 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 LYS A 622 CG CD CE NZ 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 ARG A 23 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ALA A 121 O - C - N ANGL. DEV. = -10.6 DEGREES REMARK 500 ALA A 121 O - C - N ANGL. DEV. = 12.7 DEGREES REMARK 500 ARG A 148 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 148 NE - CZ - NH2 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP A 200 CB - CG - OD1 ANGL. DEV. = 8.8 DEGREES REMARK 500 LYS A 232 C - N - CA ANGL. DEV. = -15.7 DEGREES REMARK 500 LYS A 232 CB - CA - C ANGL. DEV. = -13.7 DEGREES REMARK 500 LYS A 232 N - CA - CB ANGL. DEV. = -11.6 DEGREES REMARK 500 LYS A 232 CA - CB - CG ANGL. DEV. = -15.5 DEGREES REMARK 500 ASP A 313 CB - CG - OD1 ANGL. DEV. = 7.9 DEGREES REMARK 500 ASP A 313 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG A 334 NE - CZ - NH2 ANGL. DEV. = -7.3 DEGREES REMARK 500 GLN A 367 OE1 - CD - NE2 ANGL. DEV. = -17.6 DEGREES REMARK 500 GLN A 367 CG - CD - OE1 ANGL. DEV. = 19.4 DEGREES REMARK 500 ARG A 395 NE - CZ - NH1 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 395 NE - CZ - NH2 ANGL. DEV. = 8.2 DEGREES REMARK 500 TYR A 447 CB - CG - CD1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 471 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 474 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ASP A 486 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 542 CD - NE - CZ ANGL. DEV. = 9.1 DEGREES REMARK 500 ARG A 555 NH1 - CZ - NH2 ANGL. DEV. = -7.0 DEGREES REMARK 500 ARG A 555 NE - CZ - NH2 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 594 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 594 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 609 NE - CZ - NH2 ANGL. DEV. = -3.6 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 HIS A 54 -53.18 -142.49 REMARK 500 PHE A 142 -64.44 -103.96 REMARK 500 ARG A 186 -26.45 81.73 REMARK 500 GLN A 196 -127.86 49.42 REMARK 500 TYR A 363 -169.14 66.20 REMARK 500 ALA A 365 71.40 -162.27 REMARK 500 THR A 442 -3.23 76.38 REMARK 500 PHE A 535 -65.06 73.27 REMARK 500 PHE A 535 -65.06 72.21 REMARK 500 PRO A 593 -158.65 -78.37 REMARK 500 PRO A 593 -156.59 -82.38 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 A 23 0.10 SIDE CHAIN REMARK 500 ARG A 101 0.09 SIDE CHAIN REMARK 500 ARG A 302 0.10 SIDE CHAIN REMARK 500 ARG A 358 0.12 SIDE CHAIN REMARK 500 ARG A 550 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 DX5 A1016 IS A HYDROLYZED D-XYULOSE-5-PHOSPHATE COVALENTLY LINKED REMARK 600 TO TDP A1015 REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 DX5 A 1017 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 MG A1001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 155 OD1 REMARK 620 2 ASN A 185 OD1 94.5 REMARK 620 3 LEU A 187 O 102.5 90.0 REMARK 620 4 TPP A1015 O2A 84.9 176.5 93.5 REMARK 620 5 TPP A1015 O1B 164.0 94.5 90.7 85.3 REMARK 620 6 HOH A7001 O 82.5 85.0 173.2 91.5 85.