HEADER PHOSPHOTRANSFERASE 29-DEC-95 4AKE TITLE ADENYLATE KINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENYLATE KINASE; COMPND 3 CHAIN: A, B; 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: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 CELLULAR_LOCATION: CYTOSOL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PAK601 KEYWDS NUCLEOSIDE MONOPHOSPHATE KINASE, ATP:AMP PHOSPHOTRANSFERASE, KEYWDS 2 MYOKINASE, PHOSPHOTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.J.SCHLAUDERER,G.E.SCHULZ REVDAT 3 28-FEB-24 4AKE 1 REMARK REVDAT 2 24-FEB-09 4AKE 1 VERSN REVDAT 1 10-JUN-96 4AKE 0 JRNL AUTH C.W.MULLER,G.J.SCHLAUDERER,J.REINSTEIN,G.E.SCHULZ JRNL TITL ADENYLATE KINASE MOTIONS DURING CATALYSIS: AN ENERGETIC JRNL TITL 2 COUNTERWEIGHT BALANCING SUBSTRATE BINDING. JRNL REF STRUCTURE V. 4 147 1996 JRNL REFN ISSN 0969-2126 JRNL PMID 8805521 JRNL DOI 10.1016/S0969-2126(96)00018-4 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 C.W.MULLER,G.E.SCHULZ REMARK 1 TITL STRUCTURE OF THE COMPLEX BETWEEN ADENYLATE KINASE FROM REMARK 1 TITL 2 ESCHERICHIA COLI AND THE INHIBITOR AP5A REFINED AT 1.9 A REMARK 1 TITL 3 RESOLUTION. A MODEL FOR A CATALYTIC TRANSITION STATE REMARK 1 REF J.MOL.BIOL. V. 224 159 1992 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 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) (%) : 82.0 REMARK 3 NUMBER OF REFLECTIONS : 17932 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) : 0.183 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 : 3312 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 147 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.00 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) : 0.30 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) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.700 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) : 4.400 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 6.400 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 6.600 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 9.600 ; 2.500 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 4AKE 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_1000179257. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 1991 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 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17932 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 (%) : 82.0 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.06300 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: 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 (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 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: 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 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 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 ILE A 72 1.30 -67.56 REMARK 500 SER A 129 -32.57 179.14 REMARK 500 VAL A 135 -34.61 -30.52 REMARK 500 LYS A 136 -60.64 -100.30 REMARK 500 PHE B 137 -101.77 -84.33 REMARK 500 VAL B 148 -80.36 -77.91 REMARK 500 GLU B 161 -37.64 -39.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 24 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 4AKE A 1 214 UNP P69441 KAD_ECOLI 1 214 DBREF 4AKE B 1 214 UNP P69441 KAD_ECOLI 1 214 SEQRES 1 A 214 MET ARG ILE ILE LEU LEU GLY ALA PRO GLY ALA GLY LYS SEQRES 2 A 214 GLY THR GLN ALA GLN PHE ILE MET GLU LYS TYR GLY ILE SEQRES 3 A 214 PRO GLN ILE SER THR GLY ASP MET LEU ARG ALA ALA VAL SEQRES 4 A 214 LYS SER GLY SER GLU LEU GLY LYS GLN ALA LYS ASP ILE SEQRES 5 A 214 MET ASP ALA GLY LYS LEU VAL THR ASP GLU LEU VAL ILE SEQRES 6 A 214 ALA LEU VAL LYS GLU ARG ILE