HEADER PHOSPHOTRANSFERASE 29-DEC-95 1AK2 TITLE ADENYLATE KINASE ISOENZYME-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENYLATE KINASE ISOENZYME-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ATP\:AMP PHOSPHOTRANSFERASE, MYOKINASE; COMPND 5 EC: 2.7.4.3; COMPND 6 OTHER_DETAILS: PRECIPITANT POLYETHYLENE GLYCOL SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 ORGAN: LIVER; SOURCE 6 ORGANELLE: MITOCHONDRIA INTERMEMBRANE SPACE KEYWDS NUCLEOSIDE MONOPHOSPHATE KINASE, PHOSPHOTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.J.SCHLAUDERER,G.E.SCHULZ REVDAT 3 30-OCT-24 1AK2 1 REMARK REVDAT 2 24-FEB-09 1AK2 1 VERSN REVDAT 1 10-JUN-96 1AK2 0 JRNL AUTH G.J.SCHLAUDERER,G.E.SCHULZ JRNL TITL THE STRUCTURE OF BOVINE MITOCHONDRIAL ADENYLATE KINASE: JRNL TITL 2 COMPARISON WITH ISOENZYMES IN OTHER COMPARTMENTS. JRNL REF PROTEIN SCI. V. 5 434 1996 JRNL REFN ISSN 0961-8368 JRNL PMID 8868479 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.VONRHEIN,G.J.SCHLAUDERER,G.E.SCHULZ REMARK 1 TITL MOVIE OF THE STRUCTURAL CHANGES DURING A CATALYTIC CYCLE OF REMARK 1 TITL 2 NUCLEOSIDE MONOPHOSPHATE KINASES REMARK 1 REF STRUCTURE V. 3 483 1995 REMARK 1 REFN ISSN 0969-2126 REMARK 1 REFERENCE 2 REMARK 1 AUTH F.KISHI,Y.TANIZAWA,A.NAKAZAWA REMARK 1 TITL ISOLATION AND CHARACTERIZATION OF TWO TYPES OF CDNA FOR REMARK 1 TITL 2 MITOCHONDRIAL ADENYLATE KINASE AND THEIR EXPRESSION IN REMARK 1 TITL 3 ESCHERICHIA COLI REMARK 1 REF J.BIOL.CHEM. V. 262 11785 1987 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 3 REMARK 1 AUTH R.FRANK,M.TROSIN,A.G.TOMASSELLI,L.NODA,R.L.KRAUTH-SIEGEL, REMARK 1 AUTH 2 R.H.SCHIRMER REMARK 1 TITL MITOCHONDRIAL ADENYLATE KINASE (AK2) FROM BOVINE HEART. THE REMARK 1 TITL 2 COMPLETE PRIMARY STRUCTURE REMARK 1 REF EUR.J.BIOCHEM. V. 154 205 1986 REMARK 1 REFN ISSN 0014-2956 REMARK 1 REFERENCE 4 REMARK 1 AUTH A.G.TOMASSELLI,L.H.NODA REMARK 1 TITL MITOCHONDRIAL ATP:AMP PHOSPHOTRANSFERASE FROM BEEF HEART: REMARK 1 TITL 2 PURIFICATION AND PROPERTIES REMARK 1 REF EUR.J.BIOCHEM. V. 103 481 1980 REMARK 1 REFN ISSN 0014-2956 REMARK 2 REMARK 2 RESOLUTION. 1.92 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) : 1.92 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) (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 20850 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) : 0.222 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 : 1699 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 117 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.00 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) : 0.27 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) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.600 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) : 1.300 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.400 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.700 ; 3.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.400 ; 5.000 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 1AK2 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_1000170913. