HEADER TRANSFERASE 09-MAR-07 2P3S TITLE CRYSTAL STRUCTURE OF A THERMOSTABLE MUTANT OF BACILLUS SUBTILIS TITLE 2 ADENYLATE KINASE (G214R/Q199R) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENYLATE KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ATP-AMP TRANSPHOSPHORYLASE, AK, SUPEROXIDE-INDUCIBLE PROTEIN COMPND 5 16, SOI16; COMPND 6 EC: 2.7.4.3; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: ADK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS THERMOSTABILITY, ADENYLATE KINASE, EXPERIMENTAL ADAPTIVE EVOLUTION, KEYWDS 2 DIRECTED EVOLUTION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.COUNAGO,C.J.WILSON,J.MYERS,G.WU,Y.SHAMOO REVDAT 5 30-AUG-23 2P3S 1 REMARK REVDAT 4 20-OCT-21 2P3S 1 REMARK SEQADV REVDAT 3 18-OCT-17 2P3S 1 REMARK REVDAT 2 24-FEB-09 2P3S 1 VERSN REVDAT 1 22-JAN-08 2P3S 0 JRNL AUTH R.COUNAGO,C.J.WILSON,J.MYERS,G.WU,Y.SHAMOO, JRNL AUTH 2 P.WITTUNG-STAFSHEDE JRNL TITL CRYSTAL STRUCTURE OF A THERMOSTABLE MUTANT OF BACILLUS JRNL TITL 2 SUBTILIS ADENYLATE KINASE (G214R/Q199R) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.95 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) (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 17611 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.400 REMARK 3 FREE R VALUE TEST SET COUNT : 844 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 : 1689 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 59 REMARK 3 SOLVENT ATOMS : 275 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : 2.82900 REMARK 3 B33 (A**2) : -2.78900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : NULL 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 43.96 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : AP5_PAR REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2P3S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000041929. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 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 : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18560 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 26.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 3.380 REMARK 200 R MERGE (I) : 0.03200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.5000 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 2EU8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CHESS, PEG 1500, CACL2, PH 9.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 22.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.07900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.76100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.07900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.76100 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 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 LYS A 217 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 142 68.57 -166.81 REMARK 500 GLN A 198 58.32 -97.44 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 ZN A 320 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 323 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AP5 A 318 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2EU8 RELATED DB: PDB REMARK 900 THERMOSTABLE MUTANT OF BACILLUS SUBTILIS ADENYLATE KINASE (Q199R) REMARK 