HEADER TRANSFERASE 01-MAY-00 1EX7 TITLE CRYSTAL STRUCTURE OF YEAST GUANYLATE KINASE IN COMPLEX WITH GUANOSINE- TITLE 2 5'-MONOPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GUANYLATE KINASE; COMPND 3 CHAIN: A; 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, GMP, ATP, KEYWDS 2 SUBSTRATE SPECIFICITY, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.BLASZCZYK,X.JI REVDAT 4 30-AUG-23 1EX7 1 AUTHOR JRNL REVDAT 3 09-AUG-23 1EX7 1 REMARK REVDAT 2 24-FEB-09 1EX7 1 VERSN REVDAT 1 16-MAR-01 1EX7 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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.7 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) : 0.170 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 11.111 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1575 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 14174 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)) : 0.156 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 11.231 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1304 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 11611 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1446 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 208 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1688.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 6733 REMARK 3 NUMBER OF RESTRAINTS : 6051 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 ANGLE DISTANCES (A) : 0.033 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.021 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.035 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.044 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.013 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.085 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 1EX7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAY-00. REMARK 100 THE DEPOSITION ID IS D_1000010987. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-96 REMARK 200 TEMPERATURE (KELVIN) : 293 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 : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAC SCIENCE DIP-2000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15836 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.37800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.846 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: REFINEMENT OF THE MODEL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: 1GKY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, SODIUM PHOSPHATE, PH REMARK 280 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 77.66350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.31250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.31250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 116.49525 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.31250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.31250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 38.83175 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.31250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.31250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 116.49525 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.31250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.31250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 38.83175 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 77.66350 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 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 38 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 TYR A 78 CB - CG - CD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 TYR A 78 CB - CG - CD1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 116 NE - CZ - NH2 ANGL. DEV. = -4.7 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 LYS A 48 -51.99 -121.63 REMARK 500 ILE A 110 72.60 -118.82 REMARK 500 ASP A 170 120.86 -177.84 REMARK 500 GLU A 185 -49.19 102.54 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 SO4 A 188 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 189 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5GP A 187 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: 1EX6 RELATED DB: PDB REMARK 900 1EX6 IS THE CRYSTAL STRUCTURE OF UNLIGANDED GUANYLATE KINASE FROM REMARK 900 YEAST DBREF 1EX7 A 1 186 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 HET SO4 A 188 5 HET SO4 A 189 5 HET 5GP A 187 24 HETNAM SO4 SULFATE ION HETNAM 5GP GUANOSINE-5'-MONOPHOSPHATE FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 5GP C10 H14 N5 O8 P FORMUL 5 HOH *208(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 GLY A 92 1 11 HELIX 4 4 ASP A 100 ALA A 109 1 10 HELIX 5 5 ILE A 110 ASN A 114 5 5 HELIX 6 6 SER A 124 GLY A 136 1 13 HELIX 7 7 THR A 139 GLU A 158 1 20 HELIX 8 8 ASP A 170 PHE A 183 1 14 SHEET 1 A 5 PHE A 29 PHE A 31 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 O ILE A 4 N LEU A 97 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 SITE 1 AC1 8 THR A 12 GLY A 13 SER A 60 LYS A 63 SITE 2 AC1 8 ASN A 168 LEU A 171 HOH A 230 HOH A 235 SITE 1 AC2 9 SER A 10 GLY A 11 THR A 12 GLY A 13 SITE 2 AC2 9 LYS A 14 SER A 15 ARG A 135 HOH A 253 SITE 3 AC2 9 HOH A 329 SITE 1 AC3 15 SER A 34 ARG A 38 ARG A 41 TYR A 50 SITE 2 AC3 15 GLU A 69 TYR A 78 GLY A 79 SER A 80 SITE 3 AC3 15 ILE A 99 ASP A 100 GLY A 103 HOH A 213 SITE 4 AC3 15 HOH A 248 HOH A 344 HOH A 390 CRYST1 50.625 50.625 155.327 90.00 90.00 90.00 P 43 21 2 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 0.019753 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019753 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006438 0.00000