HEADER TRANSFERASE 03-APR-23 8SBN TITLE CRYSTAL STRUCTURE OF DEPHOSPHO-COA KINASE FROM KLEBSIELLA AEROGENES TITLE 2 (P21 FORM 1) 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; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA AEROGENES KCTC 2190; SOURCE 3 ORGANISM_TAXID: 1028307; SOURCE 4 GENE: COAE, EAE_11320; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: KLAEA.00139.A.B1 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 1 12-APR-23 8SBN 0 JRNL AUTH S.SEIBOLD,S.LOVELL,L.LIU,K.P.BATTAILE JRNL TITL CRYSTAL STRUCTURE OF DEPHOSPHO-COA KINASE FROM KLEBSIELLA JRNL TITL 2 AEROGENES (P21 FORM 1) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21RC1_4918: ???) 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) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 68044 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 3343 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 30.7700 - 3.3200 1.00 2816 146 0.1479 0.1644 REMARK 3 2 3.3200 - 2.6300 1.00 2749 162 0.1433 0.1948 REMARK 3 3 2.6300 - 2.3000 1.00 2785 119 0.1384 0.1603 REMARK 3 4 2.3000 - 2.0900 1.00 2743 139 0.1297 0.1552 REMARK 3 5 2.0900 - 1.9400 1.00 2742 128 0.1283 0.1326 REMARK 3 6 1.9400 - 1.8300 1.00 2705 157 0.1340 0.1544 REMARK 3 7 1.8300 - 1.7300 1.00 2768 139 0.1196 0.1420 REMARK 3 8 1.7300 - 1.6600 1.00 2764 131 0.1200 0.1548 REMARK 3 9 1.6600 - 1.5900 1.00 2710 147 0.1175 0.1355 REMARK 3 10 1.5900 - 1.5400 1.00 2720 131 0.1234 0.1374 REMARK 3 11 1.5400 - 1.4900 1.00 2736 151 0.1225 0.1621 REMARK 3 12 1.4900 - 1.4500 1.00 2735 151 0.1302 0.1845 REMARK 3 13 1.4500 - 1.4100 1.00 2684 153 0.1340 0.1454 REMARK 3 14 1.4100 - 1.3800 1.00 2760 136 0.1340 0.1686 REMARK 3 15 1.3800 - 1.3500 1.00 2685 131 0.1335 0.1683 REMARK 3 16 1.3500 - 1.3200 1.00 2763 134 0.1427 0.1513 REMARK 3 17 1.3200 - 1.2900 1.00 2705 125 0.1466 0.1778 REMARK 3 18 1.2900 - 1.2700 1.00 2744 160 0.1528 0.2123 REMARK 3 19 1.2700 - 1.2400 1.00 2697 143 0.1622 0.1772 REMARK 3 20 1.2400 - 1.2200 1.00 2737 138 0.1750 0.1858 REMARK 3 21 1.2200 - 1.2000 0.99 2671 146 0.1883 0.2445 REMARK 3 22 1.2000 - 1.1800 0.98 2656 143 0.2037 0.2028 REMARK 3 23 1.1800 - 1.1700 0.90 2448 129 0.2217 0.2460 REMARK 3 24 1.1700 - 1.1500 0.80 2178 104 0.2436 0.2633 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.790 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 : 0.007 1736 REMARK 3 ANGLE : 0.914 2364 REMARK 3 CHIRALITY : 0.070 273 REMARK 3 PLANARITY : 0.012 311 REMARK 3 DIHEDRAL : 13.578 696 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 8SBN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-APR-23. REMARK 100 THE DEPOSITION ID IS D_1000273441. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68101 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 48.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.17 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.63700 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BERKELEY H6: 20% (W/V) PEG 1500, 12% REMARK 280 (W/V) 1,6-HEXANEDIOL, 100 MM MES PH5.5, 100 MM CACL2. 