HEADER TRANSFERASE 18-SEP-23 8U94 TITLE CRYSTAL STRUCTURE OF DEPHOSPHO-COA KINASE FROM KLEBSIELLA AEROGENES TITLE 2 (ADP 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 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 8U94 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 (ADP BOUND) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21RC1_4933: ???) 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) : 24.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 39236 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1955 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 24.0400 - 3.3700 1.00 2743 147 0.1666 0.1974 REMARK 3 2 3.3700 - 2.6800 1.00 2674 142 0.1713 0.1785 REMARK 3 3 2.6800 - 2.3400 1.00 2665 140 0.1613 0.1833 REMARK 3 4 2.3400 - 2.1300 1.00 2691 132 0.1471 0.1682 REMARK 3 5 2.1200 - 1.9700 1.00 2650 161 0.1511 0.1850 REMARK 3 6 1.9700 - 1.8600 1.00 2666 126 0.1677 0.2096 REMARK 3 7 1.8600 - 1.7600 1.00 2676 138 0.1487 0.1814 REMARK 3 8 1.7600 - 1.6900 1.00 2623 147 0.1423 0.2011 REMARK 3 9 1.6900 - 1.6200 1.00 2672 112 0.1603 0.1989 REMARK 3 10 1.6200 - 1.5700 1.00 2679 138 0.1733 0.2445 REMARK 3 11 1.5700 - 1.5200 1.00 2638 127 0.1801 0.2388 REMARK 3 12 1.5200 - 1.4700 1.00 2637 133 0.1882 0.2675 REMARK 3 13 1.4700 - 1.4400 1.00 2655 148 0.2072 0.2733 REMARK 3 14 1.4300 - 1.4000 1.00 2612 164 0.2418 0.3014 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.850 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 1629 REMARK 3 ANGLE : 1.064 2224 REMARK 3 CHIRALITY : 0.070 261 REMARK 3 PLANARITY : 0.013 287 REMARK 3 DIHEDRAL : 14.361 608 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 8U94 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_1000277617. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-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 : 39276 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 49.020 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) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.2000 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) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.92100 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 (%): 41.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 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. 2 HOUR SOAK IN 20MM ADP REMARK 280 IN CRYSTALLANT. PLATE: SS-CLOVER-3/17/23 H7/8, PUCK: PSL-0112, 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 24.50800 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 1 REMARK 465 ALA A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 MET A 9 REMARK 465 GLN A 211 REMARK 465 GLU A 212 REMARK 465 LYS A 213 REMARK 465 PRO A 214 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 HIS A 32 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 127 CG CD NE CZ NH1 NH2 REMARK 470 THR A 129 OG1 CG2 REMARK 470 GLU A 147 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 587 DISTANCE = 6.87 ANGSTROMS DBREF1 8U94 A 9 214 UNP A0A0H3FR62_KLEAK DBREF2 8U94 A A0A0H3FR62 1 206 SEQADV 8U94 MET A 1 UNP A0A0H3FR6 INITIATING METHIONINE SEQADV 8U94 ALA A 2 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8U94 HIS A 3 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8U94 HIS A 4 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8U94 HIS A 5 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8U94 HIS A 6 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8U94 HIS A 7 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8U94 HIS A 8 UNP A0A0H3FR6 EXPRESSION TAG SEQADV 8U94 THR A 10 UNP A0A0H3FR6 GLY 2 ENGINEERED MUTATION SEQADV 8U94 ILE A 135 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 ADP A 301 27 HET MPD A 302 8 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 MPD C6 H14 O2 FORMUL 4 HOH *187(H2 O) HELIX 1 AA1 GLY A 22 LEU A 33 1 12 HELIX 2 AA2 ALA A 40 VAL A 48 1 9 HELIX 3 AA3 THR A 52 GLY A 63 1 12 HELIX 4 AA4 PRO A 64 ILE A 67 5 4 HELIX 5 AA5 ASN A 74 HIS A 85 1 12 HELIX 6 AA6 SER A 86 SER A 111 1 26 HELIX 7 AA7 PRO A 141 GLY A 154 1 14 HELIX 8 AA8 SER A 156 GLN A 167 1 12 HELIX 9 AA9 THR A 169 ALA A 177 1 9 HELIX 10 AB1 SER A 186 SER A 210 1 25 SHEET 1 AA1 5 THR A 36 ASP A 39 0 SHEET 2 AA1 5 LEU A 116 VAL A 119 1 O LEU A 117 N ILE A 38 SHEET 3 AA1 5 THR A 12 THR A 16 1 N LEU A 15 O TRP A 118 SHEET 4 AA1 5 ARG A 134 ASP A 139 1 O LEU A 136 N ALA A 14 SHEET 5 AA1 5 ASP A 179 GLU A 182 1 O ILE A 181 N VAL A 137 CRYST1 32.505 49.016 63.690 90.00 96.71 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 0.030764 0.000000 0.003618 0.00000 SCALE2 0.000000 0.020402 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015809 0.00000