HEADER TRANSFERASE 18-SEP-23 8U97 TITLE CRYSTAL STRUCTURE OF DEPHOSPHO-COA KINASE FROM KLEBSIELLA AEROGENES TITLE 2 (AMP-PNP 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 (SSGCID) REVDAT 1 27-SEP-23 8U97 0 JRNL AUTH L.LIU,S.LOVELL,K.P.BATTAILE,S.SEIBOLD JRNL TITL CRYSTAL STRUCTURE OF DEPHOSPHO-COA KINASE FROM KLEBSIELLA JRNL TITL 2 AEROGENES (AMP-PNP 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 (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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 31746 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1597 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 24.4200 - 3.3300 1.00 2831 133 0.1828 0.2080 REMARK 3 2 3.3300 - 2.6500 1.00 2750 162 0.1929 0.2085 REMARK 3 3 2.6500 - 2.3100 1.00 2732 145 0.1842 0.2111 REMARK 3 4 2.3100 - 2.1000 1.00 2739 172 0.1808 0.2166 REMARK 3 5 2.1000 - 1.9500 1.00 2710 150 0.2015 0.2344 REMARK 3 6 1.9500 - 1.8400 1.00 2722 159 0.2044 0.2530 REMARK 3 7 1.8400 - 1.7400 1.00 2754 127 0.2107 0.2234 REMARK 3 8 1.7400 - 1.6700 1.00 2707 148 0.2276 0.2569 REMARK 3 9 1.6700 - 1.6000 1.00 2749 137 0.2532 0.3622 REMARK 3 10 1.6000 - 1.5500 1.00 2718 127 0.2439 0.3170 REMARK 3 11 1.5500 - 1.5000 1.00 2737 137 0.2729 0.3253 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.550 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 : 0.002 1663 REMARK 3 ANGLE : 0.523 2275 REMARK 3 CHIRALITY : 0.041 265 REMARK 3 PLANARITY : 0.006 295 REMARK 3 DIHEDRAL : 12.990 619 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 8U97 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1000277619. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-23 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 : 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 : 31784 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 63.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.4000 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 : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.93300 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 (%): 41.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MORPHEUS E4: 12.5%(V/V) MPD, REMARK 280 12.5%(V/V) PEG 1000, 12.5%(W/V) PEG 3350, 100 MM IMIDAZOLE/MES, REMARK 280 PH 6.5, 30 MM DIETHYLENE GLYCOL, 30 MM TRIETHYLENEGLYCOL, 30 MM REMARK 280 TETRAETHYLENE GLYCOL AND 30 MM PENTAETHYLENE GLYCOL. REMARK 280 KLAEA.00139.A.B1.PW39166 AT 24.8 MG/ML. 10 MM SOAK IN AMP-PNP REMARK 280 OVERNIGHT. PLATE: SS-CLOVER-3/17/23 WELLS H7, PUCK: PSL-0116, REMARK 280 CRYO: DIRECT, 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 24.42450 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 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 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 THR A 121 45.90 -82.63 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8U97 A 1 206 UNP A0A0H3FR62_KLEAK DBREF2 8U97 A A0A0H3FR62 1 206 SEQADV 8U97 MET A -7 UNP A0A0H3FR6 INITIATING METHIONINE SEQADV 8U97 ALA A -6 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8U97 HIS A -5 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8U97 HIS A -4 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8U97 HIS A -3 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8U97 HIS A -2 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8U97 HIS A -1 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8U97 HIS A 0 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8U97 THR A 2 UNP A0A0H3FR6 GLY 2 ENGINEERED MUTATION SEQADV 8U97 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 ANP A 301 31 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER FORMUL 2 ANP C10 H17 N6 O12 P3 FORMUL 3 HOH *117(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 SER A 78 SER A 103 1 26 HELIX 7 AA7 PRO A 133 GLY A 146 1 14 HELIX 8 AA8 SER A 148 ALA A 158 1 11 HELIX 9 AA9 THR A 161 ALA A 169 1 9 HELIX 10 AB1 SER A 178 SER A 202 1 25 SHEET 1 AA1 5 THR A 28 ASP A 31 0 SHEET 2 AA1 5 LEU A 108 VAL A 111 1 O LEU A 109 N THR A 28 SHEET 3 AA1 5 THR A 4 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 32.306 48.849 63.878 90.00 96.61 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 0.030954 0.000000 0.003587 0.00000 SCALE2 0.000000 0.020471 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015760 0.00000