HEADER TRANSFERASE 22-DEC-80 1HKG TITLE STRUCTURAL DYNAMICS OF YEAST HEXOKINASE DURING CATALYSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEXOKINASE A; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.1.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932 KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR W.S.BENNETT JR.,T.A.STEITZ REVDAT 13 07-FEB-24 1HKG 1 REMARK REVDAT 12 25-APR-12 1HKG 1 AUTHOR REMARK VERSN REVDAT 11 25-AUG-09 1HKG 1 SOURCE REVDAT 10 24-FEB-09 1HKG 1 VERSN REVDAT 9 01-APR-03 1HKG 1 JRNL REVDAT 8 15-OCT-91 1HKG 1 AUTHOR REVDAT 7 16-APR-87 1HKG 3 SOURCE ATOM REVDAT 6 22-OCT-84 1HKG 1 SEQRES REVDAT 5 17-FEB-84 1HKG 1 REMARK REVDAT 4 30-SEP-83 1HKG 1 REVDAT REVDAT 3 13-JUN-83 1HKG 1 REMARK REVDAT 2 13-OCT-81 1HKG 1 REMARK REVDAT 1 26-FEB-81 1HKG 0 JRNL AUTH T.A.STEITZ,M.SHOHAM,W.S.BENNETT JR. JRNL TITL STRUCTURAL DYNAMICS OF YEAST HEXOKINASE DURING CATALYSIS. JRNL REF PHILOS.TRANS.R.SOC.LONDON, V. 293 43 1981 JRNL REF 2 SER.B JRNL REFN ISSN 0080-4622 JRNL PMID 6115422 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.S.BENNETT JR.,T.A.STEITZ REMARK 1 TITL STRUCTURE OF A COMPLEX BETWEEN YEAST HEXOKINASE A AND REMARK 1 TITL 2 GLUCOSE. II. DETAILED COMPARISONS OF CONFORMATION AND ACTIVE REMARK 1 TITL 3 SITE CONFIGURATION WITH THE NATIVE HEXOKINASE B MONOMER AND REMARK 1 TITL 4 DIMER. REMARK 1 REF J.MOL.BIOL. V. 140 211 1980 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 7001032 REMARK 1 REFERENCE 2 REMARK 1 AUTH W.S.BENNETT JR.,T.A.STEITZ REMARK 1 TITL STRUCTURE OF A COMPLEX BETWEEN YEAST HEXOKINASE A AND REMARK 1 TITL 2 GLUCOSE. I. STRUCTURE DETERMINATION AND REFINEMENT AT 3.5 A REMARK 1 TITL 3 RESOLUTION. REMARK 1 REF J.MOL.BIOL. V. 140 183 1980 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 7001031 REMARK 1 REFERENCE 3 REMARK 1 AUTH W.S.BENNETT JR.,T.A.STEITZ REMARK 1 TITL GLUCOSE-INDUCED CONFORMATIONAL CHANGE IN YEAST HEXOKINASE. REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 75 4848 1978 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 283394 REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : NULL 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 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3298 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HKG 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_1000173887. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 72.40000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.95000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.95000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 72.40000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.40000 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: MONOMERIC 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 DBREF 1HKG A 2 458 PDB 1HKG 1HKG 2 458 SEQRES 1 A 457 ALA ALA SER UNK ASP UNK SER LEU VAL GLU VAL HIS UNK SEQRES 2 A 457 UNK VAL PHE ILE VAL PRO PRO UNK ILE LEU GLN ALA VAL SEQRES 3 A 457 VAL SER ILE ALA THR THR ARG UNK ASP ASP UNK ASP SER SEQRES 4 A 457 ALA ALA ALA SER ILE PRO MET VAL PRO GLY TRP VAL LEU SEQRES 5 A 457 LYS GLN VAL UNK GLY SER GLN ALA GLY SER PHE LEU ALA SEQRES 6 A 457 ILE VAL MET GLY GLY GLY ASP LEU GLU VAL ILE LEU ILE SEQRES 7 A 