HEADER TRANSFERASE 22-JUN-14 4TTP TITLE CRYSTAL STRUCTURE OF LEGIONELLA PNEUMOPHILA DEPHOSPHO-COA KINASE IN TITLE 2 APO-FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEPHOSPHO-COA KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DEPHOSPHOCOENZYME A KINASE; COMPND 5 EC: 2.7.1.24; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA; SOURCE 3 ORGANISM_TAXID: 272624; SOURCE 4 STRAIN: PHILADELPHIA 1 / ATCC 33152 / DSM 7513; SOURCE 5 GENE: COAE, LPG1467; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA KEYWDS KINASE, P-LOOP, COENZYME METABOLISM, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR X.GONG,H.GE REVDAT 6 27-SEP-23 4TTP 1 REMARK REVDAT 5 08-JAN-20 4TTP 1 REMARK REVDAT 4 11-OCT-17 4TTP 1 REMARK REVDAT 3 07-OCT-15 4TTP 1 REMARK REVDAT 2 24-DEC-14 4TTP 1 JRNL REVDAT 1 10-DEC-14 4TTP 0 JRNL AUTH X.GONG,X.CHEN,D.YU,N.ZHANG,Z.ZHU,L.NIU,Y.MAO,H.GE JRNL TITL CRYSTAL STRUCTURE OF LEGIONELLA PNEUMOPHILA DEPHOSPHO-COA JRNL TITL 2 KINASE REVEALS A NON-CANONICAL CONFORMATION OF P-LOOP. JRNL REF J.STRUCT.BIOL. V. 188 233 2014 JRNL REFN ESSN 1095-8657 JRNL PMID 25449315 JRNL DOI 10.1016/J.JSB.2014.10.008 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 12938 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 639 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.9020 - 3.7603 0.93 2497 126 0.1775 0.1948 REMARK 3 2 3.7603 - 2.9852 0.96 2458 120 0.1814 0.2316 REMARK 3 3 2.9852 - 2.6081 0.97 2442 131 0.1983 0.2378 REMARK 3 4 2.6081 - 2.3697 0.98 2471 124 0.2019 0.2458 REMARK 3 5 2.3697 - 2.2000 0.98 2431 138 0.2090 0.2250 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 1648 REMARK 3 ANGLE : 0.699 2231 REMARK 3 CHIRALITY : 0.030 264 REMARK 3 PLANARITY : 0.003 281 REMARK 3 DIHEDRAL : 15.613 636 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4TTP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000202263. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12960 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.15700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 4TTR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CITRATE (PH 5.6), 12%(W/V) REMARK 280 PEG4000, 18%(V/V) 2-PROPANOL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 285K 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 18.11450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.02650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.16500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.02650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.11450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.16500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 MET A -7 REMARK 465 GLY A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 LYS A 2 REMARK 465 GLU A 3 REMARK 465 PRO A 4 REMARK 465 THR A 5 REMARK 465 GLN A 6 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 91 CD REMARK 480 GLU A 117 CD REMARK 480 LEU A 121 C REMARK 480 ASN A 123 CG REMARK 480 GLU A 141 CD 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 183 -145.75 -132.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4TTQ RELATED DB: PDB REMARK 900 RELATED ID: 4TTR RELATED DB: PDB DBREF 4TTP A 7 207 UNP Q5ZVH3 COAE_LEGPH 1 201 SEQADV 4TTP MET A -7 UNP Q5ZVH3 INITIATING METHIONINE SEQADV 4TTP GLY A -6 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTP HIS A -5 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTP HIS A -4 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTP HIS A -3 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTP HIS A -2 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTP HIS A -1 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTP HIS A 0 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTP MET A 1 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTP LYS A 2 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTP GLU A 3 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTP PRO A 4 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTP THR A 5 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTP GLN A 6 UNP Q5ZVH3 EXPRESSION TAG SEQRES 1 A 215 MET GLY HIS HIS HIS HIS HIS HIS MET LYS GLU PRO THR SEQRES 2 A 215 GLN MET VAL TYR SER VAL GLY LEU THR GLY ASN ILE ALA SEQRES 3 A 215 SER GLY LYS SER THR VAL ALA GLU PHE PHE SER GLU LEU SEQRES 4 A 215 GLY ILE ASN VAL ILE TYR ALA ASP LYS ILE ALA LYS GLU SEQRES 5 A 215 LEU THR SER LYS ASN THR PRO CYS TYR GLN ASP ILE ILE SEQRES 6 A 215 SER HIS PHE GLY SER SER VAL VAL LEU ASN ASN GLY GLU SEQRES 7 A 215 LEU ASP ARG LYS ARG ILE ARG ASP ILE ILE PHE SER ASN SEQRES 8 A 215 SER ASN GLU ARG LEU TRP LEU GLU SER LEU LEU HIS PRO SEQRES 9 A 215 VAL ILE ARG LYS LYS ILE GLU GLU GLN LEU ILE VAL CYS SEQRES 10 A 215 THR SER PRO TYR CYS LEU ILE GLU ILE PRO LEU LEU PHE SEQRES 11 A 215 ASN LYS HIS HIS TYR PRO TYR LEU GLN LYS VAL LEU LEU SEQRES 12 A 215 VAL ILE ALA PRO LEU GLU SER GLN LEU ASP ARG ILE VAL SEQRES 13 A 215 LYS ARG ASP HIS CYS THR LYS LYS GLN ALA LEU ALA ILE SEQRES 14 A 215 LEU ALA THR GLN PRO ASN LEU GLU GLN ARG LEU GLU ALA SEQRES 15 A 215 ALA ASP ASP VAL LEU ILE ASN GLU SER GLY LEU SER GLU SEQRES 16 A 215 LEU LYS ALA LYS VAL ASN LYS LEU HIS GLN LYS TYR LEU SEQRES 17 A 215 ARG GLU ALA LYS ILE LYS GLN FORMUL 2 HOH *91(H2 O) HELIX 1 AA1 ILE A 17 SER A 19 5 3 HELIX 2 AA2 GLY A 20 GLU A 30 1 11 HELIX 3 AA3 ALA A 38 THR A 46 1 9 HELIX 4 AA4 THR A 50 GLY A 61 1 12 HELIX 5 AA5 SER A 62 VAL A 65 5 4 HELIX 6 AA6 ASP A 72 ASN A 83 1 12 HELIX 7 AA7 ASN A 83 VAL A 108 1 26 HELIX 8 AA8 ASN A 123 TYR A 127 5 5 HELIX 9 AA9 PRO A 139 HIS A 152 1 14 HELIX 10 AB1 THR A 154 THR A 164 1 11 HELIX 11 AB2 ASN A 167 ALA A 174 1 8 HELIX 12 AB3 GLY A 184 LYS A 206 1 23 SHEET 1 AA1 5 ASN A 34 TYR A 37 0 SHEET 2 AA1 5 CYS A 114 GLU A 117 1 O LEU A 115 N ILE A 36 SHEET 3 AA1 5 SER A 10 GLY A 15 1 N VAL A 11 O ILE A 116 SHEET 4 AA1 5 LYS A 132 ILE A 137 1 O LEU A 134 N GLY A 12 SHEET 5 AA1 5 ASP A 177 ILE A 180 1 O LEU A 179 N LEU A 135 CRYST1 36.229 72.330 96.053 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 0.027602 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013826 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010411 0.00000