HEADER TRANSFERASE (PHOSPHOTRANSFERASE) 28-JUL-95 1AKY TITLE HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED WITH TITLE 2 INHIBITOR AP5A, SHOWING THE PATHWAY OF PHOSPHORYL TRANSFER COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENYLATE KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ATP\:AMP PHOSPHOTRANSFERASE, MYOKINASE; COMPND 5 EC: 2.7.4.3; COMPND 6 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 STRAIN: FALA STRASBOURG; SOURCE 6 CELLULAR_LOCATION: CYTOSOL; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ATP:AMP PHOSPHOTRANSFERASE, MYOKINASE, TRANSFERASE KEYWDS 2 (PHOSPHOTRANSFERASE) EXPDTA X-RAY DIFFRACTION AUTHOR U.ABELE,G.E.SCHULZ REVDAT 3 07-FEB-24 1AKY 1 REMARK REVDAT 2 24-FEB-09 1AKY 1 VERSN REVDAT 1 14-NOV-95 1AKY 0 JRNL AUTH U.ABELE,G.E.SCHULZ JRNL TITL HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST JRNL TITL 2 LIGATED WITH INHIBITOR AP5A, SHOWING THE PATHWAY OF JRNL TITL 3 PHOSPHORYL TRANSFER. JRNL REF PROTEIN SCI. V. 4 1262 1995 JRNL REFN ISSN 0961-8368 JRNL PMID 7670369 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.SPUERGIN,U.ABELE,G.E.SCHULZ REMARK 1 TITL STABILITY, ACTIVITY AND STRUCTURE OF ADENYLATE KINASE REMARK 1 TITL 2 MUTANTS REMARK 1 REF EUR.J.BIOCHEM. V. 231 405 1995 REMARK 1 REFN ISSN 0014-2956 REMARK 1 REFERENCE 2 REMARK 1 AUTH K.PROBA,A.G.TOMASSELLI,P.NIELSEN,G.E.SCHULZ REMARK 1 TITL THE C-DNA SEQUENCE ENCODING CYTOSOLIC ADENYLATE KINASE FROM REMARK 1 TITL 2 BAKER'S YEAST (SACCHAROMYCES CEREVISIAE) REMARK 1 REF NUCLEIC ACIDS RES. V. 15 7187 1987 REMARK 1 REFN ISSN 0305-1048 REMARK 1 REFERENCE 3 REMARK 1 AUTH U.EGNER,A.G.TOMASSELLI,G.E.SCHULZ REMARK 1 TITL STRUCTURE OF THE COMPLEX OF YEAST ADENYLATE KINASE WITH THE REMARK 1 TITL 2 INHIBITOR AP5A AT 2.6 ANGSTROMS RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 195 649 1987 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 4 REMARK 1 AUTH A.G.TOMASSELLI,E.MAST,W.JANES,E.SCHILTZ REMARK 1 TITL THE COMPLETE AMINO ACID SEQUENCE OF ADENYLATE KINASE FROM REMARK 1 TITL 2 BAKER'S YEAST REMARK 1 REF EUR.J.BIOCHEM. V. 155 111 1986 REMARK 1 REFN ISSN 0014-2956 REMARK 2 REMARK 2 RESOLUTION. 1.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 25745 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 SET) : 0.194 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 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1675 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 131 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.00 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) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.290 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.500 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.000 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 3.500 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.000 ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1AKY 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_1000170945. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 1990 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS-NICOLET X100 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS, SYNDUC REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27634 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 SER A 1 REMARK 465 SER A 2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 H1 HOH A 506 H2 HOH A 513 0.74 REMARK 500 H2 HOH A 613 H2 HOH A 620 0.87 REMARK 500 HE21 GLN A 48 H2 HOH A 582 0.91 REMARK 500 H2 HOH A 502 H1 HOH A 507 0.96 REMARK 500 H2 HOH A 509 H2 HOH A 522 0.97 REMARK 500 H ASP A 122 H1 HOH A 614 1.00 REMARK 500 H2 HOH A 611 H1 HOH A 616 1.01 REMARK 500 H1 HOH