HEADER TRANSFERASE 27-JUL-22 8DV0 TITLE CRYSTAL STRUCTURE OF A DEPHOSPHO-COA KINASE FROM RICKETTSIA FELIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEPHOSPHO-COA KINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RIFEA.01444.A.B1; COMPND 5 SYNONYM: DEPHOSPHOCOENZYME A KINASE; COMPND 6 EC: 2.7.1.24; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RICKETTSIA FELIS URRWXCAL2; SOURCE 3 ORGANISM_TAXID: 315456; SOURCE 4 STRAIN: ATCC VR-1525 / URRWXCAL2; SOURCE 5 GENE: COAE, RF_0177; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR KEYWDS 2 INFECTIOUS DISEASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID) REVDAT 2 18-OCT-23 8DV0 1 REMARK REVDAT 1 28-SEP-22 8DV0 0 JRNL AUTH S.J.MAYCLIN,J.ABENDROTH,D.D.LORIMER,P.S.HORANYI,T.E.EDWARDS JRNL TITL CRYSTAL STRUCTURE OF A DEPHOSPHO-COA KINASE FROM RICKETTSIA JRNL TITL 2 FELIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 35776 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.730 REMARK 3 FREE R VALUE TEST SET COUNT : 2051 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 30.6000 - 3.4500 0.98 2287 155 0.1483 0.1851 REMARK 3 2 3.4500 - 2.7400 0.98 2321 123 0.1630 0.2085 REMARK 3 3 2.7400 - 2.3900 0.97 2288 156 0.1652 0.2045 REMARK 3 4 2.3900 - 2.1700 0.97 2250 155 0.1502 0.1909 REMARK 3 5 2.1700 - 2.0200 0.96 2284 130 0.1513 0.2011 REMARK 3 6 2.0200 - 1.9000 0.96 2233 161 0.1529 0.1808 REMARK 3 7 1.9000 - 1.8000 0.95 2272 124 0.1587 0.2277 REMARK 3 8 1.8000 - 1.7300 0.95 2237 133 0.1585 0.1942 REMARK 3 9 1.7300 - 1.6600 0.95 2244 141 0.1462 0.1775 REMARK 3 10 1.6600 - 1.6000 0.94 2229 138 0.1373 0.1885 REMARK 3 11 1.6000 - 1.5500 0.94 2252 132 0.1425 0.1919 REMARK 3 12 1.5500 - 1.5100 0.94 2191 142 0.1477 0.2152 REMARK 3 13 1.5100 - 1.4700 0.94 2196 124 0.1650 0.2385 REMARK 3 14 1.4700 - 1.4300 0.93 2253 126 0.2059 0.2785 REMARK 3 15 1.4300 - 1.4000 0.93 2188 111 0.2429 0.3177 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.49 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.07 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 8DV0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1000267415. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : DIAMOND [111] REMARK 200 OPTICS : BERYLLIUM LENSES REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35777 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 3.957 REMARK 200 R MERGE (I) : 0.02800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.7600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.99 REMARK 200 R MERGE FOR SHELL (I) : 0.62300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.130 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MR-ROSETTA REMARK 200 STARTING MODEL: 4I1U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: WIZARD 3/4 D11 (307537D11): 100 MM REMARK 280 MES/NAOH PH6.5, 200 MM AMMONIUM SULFATE, 30% (W/V) PEG 5000 MME: REMARK 280 RIFEA.01444.A.B1.PW308220 @ 26.35 MG/ML: DEPHOSPHOCOENZYME A @ REMARK 280 6.6MM (DOES NOT APPEAR IN STRUCTURE): CRYOPROTECTED IN RESERVOIR REMARK 280 SUPPLEMENTED WITH 15% ETHYLENE GLYCOL: PUCK/PIN ID: PSD0-3, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 287K 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 