ALA GLN GLU ASP CYS ARG SEQRES 7 A 214 ASN GLY PHE LEU LEU ASP GLY PHE PRO ARG THR ILE PRO SEQRES 8 A 214 GLN ALA ASP ALA MET LYS GLU ALA GLY ILE ASN VAL ASP SEQRES 9 A 214 TYR VAL LEU GLU PHE ASP VAL PRO ASP GLU LEU ILE VAL SEQRES 10 A 214 ASP ARG ILE VAL GLY ARG ARG VAL HIS ALA PRO SER GLY SEQRES 11 A 214 ARG VAL TYR HIS VAL LYS PHE ASN PRO PRO LYS VAL GLU SEQRES 12 A 214 GLY LYS ASP ASP VAL THR GLY GLU GLU LEU THR THR ARG SEQRES 13 A 214 LYS ASP ASP GLN GLU GLU THR VAL ARG LYS ARG LEU VAL SEQRES 14 A 214 GLU TYR HIS GLN MET THR ALA PRO LEU ILE GLY TYR TYR SEQRES 15 A 214 SER LYS GLU ALA GLU ALA GLY ASN THR LYS TYR ALA LYS SEQRES 16 A 214 VAL ASP GLY THR LYS PRO VAL ALA GLU VAL ARG ALA ASP SEQRES 17 A 214 LEU GLU LYS ILE LEU GLY SEQRES 1 B 214 MET ARG ILE ILE LEU LEU GLY ALA PRO GLY ALA GLY LYS SEQRES 2 B 214 GLY THR GLN ALA GLN PHE ILE MET GLU LYS TYR GLY ILE SEQRES 3 B 214 PRO GLN ILE SER THR GLY ASP MET LEU ARG ALA ALA VAL SEQRES 4 B 214 LYS SER GLY SER GLU LEU GLY LYS GLN ALA LYS ASP ILE SEQRES 5 B 214 MET ASP ALA GLY LYS LEU VAL THR ASP GLU LEU VAL ILE SEQRES 6 B 214 ALA LEU VAL LYS GLU ARG ILE ALA GLN GLU ASP CYS ARG SEQRES 7 B 214 ASN GLY PHE LEU LEU ASP GLY PHE PRO ARG THR ILE PRO SEQRES 8 B 214 GLN ALA ASP ALA MET LYS GLU ALA GLY ILE ASN VAL ASP SEQRES 9 B 214 TYR VAL LEU GLU PHE ASP VAL PRO ASP GLU LEU ILE VAL SEQRES 10 B 214 ASP ARG ILE VAL GLY ARG ARG VAL HIS ALA PRO SER GLY SEQRES 11 B 214 ARG VAL TYR HIS VAL LYS PHE ASN PRO PRO LYS VAL GLU SEQRES 12 B 214 GLY LYS ASP ASP VAL THR GLY GLU GLU LEU THR THR ARG SEQRES 13 B 214 LYS ASP ASP GLN GLU GLU THR VAL ARG LYS ARG LEU VAL SEQRES 14 B 214 GLU TYR HIS GLN MET THR ALA PRO LEU ILE GLY TYR TYR SEQRES 15 B 214 SER LYS GLU ALA GLU ALA GLY ASN THR LYS TYR ALA LYS SEQRES 16 B 214 VAL ASP GLY THR LYS PRO VAL ALA GLU VAL ARG ALA ASP SEQRES 17 B 214 LEU GLU LYS ILE LEU GLY FORMUL 3 HOH *147(H2 O) HELIX 1 1 LYS A 13 TYR A 24 5 12 HELIX 2 2 THR A 31 LYS A 40 1 10 HELIX 3 3 GLU A 44 ASP A 54 1 11 HELIX 4 4 ASP A 61 ALA A 73 1 13 HELIX 5 5 GLU A 75 CYS A 77 5 3 HELIX 6 6 ILE A 90 GLU A 98 1 9 HELIX 7 7 ASP A 113 VAL A 121 1 9 HELIX 8 8 GLU A 161 GLU A 187 1 27 HELIX 9 9 VAL A 202 LEU A 213 1 12 HELIX 10 10 LYS B 13 TYR B 24 5 12 HELIX 11 11 THR B 31 LYS B 40 1 10 HELIX 12 12 GLU B 44 ASP B 54 1 11 HELIX 13 13 ASP B 61 ALA B 73 1 13 HELIX 14 14 GLU B 75 CYS B 77 5 3 HELIX 15 15 ILE B 90 GLU B 98 1 9 HELIX 16 16 ASP B 113 VAL B 121 1 9 HELIX 17 17 LYS B 157 ASP B 159 5 3 HELIX 18 18 GLU B 161 ALA B 188 1 28 HELIX 19 19 VAL B 202 ILE B 212 1 11 SHEET 1 A 5 LYS A 192 ASP A 197 0 SHEET 2 A 5 TYR A 105 ASP A 110 1 N VAL A 106 O LYS A 192 SHEET 3 A 5 ARG A 2 GLY A 7 1 N ILE A 4 O TYR A 105 SHEET 4 A 5 PHE A 81 ASP A 84 1 N PHE A 81 O ILE A 3 SHEET 5 A 5 PRO A 27 ILE A 29 1 N PRO A 27 O LEU A 82 SHEET 1 B 2 ARG A 123 HIS A 126 0 SHEET 2 B 2 ARG A 131 HIS A 134 -1 N TYR A 133 O ARG A 124 SHEET 1 C 5 LYS B 192 ASP B 197 0 SHEET 2 C 5 TYR B 105 ASP B 110 1 N VAL B 106 O LYS B 192 SHEET 3 C 5 ARG B 2 GLY B 7 1 N ILE B 4 O TYR B 105 SHEET 4 C 5 PHE B 81 ASP B 84 1 N PHE B 81 O ILE B 3 SHEET 5 C 5 PRO B 27 ILE B 29 1 N PRO B 27 O LEU B 82 SHEET 1 D 2 ARG B 124 HIS B 126 0 SHEET 2 D 2 ARG B 131 TYR B 133 -1 N TYR B 133 O ARG B 124 CISPEP 1 PHE A 86 PRO A 87 0 0.62 CISPEP 2 PHE B 86 PRO B 87 0 0.07 CRYST1 31.800 54.500 71.300 67.70 77.90 88.40 P 1 2 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 0.031447 -0.000878 -0.006932 0.00000 SCALE2 0.000000 0.018356 -0.007593 0.00000 SCALE3 0.000000 0.000000 0.015523 0.00000 MTRIX1 1 0.999606 -0.012438 0.025179 0.88440 1 MTRIX2 1 -0.012961 -0.999702 0.020699 0.97090 1 MTRIX3 1 0.024914 -0.021017 -0.999469 1.34950 1