HEADER TRANSFERASE 22-JUN-14 4TTR TITLE CRYSTAL STRUCTURE OF LEGIONELLA PNEUMOPHILA DEPHOSPHO-COA KINASE IN TITLE 2 COMPLEX WITH BU2 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 D.YU,H.GE REVDAT 5 27-SEP-23 4TTR 1 REMARK REVDAT 4 08-JAN-20 4TTR 1 REMARK REVDAT 3 07-OCT-15 4TTR 1 REMARK REVDAT 2 24-DEC-14 4TTR 1 JRNL REVDAT 1 10-DEC-14 4TTR 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. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.2 REMARK 3 NUMBER OF REFLECTIONS : 12698 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 : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 651 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 22.7225 - 3.5875 0.87 2617 109 0.1714 0.1816 REMARK 3 2 3.5875 - 2.8492 0.94 2639 166 0.1812 0.2258 REMARK 3 3 2.8492 - 2.4896 0.86 2371 134 0.2071 0.2745 REMARK 3 4 2.4896 - 2.2622 0.90 2460 136 0.2026 0.2510 REMARK 3 5 2.2622 - 2.1002 0.83 1960 106 0.2187 0.2682 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.810 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 1664 REMARK 3 ANGLE : 0.764 2254 REMARK 3 CHIRALITY : 0.031 266 REMARK 3 PLANARITY : 0.002 283 REMARK 3 DIHEDRAL : 14.629 643 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 4TTR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000202265. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 0.97907 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 : 12710 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 22.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.9 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.46700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.600 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: 1JJV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.23 M AMMONIUM CITRATE DIBASIC, REMARK 280 17.5%(W/V) PEG 3350, 0.01 M ATP, 5%(V/V) 1,3-BUTANEDIOL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 18.14500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.10000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.14500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.10000 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: 490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 141 CG CD OE1 OE2 REMARK 470 GLN A 157 CG CD OE1 NE2 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 O HOH A 470 O HOH A 519 1.91 REMARK 500 O HOH A 496 O HOH A 506 1.95 REMARK 500 O THR A 110 O HOH A 401 2.09 REMARK 500 OE2 GLU A 70 O HOH A 402 2.18 REMARK 500 OE2 GLU A 187 O HOH A 477 2.19 REMARK 500 ND2 ASN A 123 O HOH A 511 2.19 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 ASN A 16 -166.24 -77.14 REMARK 500 LEU A 121 50.48 -99.24 REMARK 500 SER A 183 64.89 -162.21 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 BU2 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4TTP RELATED DB: PDB REMARK 900 4TTP CONTAINS THE SAME PROTEIN IN APO-FORM 4TTQ CONTAINS THE SAME REMARK 900 PROTEIN COMPLEXED WITH ATP REMARK 900 RELATED ID: 4TTQ RELATED DB: PDB DBREF 4TTR A 7 207 UNP Q5ZVH3 COAE_LEGPH 1 201 SEQADV 4TTR MET A -7 UNP Q5ZVH3 INITIATING METHIONINE SEQADV 4TTR GLY A -6 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTR HIS A -5 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTR HIS A -4 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTR HIS A -3 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTR HIS A -2 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTR HIS A -1 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTR HIS A 0 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTR MET A 1 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTR LYS A 2 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTR GLU A 3 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTR PRO A 4 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTR THR A 5 UNP Q5ZVH3 EXPRESSION TAG SEQADV 4TTR 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 HET BU2 A 301 6 HET PO4 A 302 5 HETNAM BU2 1,3-BUTANEDIOL HETNAM PO4 PHOSPHATE ION FORMUL 2 BU2 C4 H10 O2 FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *123(H2 O) HELIX 1 AA1 GLY A 20 LEU A 31 1 12 HELIX 2 AA2 ALA A 38 LEU A 45 1 8 HELIX 3 AA3 THR A 50 GLY A 61 1 12 HELIX 4 AA4 SER A 62 VAL A 65 5 4 HELIX 5 AA5 ASP A 72 ASN A 83 1 12 HELIX 6 AA6 ASN A 83 VAL A 108 1 26 HELIX 7 AA7 ASN A 123 TYR A 127 5 5 HELIX 8 AA8 PRO A 139 HIS A 152 1 14 HELIX 9 AA9 THR A 154 THR A 164 1 11 HELIX 10 AB1 LEU A 168 ALA A 175 1 8 HELIX 11 AB2 SER A 183 LYS A 206 1 24 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 CYS A 114 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 ILE A 137 SITE 1 AC1 6 ALA A 18 SER A 19 GLY A 20 LYS A 21 SITE 2 AC1 6 SER A 22 HOH A 490 SITE 1 AC2 2 ARG A 73 HOH A 457 CRYST1 36.290 82.200 81.800 90.00 90.00 90.00 P 21 21 2 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 0.027556 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012165 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012225 0.00000