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 1992 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 : ROTATING ANODE 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) : 1.5418 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 REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20850 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : 0.07700 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 (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 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 22.10000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.15000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.05000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.15000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.10000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.05000 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 REMARK 400 REMARK 400 COMPOUND REMARK 400 THE SECONDARY STRUCTURAL ELEMENTS PRESENTED BELOW ARE FROM REMARK 400 PROGRAM DSSP. FOR MANUAL ASSIGNMENTS PLEASE SEE THE REMARK 400 PUBLICATION. 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 ALA A 1 REMARK 465 PRO A 2 REMARK 465 ASN A 3 REMARK 465 VAL A 4 REMARK 465 PRO A 5 REMARK 465 ALA A 6 REMARK 465 ALA A 7 REMARK 465 GLU A 8 REMARK 465 PRO A 9 REMARK 465 VAL A 10 REMARK 465 PRO A 11 REMARK 465 GLU A 12 REMARK 465 SER A 13 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 ASN A 158 75.11 -150.85 REMARK 500 SER A 177 31.14 -68.47 REMARK 500 ASN A 180 48.34 -151.38 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 301 DBREF 1AK2 A 1 232 UNP P08166 KAD2_BOVIN 1 232 SEQRES 1 A 233 ALA PRO ASN VAL PRO ALA ALA GLU PRO VAL PRO GLU SER SEQRES 2 A 233 PRO LYS GLY VAL ARG ALA VAL LEU LEU GLY PRO PRO GLY SEQRES 3 A 233 ALA GLY LYS GLY THR GLN ALA PRO LYS LEU ALA LYS ASN SEQRES 4 A 233 PHE CYS VAL CYS HIS LEU ALA THR GLY ASP MET LEU ARG SEQRES 5 A 233 ALA MET VAL ALA SER GLY SER GLU LEU GLY LYS LYS LEU SEQRES 6 A 233 LYS ALA THR MET ASP ALA GLY LYS LEU VAL SER ASP GLU SEQRES 7 A 233 MET VAL LEU GLU LEU ILE GLU LYS ASN LEU GLU THR PRO SEQRES 8 A 233 PRO CYS LYS ASN GLY PHE LEU LEU ASP GLY PHE PRO ARG SEQRES 9 A 233 THR VAL ARG GLN ALA GLU MET LEU ASP ASP LEU MET GLU SEQRES 10 A 233 LYS ARG LYS GLU LYS LEU ASP SER VAL ILE GLU PHE SER SEQRES 11 A 233 ILE PRO ASP SER LEU LEU ILE ARG ARG ILE THR GLY ARG SEQRES 12 A 233 LEU ILE HIS PRO GLN SER GLY ARG SER TYR HIS GLU GLU SEQRES 13 A 233 PHE ASN PRO PRO LYS GLU PRO MET LYS ASP ASP ILE THR SEQRES 14 A 233 GLY GLU PRO LEU ILE ARG ARG SER ASP ASP ASN LYS LYS SEQRES 15 A 233 ALA LEU LYS ILE ARG LEU GLU ALA TYR HIS THR GLN THR SEQRES 16 A 233 THR PRO LEU VAL GLU TYR TYR SER LYS ARG GLY ILE HIS SEQRES 17 A 233 SER ALA ILE ASP ALA SER GLN THR PRO ASP VAL VAL PHE SEQRES 18 A 233 ALA SER ILE LEU ALA ALA PHE SER LYS ALA THR SER HET SO4 A 301 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *117(H2 O) HELIX 1 1 LYS A 29 PHE A 40 1 12 HELIX 2 2 THR A 47 SER A 57 1 11 HELIX 3 3 GLU A 60 ASP A 70 1 11 HELIX 4 4 ASP A 77 LEU A 88 1 12 HELIX 5 5 PRO A 91 CYS A 93 5 3 HELIX 6 6 VAL A 106 LYS A 118 1 13 HELIX 7 7 ASP A 133 THR A 141 1 9 HELIX 8 8 LYS A 181 LYS A 204 1 24 HELIX 9 9 PRO A 217 ALA A 231 1 15 SHEET 1 A 5 HIS A 208 ASP A 212 0 SHEET 2 A 5 SER A 125 SER A 130 1 N VAL A 126 O SER A 209 SHEET 3 A 5 ARG A 18 GLY A 23 1 N VAL A 20 O SER A 125 SHEET 4 A 5 PHE A 97 ASP A 100 1 N PHE A 97 O ALA A 19 SHEET 5 A 5 CYS A 43 ALA A 46 1 N CYS A 43 O LEU A 98 SSBOND 1 CYS A 43 CYS A 93 1555 1555 2.02 CISPEP 1 PHE A 102 PRO A 103 0 -0.04 SITE 1 AC1 6 PRO A 24 GLY A 26 ALA A 27 GLY A 28 SITE 2 AC1 6 LYS A 29 GLY A 30 CRYST1 44.200 50.100 122.300 90.00 90.00 90.00 P 21 21 21 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 0.022624 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019960 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008177 0.00000