ALA 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 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 56 CG CD OE1 OE2 REMARK 470 LYS A 116 CG CD CE NZ REMARK 470 GLU A 128 CG CD OE1 OE2 REMARK 470 LYS A 178 CG CD CE NZ REMARK 470 LYS A 190 CG CD CE NZ 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 413 O HOH A 567 1.76 REMARK 500 O HOH A 443 O HOH A 481 1.80 REMARK 500 O HOH A 519 O HOH A 560 2.10 REMARK 500 SG CYS A 34 O HOH A 550 2.10 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 GLU A 56 -38.08 72.05 REMARK 500 SER A 57 156.62 160.85 REMARK 500 LEU A 109 -8.03 81.14 REMARK 500 REMARK 500 REMARK: NULL DBREF 8DV0 A 1 191 UNP Q4UN30 COAE_RICFE 1 191 SEQADV 8DV0 MET A -7 UNP Q4UN30 INITIATING METHIONINE SEQADV 8DV0 ALA A -6 UNP Q4UN30 EXPRESSION TAG SEQADV 8DV0 HIS A -5 UNP Q4UN30 EXPRESSION TAG SEQADV 8DV0 HIS A -4 UNP Q4UN30 EXPRESSION TAG SEQADV 8DV0 HIS A -3 UNP Q4UN30 EXPRESSION TAG SEQADV 8DV0 HIS A -2 UNP Q4UN30 EXPRESSION TAG SEQADV 8DV0 HIS A -1 UNP Q4UN30 EXPRESSION TAG SEQADV 8DV0 HIS A 0 UNP Q4UN30 EXPRESSION TAG SEQRES 1 A 199 MET ALA HIS HIS HIS HIS HIS HIS MET LEU ALA ILE GLY SEQRES 2 A 199 ILE THR GLY SER TYR ALA SER GLY LYS THR PHE ILE LEU SEQRES 3 A 199 ASP TYR LEU ALA GLU LYS GLY TYR LYS THR PHE CYS ALA SEQRES 4 A 199 ASP ARG CYS ILE LYS GLU LEU TYR GLN ASP LEU SER VAL SEQRES 5 A 199 GLN THR GLN ILE LEU LYS LEU LEU PRO GLU LEU GLU SER SEQRES 6 A 199 PHE ASN ILE GLY LYS ILE SER ASN LEU ILE TYR ASN ASN SEQRES 7 A 199 ASP LEU ALA ARG GLU LYS LEU GLN ASN PHE ILE TYR PRO SEQRES 8 A 199 LEU LEU ILE ASP LYS LEU ILE LEU PHE LYS LYS GLU ASN SEQRES 9 A 199 ALA ASN SER LYS PHE GLY PHE ALA GLU ILE PRO LEU LEU SEQRES 10 A 199 TYR GLU ALA LYS PHE ASP LYS TYR PHE ASP PHE VAL VAL SEQRES 11 A 199 THR ILE TYR CYS SER GLU GLU ILE ARG MET GLN ARG ALA SEQRES 12 A 199 ILE THR ARG THR SER PHE ASP ILE GLU ILE TYR ASN LYS SEQRES 13 A 199 ILE LYS GLU ILE GLN LEU SER GLN GLU SER LYS ILE ALA SEQRES 14 A 199 LYS ALA ASP PHE ALA ILE ASN SER GLY VAL ASP MET LEU SEQRES 15 A 199 ASP LEU GLU LYS GLN ILE GLU LYS LEU ILE LEU VAL ILE SEQRES 16 A 199 ALA ARG LYS LEU HET SO4 A 301 5 HET EDO A 302 4 HET EDO A 303 4 HET SO4 A 304 5 HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 SO4 2(O4 S 2-) FORMUL 3 EDO 2(C2 H6 O2) FORMUL 6 HOH *180(H2 O) HELIX 1 AA1 GLY A 13 LYS A 24 1 12 HELIX 2 AA2 ALA A 31 GLN A 40 1 10 HELIX 3 AA3 ASP A 41 LEU A 52 1 12 HELIX 4 AA4 PRO A 53 GLU A 56 5 4 HELIX 5 AA5 ASN A 59 ASN A 70 1 12 HELIX 6 AA6 ASN A 70 ASN A 96 1 27 HELIX 7 AA7 SER A 127 ARG A 138 1 12 HELIX 8 AA8 ASP A 142 GLN A 153 1 12 HELIX 9 AA9 SER A 155 LYS A 162 1 8 HELIX 10 AB1 ASP A 172 LEU A 191 1 20 SHEET 1 AA1 5 THR A 28 CYS A 30 0 SHEET 2 AA1 5 PHE A 101 GLU A 105 1 O GLU A 105 N PHE A 29 SHEET 3 AA1 5 LEU A 2 GLY A 8 1 N ILE A 4 O GLY A 102 SHEET 4 AA1 5 PHE A 120 TYR A 125 1 O VAL A 122 N GLY A 5 SHEET 5 AA1 5 PHE A 165 ASN A 168 1 O ILE A 167 N THR A 123 CRYST1 35.130 39.680 42.850 107.05 106.87 108.30 P 1 1 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 0.028466 0.009414 0.013921 0.00000 SCALE2 0.000000 0.026544 0.012391 0.00000 SCALE3 0.000000 0.000000 0.026913 0.00000