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1013 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 411 OD1 REMARK 620 2 ALA A 461 O 86.6 REMARK 620 3 THR A 464 O 161.4 94.5 REMARK 620 4 HOH A7070 O 95.9 91.7 102.6 REMARK 620 5 HOH A7081 O 95.6 177.7 83.3 88.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1008 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1009 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1010 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1011 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1012 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1013 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1014 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TPP A 1015 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DX5 A 1016 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DX5 A 1017 DBREF 4KXW A 1 623 UNP P29401 TKT_HUMAN 1 623 SEQADV 4KXW LEU A 624 UNP P29401 EXPRESSION TAG SEQADV 4KXW VAL A 625 UNP P29401 EXPRESSION TAG SEQADV 4KXW PRO A 626 UNP P29401 EXPRESSION TAG SEQADV 4KXW ARG A 627 UNP P29401 EXPRESSION TAG SEQADV 4KXW GLY A 628 UNP P29401 EXPRESSION TAG SEQADV 4KXW SER A 629 UNP P29401 EXPRESSION TAG SEQADV 4KXW LEU A 630 UNP P29401 EXPRESSION TAG SEQADV 4KXW GLU A 631 UNP P29401 EXPRESSION TAG SEQADV 4KXW HIS A 632 UNP P29401 EXPRESSION TAG SEQADV 4KXW HIS A 633 UNP P29401 EXPRESSION TAG SEQADV 4KXW HIS A 634 UNP P29401 EXPRESSION TAG SEQADV 4KXW HIS A 635 UNP P29401 EXPRESSION TAG SEQADV 4KXW HIS A 636 UNP P29401 EXPRESSION TAG SEQADV 4KXW HIS A 637 UNP P29401 EXPRESSION TAG SEQRES 1 A 637 MET GLU SER TYR HIS LYS PRO ASP GLN GLN LYS LEU GLN SEQRES 2 A 637 ALA LEU LYS ASP THR ALA ASN ARG LEU ARG ILE SER SER SEQRES 3 A 637 ILE GLN ALA THR THR ALA ALA GLY SER GLY HIS PRO THR SEQRES 4 A 637 SER CYS CYS SER ALA ALA GLU ILE MET ALA VAL LEU PHE SEQRES 5 A 637 PHE HIS THR MET ARG TYR LYS SER GLN ASP PRO ARG ASN SEQRES 6 A 637 PRO HIS ASN ASP ARG PHE VAL LEU SER LYS GLY HIS ALA SEQRES 7 A 637 ALA PRO ILE LEU TYR ALA VAL TRP ALA GLU ALA GLY PHE SEQRES 8 A 637 LEU ALA GLU ALA GLU LEU LEU ASN LEU ARG LYS ILE SER SEQRES 9 A 637 SER ASP LEU ASP GLY HIS PRO VAL PRO LYS GLN ALA PHE SEQRES 10 A 637 THR ASP VAL ALA THR GLY SER LEU GLY GLN GLY LEU GLY SEQRES 11 A 637 ALA ALA CYS GLY MET ALA TYR THR GLY LYS TYR PHE ASP SEQRES 12 A 637 LYS ALA SER TYR ARG VAL TYR CYS LEU LEU GLY ASP GLY SEQRES 13 A 637 GLU LEU SER GLU GLY SER VAL TRP GLU ALA MET ALA PHE SEQRES 