2MM COA REMARK 280 ADDED PRIOR TO CRYSTALLIZATION BUT NOT OBSERVED IN THE ELECTRON REMARK 280 DENSITY. KLAEA.00139.A.B1.PW39166 AT 24.8 MG/ML. PLATE: 13151, REMARK 280 WELL H6 DROP 3, PUCK: PSL-1415, CRYO: 80% BERKELEY H6 + 20% PEG REMARK 280 200, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 24.36650 REMARK 290 SMTRY3 2 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 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLN A 203 REMARK 465 GLU A 204 REMARK 465 LYS A 205 REMARK 465 PRO A 206 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 LEU A 114 CG CD1 CD2 REMARK 470 GLU A 163 CG CD OE1 OE2 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 676 DISTANCE = 6.26 ANGSTROMS DBREF1 8SBN A 1 206 UNP A0A0H3FR62_KLEAK DBREF2 8SBN A A0A0H3FR62 1 206 SEQADV 8SBN MET A -7 UNP A0A0H3FR6 INITIATING METHIONINE SEQADV 8SBN ALA A -6 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8SBN HIS A -5 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8SBN HIS A -4 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8SBN HIS A -3 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8SBN HIS A -2 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8SBN HIS A -1 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8SBN HIS A 0 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8SBN THR A 2 UNP A0A0H3FR6 GLY 2 ENGINEERED MUTATION SEQADV 8SBN ILE A 127 UNP A0A0H3FR6 VAL 127 ENGINEERED MUTATION SEQRES 1 A 214 MET ALA HIS HIS HIS HIS HIS HIS MET THR TYR THR VAL SEQRES 2 A 214 ALA LEU THR GLY GLY ILE GLY SER GLY LYS SER THR VAL SEQRES 3 A 214 ALA ASP GLU PHE ALA HIS LEU GLY VAL THR VAL ILE ASP SEQRES 4 A 214 ALA ASP ILE ILE ALA ARG GLN VAL VAL GLU PRO GLY THR SEQRES 5 A 214 PRO ALA LEU LEU ALA ILE ALA GLU ARG PHE GLY PRO GLN SEQRES 6 A 214 MET ILE ASN ASP ASP GLY SER LEU ASN ARG ARG ARG LEU SEQRES 7 A 214 ARG GLU ARG ILE PHE ALA HIS SER GLU ASP LYS ALA TRP SEQRES 8 A 214 LEU ASN ALA LEU LEU HIS PRO LEU ILE GLN GLN GLU THR SEQRES 9 A 214 ARG ARG GLN MET GLN ALA SER THR SER PRO TYR LEU LEU SEQRES 10 A 214 TRP VAL VAL PRO LEU LEU VAL GLU ASN ARG LEU THR ASP SEQRES 11 A 214 LYS ALA ASP ARG ILE LEU VAL VAL ASP VAL PRO LYS GLU SEQRES 12 A 214 THR GLN ILE GLU ARG THR ILE ARG ARG ASP GLY VAL SER SEQRES 13 A 214 ARG GLU HIS ALA GLU HIS ILE LEU ALA ALA GLN ALA THR SEQRES 14 A 214 ARG GLU GLN ARG LEU ALA ALA ALA ASP ASP VAL ILE GLU SEQRES 15 A 214 ASN MET GLY SER ALA ASP ALA VAL ALA SER HIS VAL ALA SEQRES 16 A 214 ARG LEU HIS ASP LYS TYR LEU MET LEU ALA SER GLN ALA SEQRES 17 A 214 ALA SER GLN GLU LYS PRO HET HEZ A 301 8 HET HEZ A 302 16 HET HEZ A 303 8 HET GOL A 304 6 HET GOL A 305 6 HET CL A 306 1 HETNAM HEZ HEXANE-1,6-DIOL HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 HEZ 3(C6 H14 O2) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 7 CL CL 1- FORMUL 8 HOH *276(H2 O) HELIX 1 AA1 GLY A 14 LEU A 25 1 12 HELIX 2 AA2 ALA A 32 VAL A 39 1 8 HELIX 3 AA3 THR A 44 GLY A 55 1 12 HELIX 4 AA4 PRO A 56 ILE A 59 5 4 HELIX 5 AA5 ASN A 66 HIS A 77 1 12 HELIX 6 AA6 ASP A 80 SER A 103 1 24 HELIX 7 AA7 ARG A 119 LYS A 123 5 5 HELIX 8 AA8 PRO A 133 GLY A 146 1 14 HELIX 9 AA9 SER A 148 GLN A 159 1 12 HELIX 10 AB1 THR A 161 ALA A 169 1 9 HELIX 11 AB2 SER A 178 SER A 202 1 25 SHEET 1 AA1 5 THR A 28 ASP A 31 0 SHEET 2 AA1 5 TYR A 107 VAL A 111 1 O LEU A 109 N THR A 28 SHEET 3 AA1 5 TYR A 3 THR A 8 1 N LEU A 7 O TRP A 110 SHEET 4 AA1 5 ARG A 126 ASP A 131 1 O LEU A 128 N ALA A 6 SHEET 5 AA1 5 ASP A 171 GLU A 174 1 O ILE A 173 N VAL A 129 CRYST1 30.905 48.733 65.730 90.00 95.42 90.00 P 1 21 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 0.032357 0.000000 0.003071 0.00000 SCALE2 0.000000 0.020520 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015282 0.00000