A 508 H1 HOH A 559 1.11 REMARK 500 HG SER A 64 H2 HOH A 516 1.12 REMARK 500 H1 HOH A 536 H2 HOH A 560 1.15 REMARK 500 H2 HOH A 561 H1 HOH A 625 1.16 REMARK 500 HE21 GLN A 25 H1 HOH A 619 1.16 REMARK 500 H GLY A 11 H2 HOH A 506 1.26 REMARK 500 HD1 HIS A 143 H PHE A 146 1.27 REMARK 500 HG SER A 138 H ARG A 140 1.29 REMARK 500 HG1 THR A 19 H2 HOH A 528 1.30 REMARK 500 H2 HOH A 515 H1 HOH A 605 1.30 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 SER A 138 -48.85 -151.71 REMARK 500 ARG A 140 110.32 -34.58 REMARK 500 ASN A 147 63.71 -159.52 REMARK 500 MET A 153 17.76 59.20 REMARK 500 LYS A 219 -68.38 -120.18 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 AP5 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 302 DBREF 1AKY A 1 219 UNP P07170 KAD1_YEAST 3 221 SEQRES 1 A 220 SER SER GLU SER ILE ARG MET VAL LEU ILE GLY PRO PRO SEQRES 2 A 220 GLY ALA GLY LYS GLY THR GLN ALA PRO ASN LEU GLN GLU SEQRES 3 A 220 ARG PHE HIS ALA ALA HIS LEU ALA THR GLY ASP MET LEU SEQRES 4 A 220 ARG SER GLN ILE ALA LYS GLY THR GLN LEU GLY LEU GLU SEQRES 5 A 220 ALA LYS LYS ILE MET ASP GLN GLY GLY LEU VAL SER ASP SEQRES 6 A 220 ASP ILE MET VAL ASN MET ILE LYS ASP GLU LEU THR ASN SEQRES 7 A 220 ASN PRO ALA CYS LYS ASN GLY PHE ILE LEU ASP GLY PHE SEQRES 8 A 220 PRO ARG THR ILE PRO GLN ALA GLU LYS LEU ASP GLN MET SEQRES 9 A 220 LEU LYS GLU GLN GLY THR PRO LEU GLU LYS ALA ILE GLU SEQRES 10 A 220 LEU LYS VAL ASP ASP GLU LEU LEU VAL ALA ARG ILE THR SEQRES 11 A 220 GLY ARG LEU ILE HIS PRO ALA SER GLY ARG SER TYR HIS SEQRES 12 A 220 LYS ILE PHE ASN PRO PRO LYS GLU ASP MET LYS ASP ASP SEQRES 13 A 220 VAL THR GLY GLU ALA LEU VAL GLN ARG SER ASP ASP ASN SEQRES 14 A 220 ALA ASP ALA LEU LYS LYS ARG LEU ALA ALA TYR HIS ALA SEQRES 15 A 220 GLN THR GLU PRO ILE VAL ASP PHE TYR LYS LYS THR GLY SEQRES 16 A 220 ILE TRP ALA GLY VAL ASP ALA SER GLN PRO PRO ALA THR SEQRES 17 A 220 VAL TRP ALA ASP ILE LEU ASN LYS LEU GLY LYS ASN HET AP5 A 301 65 HET IMD A 302 7 HETNAM AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE HETNAM IMD IMIDAZOLE FORMUL 2 AP5 C20 H29 N10 O22 P5 FORMUL 3 IMD C3 H5 N2 1+ FORMUL 4 HOH *131(H2 O) HELIX 1 1 LYS A 17 PHE A 28 1 12 HELIX 2 2 THR A 35 ALA A 44 1 10 HELIX 3 3 GLN A 48 ASP A 58 1 11 HELIX 4 4 ASP A 65 ASN A 78 1 14 HELIX 5 5 PRO A 80 LYS A 83 5 4 HELIX 6 6 ILE A 95 GLN A 108 1 14 HELIX 7 7 ASP A 122 THR A 130 1 9 HELIX 8 8 ALA A 170 GLN A 183 1 14 HELIX 9 9 GLU A 185 THR A 194 5 10 HELIX 10 10 PRO A 206 LEU A 217 1 12 SHEET 1 A 5 TRP A 197 ASP A 201 0 SHEET 2 A 5 LYS A 114 LYS A 119 1 N ALA A 115 O ALA A 198 SHEET 3 A 5 ARG A 6 GLY A 11 1 N VAL A 8 O LYS A 114 SHEET 4 A 5 PHE A 86 ASP A 89 1 N PHE A 86 O MET A 7 SHEET 5 A 5 ALA A 31 ALA A 34 1 N ALA A 31 O ILE A 87 SHEET 1 B 2 ARG A 132 ILE A 134 0 SHEET 2 B 2 SER A 141 HIS A 143 -1 N TYR A 142 O LEU A 133 CISPEP 1 PHE A 91 PRO A 92 0 0.16 SITE 1 AC1 39 PRO A 13 GLY A 14 ALA A 15 GLY A 16 SITE 2 AC1 39 LYS A 17 GLY A 18 THR A 19 THR A 35 SITE 3 AC1 39 GLY A 36 ARG A 40 MET A 57 GLY A 61 SITE 4 AC1 39 VAL A 63 MET A 68 GLY A 90 PHE A 91 SITE 5 AC1 39 ARG A 93 GLN A 97 ARG A 128 ARG A 132 SITE 6 AC1 39 SER A 141 TYR A 142 HIS A 143 ASN A 147 SITE 7 AC1 39 ARG A 165 ARG A 176 GLN A 204 PRO A 205 SITE 8 AC1 39 PRO A 206 IMD A 302 HOH A 501 HOH A 505 SITE 9 AC1 39 HOH A 509 HOH A 511 HOH A 528 HOH A 530 SITE 10 AC1 39 HOH A 540 HOH A 550 HOH A 575 SITE 1 AC2 6 GLY A 18 ASP A 37 ARG A 40 ASP A 89 SITE 2 AC2 6 AP5 A 301 HOH A 530 CRYST1 36.300 40.500 45.700 110.80 109.00 63.30 P 1 1 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 0.027548 -0.013855 0.006254 0.00000 SCALE2 0.000000 0.027638 0.007052 0.00000 SCALE3 0.000000 0.000000 0.023884 0.00000