457 UNK LEU ALA GLY TYR GLN GLU SER SER ILE UNK ALA SER SEQRES 8 A 457 ARG SER LEU ALA ALA SER MET UNK THR THR ALA ILE PRO SEQRES 9 A 457 SER ASP LEU TRP GLY ASN UNK ALA UNK SER ASN ALA ALA SEQRES 10 A 457 PHE SER SER UNK GLU PHE SER SER UNK ALA GLY SER VAL SEQRES 11 A 457 PRO LEU GLY PHE THR PHE UNK GLU ALA GLY ALA LYS GLU SEQRES 12 A 457 UNK VAL ILE LYS GLY GLN ILE THR UNK GLN ALA UNK ALA SEQRES 13 A 457 PHE SER LEU ALA UNK LEU UNK LYS LEU ILE SER ALA MET SEQRES 14 A 457 UNK ASN ALA UNK PHE PRO ALA GLY ASP UNK UNK UNK UNK SEQRES 15 A 457 VAL ALA ASP ILE UNK ASP SER HIS GLY ILE LEU UNK UNK SEQRES 16 A 457 VAL ASN TYR THR ASP ALA UNK ILE LYS MET GLY ILE ILE SEQRES 17 A 457 PHE GLY SER GLY VAL ASN ALA ALA TYR TRP CYS ASP SER SEQRES 18 A 457 THR UNK ILE ALA ASP ALA ALA ASP ALA GLY UNK UNK GLY SEQRES 19 A 457 GLY ALA GLY UNK MET UNK VAL CYS CYS UNK GLN ASP SER SEQRES 20 A 457 PHE ARG LYS ALA PHE PRO SER LEU PRO GLN ILE UNK TYR SEQRES 21 A 457 UNK UNK THR LEU ASN UNK UNK SER PRO UNK ALA UNK LYS SEQRES 22 A 457 THR PHE GLU LYS ASN SER UNK ALA LYS ASN UNK GLY GLN SEQRES 23 A 457 SER LEU ARG ASP VAL LEU MET UNK TYR LYS UNK UNK GLY SEQRES 24 A 457 GLN UNK HIS UNK UNK UNK ALA UNK ASP PHE UNK ALA ALA SEQRES 25 A 457 ASN VAL GLU ASN SER SER TYR PRO ALA LYS ILE GLN LYS SEQRES 26 A 457 LEU PRO HIS PHE ASP LEU ARG UNK UNK UNK ASP LEU PHE SEQRES 27 A 457 UNK GLY ASP GLN GLY ILE ALA UNK LYS THR UNK MET LYS SEQRES 28 A 457 UNK VAL VAL ARG ARG UNK LEU PHE LEU ILE ALA ALA TYR SEQRES 29 A 457 ALA PHE ARG LEU VAL VAL CYS UNK ILE UNK ALA ILE CYS SEQRES 30 A 457 GLN LYS LYS GLY TYR SER SER GLY HIS ILE ALA ALA UNK SEQRES 31 A 457 GLY SER UNK ARG ASP TYR SER GLY PHE SER UNK ASN SER SEQRES 32 A 457 ALA THR UNK ASN UNK ASN ILE TYR GLY TRP PRO GLN SER SEQRES 33 A 457 ALA UNK UNK SER LYS PRO ILE UNK ILE THR PRO ALA ILE SEQRES 34 A 457 ASP GLY GLU GLY ALA ALA UNK UNK VAL ILE UNK SER ILE SEQRES 35 A 457 ALA SER SER GLN UNK UNK UNK ALA UNK UNK SER ALA UNK SEQRES 36 A 457 UNK ALA HELIX 1 1 UNK A 5 PHE A 17 1 13 HELIX 2 2 PRO A 20 VAL A 28 1 9 HELIX 3 3 SER A 29 UNK A 38 1 10 HELIX 4 4 ASN A 111 PHE A 124 1 14 HELIX 5 5 ALA A 173 ASP A 179 1 7 HELIX 6 6 UNK A 195 ASP A 201 1 7 HELIX 7 7 UNK A 245 PHE A 249 5 5 HELIX 8 8 UNK A 263 SER A 269 1 7 HELIX 9 9 LYS A 274 ASN A 279 1 6 HELIX 10 10 UNK A 285 GLN A 287 5 3 HELIX 11 11 SER A 288 UNK A 299 1 12 HELIX 12 12 LEU A 332 GLY A 344 1 13 HELIX 13 13 MET A 351 VAL A 371 1 21 HELIX 14 14 UNK A 375 LYS A 381 1 7 HELIX 15 15 PHE A 400 TYR A 412 1 13 HELIX 16 16 GLY A 434 UNK A 449 1 16 SHEET 1 A 2 VAL A 48 PRO A 49 0 SHEET 2 A 2 VAL A 242 CYS A 243 -1 N CYS A 243 O VAL A 48 SHEET 1 B 2 THR A 102 ALA A 103 0 SHEET 2 B 2 LEU A 160 ALA A 161 1 N ALA A 161 O THR A 102 SHEET 1 C 3 VAL A 214 ALA A 217 0 SHEET 2 C 3 ILE A 204 PHE A 210 -1 O GLY A 207 N ALA A 217 SHEET 3 C 3 HIS A 387 UNK A 391 1 O HIS A 387 N LYS A 205 CRYST1 144.800 78.800 61.900 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 0.006897 0.000000 0.000000 0.00000 ORIGX2 0.000000 0.012658 0.000000 0.00000 ORIGX3 0.000000 0.000000 0.016129 0.00000 SCALE1 0.006897 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012658 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016129 0.00000