14 A 637 ALA SER ILE TYR LYS LEU ASP ASN LEU VAL ALA ILE LEU SEQRES 15 A 637 ASP ILE ASN ARG LEU GLY GLN SER ASP PRO ALA PRO LEU SEQRES 16 A 637 GLN HIS GLN MET ASP ILE TYR GLN LYS ARG CYS GLU ALA SEQRES 17 A 637 PHE GLY TRP HIS ALA ILE ILE VAL ASP GLY HIS SER VAL SEQRES 18 A 637 GLU GLU LEU CYS LYS ALA PHE GLY GLN ALA LYS HIS GLN SEQRES 19 A 637 PRO THR ALA ILE ILE ALA LYS THR PHE LYS GLY ARG GLY SEQRES 20 A 637 ILE THR GLY VAL GLU ASP LYS GLU SER TRP HIS GLY LYS SEQRES 21 A 637 PRO LEU PRO LYS ASN MET ALA GLU GLN ILE ILE GLN GLU SEQRES 22 A 637 ILE TYR SER GLN ILE GLN SER LYS LYS LYS ILE LEU ALA SEQRES 23 A 637 THR PRO PRO GLN GLU ASP ALA PRO SER VAL ASP ILE ALA SEQRES 24 A 637 ASN ILE ARG MET PRO SER LEU PRO SER TYR LYS VAL GLY SEQRES 25 A 637 ASP LYS ILE ALA THR ARG LYS ALA TYR GLY GLN ALA LEU SEQRES 26 A 637 ALA LYS LEU GLY HIS ALA SER ASP ARG ILE ILE ALA LEU SEQRES 27 A 637 ASP GLY ASP THR LYS ASN SER THR PHE SER GLU ILE PHE SEQRES 28 A 637 LYS LYS GLU HIS PRO ASP ARG PHE ILE GLU CYS TYR ILE SEQRES 29 A 637 ALA GLU GLN ASN MET VAL SER ILE ALA VAL GLY CYS ALA SEQRES 30 A 637 THR ARG ASN ARG THR VAL PRO PHE CYS SER THR PHE ALA SEQRES 31 A 637 ALA PHE PHE THR ARG ALA PHE ASP GLN ILE ARG MET ALA SEQRES 32 A 637 ALA ILE SER GLU SER ASN ILE ASN LEU CYS GLY SER HIS SEQRES 33 A 637 CYS GLY VAL SER ILE GLY GLU ASP GLY PRO SER GLN MET SEQRES 34 A 637 ALA LEU GLU ASP LEU ALA MET PHE ARG SER VAL PRO THR SEQRES 35 A 637 SER THR VAL PHE TYR PRO SER ASP GLY VAL ALA THR GLU SEQRES 36 A 637 LYS ALA VAL GLU LEU ALA ALA ASN THR LYS GLY ILE CYS SEQRES 37 A 637 PHE ILE ARG THR SER ARG PRO GLU ASN ALA ILE ILE TYR SEQRES 38 A 637 ASN ASN ASN GLU ASP PHE GLN VAL GLY GLN ALA LYS VAL SEQRES 39 A 637 VAL LEU LYS SER LYS ASP ASP GLN VAL THR VAL ILE GLY SEQRES 40 A 637 ALA GLY VAL THR LEU HIS GLU ALA LEU ALA ALA ALA GLU SEQRES 41 A 637 LEU LEU LYS LYS GLU LYS ILE ASN ILE ARG VAL LEU ASP SEQRES 42 A 637 PRO PHE THR ILE LYS PRO LEU ASP ARG LYS LEU ILE LEU SEQRES 43 A 637 ASP SER ALA ARG ALA THR LYS GLY ARG ILE LEU THR VAL SEQRES 44 A 637 GLU ASP HIS TYR TYR GLU GLY GLY ILE GLY GLU ALA VAL SEQRES 45 A 637 SER SER ALA VAL VAL GLY GLU PRO GLY ILE THR VAL THR SEQRES 46 A 637 HIS LEU ALA VAL ASN ARG VAL PRO ARG SER GLY LYS PRO SEQRES 47 A 637 ALA GLU LEU LEU LYS MET PHE GLY ILE ASP ARG ASP ALA SEQRES 48 A 637 ILE ALA GLN ALA VAL ARG GLY LEU ILE THR LYS ALA LEU SEQRES 49 A 637 VAL PRO ARG GLY SER LEU GLU HIS HIS HIS HIS HIS HIS HET MG A1001 1 HET EDO A1002 4 HET EDO A1003 4 HET EDO A1004 4 HET EDO A1005 8 HET EDO A1006 4 HET EDO A1007 4 HET EDO A1008 4 HET EDO A1009 4 HET EDO A1010 8 HET EDO A1011 4 HET EDO A1012 4 HET NA A1013 1 HET EDO A1014 4 HET TPP A1015 26 HET DX5 A1016 14 HET DX5 A1017 