HEADER TRANSFERASE 01-MAY-00 1EX6 TITLE CRYSTAL STRUCTURE OF UNLIGANDED FORM OF GUANYLATE KINASE FROM YEAST COMPND MOL_ID: 1; COMPND 2 MOLECULE: GUANYLATE KINASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.7.4.8; 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; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS GUANYLATE KINASE, SUBSTRATE-INDUCED FIT, DOMAIN MOVEMENT, ATP, GMP, KEYWDS 2 SUBSTRATE SPECIFICITY, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.BLASZCZYK,X.JI REVDAT 3 30-AUG-23 1EX6 1 AUTHOR JRNL REVDAT 2 24-FEB-09 1EX6 1 VERSN REVDAT 1 16-MAR-01 1EX6 0 JRNL AUTH J.BLASZCZYK,Y.LI,H.YAN,X.JI JRNL TITL CRYSTAL STRUCTURE OF UNLIGATED GUANYLATE KINASE FROM YEAST JRNL TITL 2 REVEALS GMP-INDUCED CONFORMATIONAL CHANGES. JRNL REF J.MOL.BIOL. V. 307 247 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11243817 JRNL DOI 10.1006/JMBI.2000.4427 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 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) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.214 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.334 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 797 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 14941 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.164 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.118 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 581 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 11353 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2892 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 424 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 3306.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 11965 REMARK 3 NUMBER OF RESTRAINTS : 11875 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 ANGLE DISTANCES (A) : 0.017 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.020 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.019 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.025 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.015 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.087 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1975)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: LEAST-SQUARES REFINEMENT USING THE REMARK 3 KONNERT-HENDRICKSON CONJUGATE-GRADIENT ALGORITHM REMARK 4 REMARK 4 1EX6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAY-00. REMARK 100 THE DEPOSITION ID IS D_1000010986. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAR-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92000 REMARK 200 MONOCHROMATOR : SILICON 111 REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15759 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 2.370 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9917 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.13 REMARK 200 R MERGE FOR SHELL (I) : 0.54300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.585 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: HGMAD REMARK 200 SOFTWARE USED: SOLVE, PHASES, DM REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, TRIS-HCL, ACETATE, PH 8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.88167 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 79.76333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 PRO A 40 160.37 -45.35 REMARK 500 LYS A 48 -54.93 -125.56 REMARK 500 VAL A 53 -166.12 -116.98 REMARK 500 THR A 139 -140.06 -121.58 REMARK 500 ASP A 170 123.38 176.84 REMARK 500 GLU A 185 120.25 -38.64 REMARK 500 ALA B 242 93.09 -58.72 REMARK 500 LYS B 248 -65.10 -106.22 REMARK 500 ILE B 310 78.93 -100.25 REMARK 500 ASN B 314 73.99 46.81 REMARK 500 GLU B 338 -154.58 -139.52 REMARK 500 ASN B 368 68.73 -100.