HEADER TRANSFERASE 02-OCT-24 9DUG TITLE CRYSTAL STRUCTURE OF DEPHOSPHO-COA KINASE FROM KLEBSIELLA AEROGENES TITLE 2 (SULFATE BOUND) 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,SEATTLE AUTHOR 2 STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID) REVDAT 1 16-OCT-24 9DUG 0 JRNL AUTH L.LIU,S.LOVELL,K.P.BATTAILE JRNL TITL CRYSTAL STRUCTURE OF DEPHOSPHO-COA KINASE FROM KLEBSIELLA JRNL TITL 2 AEROGENES (SULFATE BOUND) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_5462: ???) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 32885 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.830 REMARK 3 FREE R VALUE TEST SET COUNT : 1588 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 47.4600 - 3.3400 1.00 3027 156 0.1620 0.1919 REMARK 3 2 3.3400 - 2.6500 1.00 2902 148 0.1645 0.1825 REMARK 3 3 2.6500 - 2.3100 1.00 2849 146 0.1433 0.1970 REMARK 3 4 2.3100 - 2.1000 1.00 2831 148 0.1308 0.1857 REMARK 3 5 2.1000 - 1.9500 1.00 2825 147 0.1307 0.1827 REMARK 3 6 1.9500 - 1.8400 1.00 2833 143 0.1420 0.2008 REMARK 3 7 1.8400 - 1.7400 1.00 2826 147 0.1539 0.1941 REMARK 3 8 1.7400 - 1.6700 1.00 2805 124 0.1580 0.2597 REMARK 3 9 1.6700 - 1.6000 1.00 2798 148 0.1664 0.2322 REMARK 3 10 1.6000 - 1.5500 1.00 2801 135 0.1835 0.2634 REMARK 3 11 1.5500 - 1.5000 1.00 2800 146 0.2053 0.2622 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.580 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 : 0.008 1717 REMARK 3 ANGLE : 0.871 2341 REMARK 3 CHIRALITY : 0.051 269 REMARK 3 PLANARITY : 0.012 303 REMARK 3 DIHEDRAL : 12.992 630 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 9DUG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1000288856. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-AUG-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.9786 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 : 32947 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 94.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 8.60 REMARK 200 R MERGE FOR SHELL (I) : 1.20800 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 (%): 41.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTAL SCREEN D3: 2.0 M AMMONIUM REMARK 280 SULFATE, 0.1 M HEPES PH 7.5, 2% (V/V) PEG 400. REMARK 280 KLAEA.00139.A.B1.PW39166 AT 24.8 MG/ML. PLATE 13976 WELL D3 DROP REMARK 280 2, PUCK: PSL-2011, CRYO: 2.5 M AMMONIUM SULFATE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K 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 21.40050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.45800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.61400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.45800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.40050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.61400 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 MET A -7 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 GLN A 203 CG CD OE1 NE2 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 175 36.07 -87.73 REMARK 500 REMARK 500 REMARK: NULL DBREF1 9DUG A 1 206 UNP A0A0H3FR62_KLEAK DBREF2 9DUG A A0A0H3FR62 1 206 SEQADV 9DUG MET A -7 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 9DUG ALA A -6 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 9DUG HIS A -5 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 9DUG HIS A -4 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 9DUG HIS A -3 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 9DUG HIS A -2 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 9DUG HIS A -1 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 9DUG HIS A 0 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 9DUG THR A 2 UNP A0A0H3FR6 GLY 2 ENGINEERED MUTATION SEQADV 9DUG 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 SO4 A 301 5 HET SO4 A 302 5 HET SO4 A 303 5 HET SO4 A 304 5 HET SO4 A 305 5 HET SO4 A 306 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 6(O4 S 2-) FORMUL 8 HOH *218(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 HIS A 77 SER A 103 1 27 HELIX 7 AA7 LEU A 120 ALA A 124 5 5 HELIX 8 AA8 PRO A 133 GLY A 146 1 14 HELIX 9 AA9 SER A 148 ALA A 157 1 10 HELIX 10 AB1 THR A 161 ALA A 167 1 7 HELIX 11 AB2 SER A 178 ALA A 201 1 24 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 ILE A 30 SHEET 3 AA1 5 TYR A 3 THR A 8 1 N VAL A 5 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 ASP A 131 CRYST1 42.801 49.228 94.916 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 0.023364 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020314 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010536 0.00000