10 HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM NA SODIUM ION HETNAM TPP THIAMINE DIPHOSPHATE HETNAM DX5 D-XYLITOL-5-PHOSPHATE HETSYN EDO ETHYLENE GLYCOL HETSYN DX5 D-HYLITOL-5-PHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 EDO 12(C2 H6 O2) FORMUL 14 NA NA 1+ FORMUL 16 TPP C12 H19 N4 O7 P2 S 1+ FORMUL 17 DX5 2(C5 H13 O8 P) FORMUL 19 HOH *963(H2 O) HELIX 1 1 ASP A 8 GLY A 34 1 27 HELIX 2 2 HIS A 37 SER A 43 1 7 HELIX 3 3 ALA A 44 HIS A 54 1 11 HELIX 4 4 LYS A 75 HIS A 77 5 3 HELIX 5 5 ALA A 78 ALA A 89 1 12 HELIX 6 6 ALA A 93 LEU A 100 5 8 HELIX 7 7 GLN A 127 PHE A 142 1 16 HELIX 8 8 GLY A 156 SER A 159 5 4 HELIX 9 9 GLU A 160 TYR A 173 1 14 HELIX 10 10 GLN A 198 PHE A 209 1 12 HELIX 11 11 SER A 220 GLY A 229 1 10 HELIX 12 12 PRO A 263 SER A 276 1 14 HELIX 13 13 THR A 317 SER A 332 1 16 HELIX 14 14 THR A 342 PHE A 347 1 6 HELIX 15 15 PHE A 347 HIS A 355 1 9 HELIX 16 16 ALA A 365 THR A 378 1 14 HELIX 17 17 ARG A 379 ARG A 381 5 3 HELIX 18 18 ALA A 391 ARG A 395 5 5 HELIX 19 19 ALA A 396 SER A 406 1 11 HELIX 20 20 GLY A 418 GLY A 422 5 5 HELIX 21 21 GLY A 425 MET A 429 5 5 HELIX 22 22 GLU A 432 SER A 439 1 8 HELIX 23 23 ASP A 450 ASN A 463 1 14 HELIX 24 24 GLY A 509 LYS A 524 1 16 HELIX 25 25 ASP A 541 THR A 552 1 12 HELIX 26 26 GLY A 567 VAL A 577 1 11 HELIX 27 27 LYS A 597 PHE A 605 1 9 HELIX 28 28 ASP A 608 THR A 621 1 14 SHEET 1 A 5 ARG A 70 LEU A 73 0 SHEET 2 A 5 VAL A 149 GLY A 154 1 O TYR A 150 N ARG A 70 SHEET 3 A 5 LEU A 178 ILE A 184 1 O ASP A 183 N LEU A 153 SHEET 4 A 5 THR A 236 LYS A 241 1 O ILE A 238 N ALA A 180 SHEET 5 A 5 HIS A 212 ASP A 217 1 N ILE A 214 O ILE A 239 SHEET 1 B 2 LYS A 314 ALA A 316 0 SHEET 2 B 2 GLU A 476 ALA A 478 -1 O ASN A 477 N ILE A 315 SHEET 1 C 7 PHE A 359 GLU A 361 0 SHEET 2 C 7 ILE A 335 ASP A 339 1 N ALA A 337 O ILE A 360 SHEET 3 C 7 VAL A 383 PHE A 389 1 O PHE A 385 N LEU A 338 SHEET 4 C 7 ILE A 410 SER A 415 1 O ASN A 411 N CYS A 386 SHEET 5 C 7 ILE A 467 ARG A 471 1 O CYS A 468 N LEU A 412 SHEET 6 C 7 THR A 444 PHE A 446 1 N PHE A 446 O PHE A 469 SHEET 7 C 7 THR A 536 LYS A 538 -1 O LYS A 538 N VAL A 445 SHEET 1 D 5 LYS A 493 LEU A 496 0 SHEET 2 D 5 ASN A 528 ASP A 533 -1 O ASP A 533 N LYS A 493 SHEET 3 D 5 ASP A 501 ILE A 506 1 N VAL A 505 O ARG A 530 SHEET 4 D 5 ARG A 555 TYR A 563 1 O LEU A 557 N ILE A 506 SHEET 5 D 5 THR A 583 VAL A 589 1 O LEU A 587 N THR A 558 LINK C2 TPP A1015 C2 ADX5 A1016 1555 1555 1.54 LINK OD1 ASP A 155 MG MG A1001 1555 1555 2.03 LINK OD1 ASN A 185 MG MG A1001 1555 1555 2.11 LINK O LEU A 187 MG MG A1001 1555 1555 2.06 LINK OD1 ASN A 411 NA NA A1013 1555 1555 2.35 LINK O ALA A 461 NA NA A1013 1555 1555 2.25 LINK O THR A 464 NA NA A1013 1555 1555 2.33 LINK MG MG A1001 O2A TPP