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GKY RELATED DB: PDB REMARK 900 1GKY IS THE CRYSTAL STRUCTURE OF A COMPLEX OF N-ACETYLATED REMARK 900 GUANYLATE KINASE FROM YEAST WITH GMP REMARK 900 RELATED ID: 1EX7 RELATED DB: PDB REMARK 900 1EX7 IS THE CRYSTAL STRUCTURE OF A COMPLEX OF NON-(N-ACETYLATED) REMARK 900 GUANYLATE KINASE FROM YEAST WITH GMP DBREF 1EX6 A 1 186 UNP P15454 KGUA_YEAST 1 186 DBREF 1EX6 B 201 386 UNP P15454 KGUA_YEAST 1 186 SEQRES 1 A 186 SER ARG PRO ILE VAL ILE SER GLY PRO SER GLY THR GLY SEQRES 2 A 186 LYS SER THR LEU LEU LYS LYS LEU PHE ALA GLU TYR PRO SEQRES 3 A 186 ASP SER PHE GLY PHE SER VAL SER SER THR THR ARG THR SEQRES 4 A 186 PRO ARG ALA GLY GLU VAL ASN GLY LYS ASP TYR ASN PHE SEQRES 5 A 186 VAL SER VAL ASP GLU PHE LYS SER MET ILE LYS ASN ASN SEQRES 6 A 186 GLU PHE ILE GLU TRP ALA GLN PHE SER GLY ASN TYR TYR SEQRES 7 A 186 GLY SER THR VAL ALA SER VAL LYS GLN VAL SER LYS SER SEQRES 8 A 186 GLY LYS THR CYS ILE LEU ASP ILE ASP MET GLN GLY VAL SEQRES 9 A 186 LYS SER VAL LYS ALA ILE PRO GLU LEU ASN ALA ARG PHE SEQRES 10 A 186 LEU PHE ILE ALA PRO PRO SER VAL GLU ASP LEU LYS LYS SEQRES 11 A 186 ARG LEU GLU GLY ARG GLY THR GLU THR GLU GLU SER ILE SEQRES 12 A 186 ASN LYS ARG LEU SER ALA ALA GLN ALA GLU LEU ALA TYR SEQRES 13 A 186 ALA GLU THR GLY ALA HIS ASP LYS VAL ILE VAL ASN ASP SEQRES 14 A 186 ASP LEU ASP LYS ALA TYR LYS GLU LEU LYS ASP PHE ILE SEQRES 15 A 186 PHE ALA GLU LYS SEQRES 1 B 186 SER ARG PRO ILE VAL ILE SER GLY PRO SER GLY THR GLY SEQRES 2 B 186 LYS SER THR LEU LEU LYS LYS LEU PHE ALA GLU TYR PRO SEQRES 3 B 186 ASP SER PHE GLY PHE SER VAL SER SER THR THR ARG THR SEQRES 4 B 186 PRO ARG ALA GLY GLU VAL ASN GLY LYS ASP TYR ASN PHE SEQRES 5 B 186 VAL SER VAL ASP GLU PHE LYS SER MET ILE LYS ASN ASN SEQRES 6 B 186 GLU PHE ILE GLU TRP ALA GLN PHE SER GLY ASN TYR TYR SEQRES 7 B 186 GLY SER THR VAL ALA SER VAL LYS GLN VAL SER LYS SER SEQRES 8 B 186 GLY LYS THR CYS ILE LEU ASP ILE ASP MET GLN GLY VAL SEQRES 9 B 186 LYS SER VAL LYS ALA ILE PRO GLU LEU ASN ALA ARG PHE SEQRES 10 B 186 LEU PHE ILE ALA PRO PRO SER VAL GLU ASP LEU LYS LYS SEQRES 11 B 186 ARG LEU GLU GLY ARG GLY THR GLU THR GLU GLU SER ILE SEQRES 12 B 186 ASN LYS ARG LEU SER ALA ALA GLN ALA GLU LEU ALA TYR SEQRES 13 B 186 ALA GLU THR GLY ALA HIS ASP LYS VAL ILE VAL ASN ASP SEQRES 14 B 186 ASP LEU ASP LYS ALA TYR LYS GLU LEU LYS ASP PHE ILE SEQRES 15 B 186 PHE ALA GLU LYS FORMUL 3 HOH *424(H2 O) HELIX 1 1 GLY A 13 TYR A 25 1 13 HELIX 2 2 SER A 54 ASN A 64 1 11 HELIX 3 3 VAL A 82 SER A 91 1 10 HELIX 4 4 ASP A 100 ALA A 109 1 10 HELIX 5 5 SER A 124 GLY A 136 1 13 HELIX 6 6 GLU A 140 GLU A 158 1 19 HELIX 7 7 ASP A 170 PHE A 183 1 14 HELIX 8 8 GLY B 213 TYR B 225 1 13 HELIX 9 9 SER B 254 ASN B 264 1 11 HELIX 10 10 VAL B 282 SER B 291 1 10 HELIX 11 11 ASP B 300 ALA B 309 1 10 HELIX 12 12 SER B 324 ARG B 335 1 12 HELIX 13 13 THR B 339 THR B 359 1 21 HELIX 14 14 ASP B 370 ALA B 384 1 15 SHEET 1 A 5 PHE A 29 GLY A 30 0 SHEET 2 A 5 THR A 94 ASP A 98 1 O THR A 94 N GLY A 30 SHEET 3 A 5 ILE A 4 SER A 7 1 N ILE A 4 O CYS A 95 SHEET 4 A 5 ARG A 116 ALA A 121 1 O ARG A 116 N VAL A 5 SHEET 5 A 5 LYS A 164 VAL A 167 1 O LYS A 164 N PHE A 119 SHEET 1 B 4 ASN A 51 PHE A 52 0 SHEET 2 B 4 SER A 35 THR A 36 1 N THR A 36 O ASN A 51 SHEET 3 B 4 ASN A 76 THR A 81 -1 O GLY A 79 N SER A 35 SHEET 4 B 4 PHE A 67 PHE A 73 -1 N ILE A 68 O SER A 80 SHEET 1 C 5 PHE B 229 GLY B 230 0 SHEET 2 C 5 THR B 294 ASP B 298 1 O THR B 294 N GLY B 230 SHEET 3 C 5 ILE B 204 SER B 207 1 N ILE B 204 O CYS B 295 SHEET 4 C 5 ARG B 316 ALA B 321 1 O ARG B 316 N VAL B 205 SHEET 5 C 5 LYS B 364 VAL B 367 1 O LYS B 364 N PHE B 319 SHEET 1 D 4 ASN B 251 PHE B 252 0 SHEET 2 D 4 SER B 235 THR B 236 1 N THR B 236 O ASN B 251 SHEET 3 D 4 ASN B 276 THR B 281 -1 O GLY B 279 N SER B 235 SHEET 4 D 4 PHE B 267 PHE B 273 -1 N ILE B 268 O SER B 280 CRYST1 51.559 51.559 119.645 90.00 90.00 120.00 P 31 6 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 0.019395 0.011198 0.000000 0.00000 SCALE2 0.000000 0.022396 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008358 0.00000