900 RELATED ID: 1P3J RELATED DB: PDB REMARK 900 ADENYLATE KINASE FROM BACILLUS SUBTILIS DBREF 2P3S A 1 217 UNP P16304 KAD_BACSU 1 217 SEQADV 2P3S ARG A 199 UNP P16304 GLN 199 ENGINEERED MUTATION SEQADV 2P3S ARG A 214 UNP P16304 GLY 214 ENGINEERED MUTATION SEQRES 1 A 217 MET ASN LEU VAL LEU MET GLY LEU PRO GLY ALA GLY LYS SEQRES 2 A 217 GLY THR GLN GLY GLU ARG ILE VAL GLU ASP TYR GLY ILE SEQRES 3 A 217 PRO HIS ILE SER THR GLY ASP MET PHE ARG ALA ALA MET SEQRES 4 A 217 LYS GLU GLU THR PRO LEU GLY LEU GLU ALA LYS SER TYR SEQRES 5 A 217 ILE ASP LYS GLY GLU LEU VAL PRO ASP GLU VAL THR ILE SEQRES 6 A 217 GLY ILE VAL LYS GLU ARG LEU GLY LYS ASP ASP CYS GLU SEQRES 7 A 217 ARG GLY PHE LEU LEU ASP GLY PHE PRO ARG THR VAL ALA SEQRES 8 A 217 GLN ALA GLU ALA LEU GLU GLU ILE LEU GLU GLU TYR GLY SEQRES 9 A 217 LYS PRO ILE ASP TYR VAL ILE ASN ILE GLU VAL ASP LYS SEQRES 10 A 217 ASP VAL LEU MET GLU ARG LEU THR GLY ARG ARG ILE CYS SEQRES 11 A 217 SER VAL CYS GLY THR THR TYR HIS LEU VAL PHE ASN PRO SEQRES 12 A 217 PRO LYS THR PRO GLY ILE CYS ASP LYS ASP GLY GLY GLU SEQRES 13 A 217 LEU TYR GLN ARG ALA ASP ASP ASN GLU GLU THR VAL SER SEQRES 14 A 217 LYS ARG LEU GLU VAL ASN MET LYS GLN THR GLN PRO LEU SEQRES 15 A 217 LEU ASP PHE TYR SER GLU LYS GLY TYR LEU ALA ASN VAL SEQRES 16 A 217 ASN GLY GLN ARG ASP ILE GLN ASP VAL TYR ALA ASP VAL SEQRES 17 A 217 LYS ASP LEU LEU GLY ARG LEU LYS LYS HET ZN A 320 1 HET MG A 323 1 HET AP5 A 318 57 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE FORMUL 2 ZN ZN 2+ FORMUL 3 MG MG 2+ FORMUL 4 AP5 C20 H29 N10 O22 P5 FORMUL 5 HOH *275(H2 O) HELIX 1 1 GLY A 12 GLY A 25 1 14 HELIX 2 2 THR A 31 GLU A 41 1 11 HELIX 3 3 THR A 43 GLY A 56 1 14 HELIX 4 4 PRO A 60 GLY A 73 1 14 HELIX 5 5 LYS A 74 GLU A 78 5 5 HELIX 6 6 THR A 89 TYR A 103 1 15 HELIX 7 7 ASP A 116 ASP A 118 5 3 HELIX 8 8 VAL A 119 GLY A 126 1 8 HELIX 9 9 ARG A 160 ASP A 163 5 4 HELIX 10 10 ASN A 164 GLY A 190 1 27 HELIX 11 11 ASP A 200 GLY A 213 1 14 SHEET 1 A 5 HIS A 28 SER A 30 0 SHEET 2 A 5 PHE A 81 ASP A 84 1 O LEU A 82 N ILE A 29 SHEET 3 A 5 ASN A 2 MET A 6 1 N LEU A 3 O LEU A 83 SHEET 4 A 5 TYR A 109 GLU A 114 1 O ILE A 113 N MET A 6 SHEET 5 A 5 LEU A 192 ASN A 196 1 O VAL A 195 N ASN A 112 SHEET 1 B 3 THR A 136 HIS A 138 0 SHEET 2 B 3 ARG A 127 CYS A 130 -1 N ARG A 128 O TYR A 137 SHEET 3 B 3 LEU A 157 TYR A 158 -1 O TYR A 158 N ILE A 129 CISPEP 1 PHE A 86 PRO A 87 0 -0.21 SITE 1 AC1 4 CYS A 130 CYS A 133 CYS A 150 ASP A 153 SITE 1 AC2 3 AP5 A 318 HOH A 454 HOH A 564 SITE 1 AC3 39 PRO A 9 GLY A 10 ALA A 11 GLY A 12 SITE 2 AC3 39 LYS A 13 GLY A 14 THR A 15 THR A 31 SITE 3 AC3 39 GLY A 32 PHE A 35 ARG A 36 ILE A 53 SITE 4 AC3 39 GLU A 57 VAL A 59 THR A 64 GLY A 85 SITE 5 AC3 39 PHE A 86 ARG A 88 GLN A 92 ARG A 123 SITE 6 AC3 39 ARG A 127 THR A 136 TYR A 137 HIS A 138 SITE 7 AC3 39 PHE A 141 ARG A 160 ARG A 171 GLY A 197 SITE 8 AC3 39 ARG A 199 ILE A 201 MG A 323 HOH A 324 SITE 9 AC3 39 HOH A 325 HOH A 331 HOH A 333 HOH A 334 SITE 10 AC3 39 HOH A 343 HOH A 366 HOH A 455 CRYST1 44.000 45.522 100.158 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 0.022727 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021967 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009984 0.00000