A1015 1555 1555 2.06 LINK MG MG A1001 O1B TPP A1015 1555 1555 2.07 LINK MG MG A1001 O HOH A7001 1555 1555 2.22 LINK NA NA A1013 O HOH A7070 1555 1555 2.41 LINK NA NA A1013 O HOH A7081 1555 1555 2.25 CISPEP 1 LYS A 538 PRO A 539 0 -3.69 SITE 1 AC1 5 ASP A 155 ASN A 185 LEU A 187 TPP A1015 SITE 2 AC1 5 HOH A7001 SITE 1 AC2 8 PRO A 63 ASN A 68 ASP A 69 ARG A 70 SITE 2 AC2 8 PHE A 71 ARG A 379 HOH A7186 HOH A7847 SITE 1 AC3 7 TYR A 564 ALA A 588 ASN A 590 HOH A7051 SITE 2 AC3 7 HOH A7055 HOH A7126 HOH A7247 SITE 1 AC4 8 PHE A 71 VAL A 72 LEU A 73 LEU A 82 SITE 2 AC4 8 PHE A 117 HOH A7040 HOH A7056 HOH A7068 SITE 1 AC5 13 ASP A 155 GLY A 156 LEU A 158 SER A 159 SITE 2 AC5 13 TRP A 164 PRO A 194 LEU A 195 TYR A 202 SITE 3 AC5 13 ARG A 205 EDO A1012 HOH A7467 HOH A7960 SITE 4 AC5 13 HOH A7961 SITE 1 AC6 7 LEU A 92 LEU A 107 GLN A 115 HOH A7110 SITE 2 AC6 7 HOH A7124 HOH A7174 HOH A7920 SITE 1 AC7 4 GLN A 10 ASN A 590 ARG A 591 HOH A7260 SITE 1 AC8 6 TYR A 137 TYR A 141 TYR A 173 HOH A7409 SITE 2 AC8 6 HOH A7610 HOH A7914 SITE 1 AC9 8 ALA A 33 ARG A 101 GLU A 423 LYS A 597 SITE 2 AC9 8 HOH A7103 HOH A7586 HOH A7742 HOH A7934 SITE 1 BC1 10 ARG A 21 SER A 25 ALA A 84 GLU A 88 SITE 2 BC1 10 GLU A 94 LEU A 97 LYS A 283 HOH A7177 SITE 3 BC1 10 HOH A7472 HOH A7672 SITE 1 BC2 7 PHE A 142 ASP A 333 ARG A 358 HOH A7406 SITE 2 BC2 7 HOH A7539 HOH A7700 HOH A7894 SITE 1 BC3 9 LEU A 158 SER A 159 TRP A 164 GLU A 165 SITE 2 BC3 9 ALA A 168 PHE A 209 EDO A1005 EDO A1014 SITE 3 BC3 9 HOH A7961 SITE 1 BC4 6 ASN A 411 ALA A 461 THR A 464 CYS A 468 SITE 2 BC4 6 HOH A7070 HOH A7081 SITE 1 BC5 6 SER A 159 GLU A 165 ALA A 168 EDO A1012 SITE 2 BC5 6 HOH A7467 HOH A7715 SITE 1 BC6 26 SER A 40 LYS A 75 HIS A 77 GLY A 123 SITE 2 BC6 26 SER A 124 LEU A 125 GLY A 154 ASP A 155 SITE 3 BC6 26 GLY A 156 GLU A 157 GLU A 160 ASN A 185 SITE 4 BC6 26 LEU A 187 GLY A 188 GLN A 189 LYS A 244 SITE 5 BC6 26 HIS A 258 ASP A 341 ILE A 364 GLU A 366 SITE 6 BC6 26 PHE A 392 ARG A 395 GLN A 428 MG A1001 SITE 7 BC6 26 DX5 A1016 HOH A7001 SITE 1 BC7 19 HIS A 37 HIS A 77 HIS A 110 GLN A 189 SITE 2 BC7 19 HIS A 258 SER A 345 PHE A 389 HIS A 416 SITE 3 BC7 19 ASP A 424 GLN A 428 ARG A 474 TPP A1015 SITE 4 BC7 19 DX5 A1017 HOH A7053 HOH A7095 HOH A7108 SITE 5 BC7 19 HOH A7246 HOH A7263 HOH A7299 SITE 1 BC8 14 HIS A 37 GLN A 189 HIS A 258 ARG A 318 SITE 2 BC8 14 SER A 345 HIS A 416 ASP A 424 ARG A 474 SITE 3 BC8 14 DX5 A1016 HOH A7108 HOH A7246 HOH A7263 SITE 4 BC8 14 HOH A7272 HOH A7299 CRYST1 113.756 86.017 72.994 90.00 125.46 90.00 C 1 2 1 4 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 0.008791 0.000000 0.006261 0.00000 SCALE2 0.000000 0.011626 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016819 0.00000