HEADER TRANSFERASE 20-OCT-17 6BC5 TITLE CRYO X-RAY STRUCTURE OF COENZYME A BOUND AAC-VIA COMPND MOL_ID: 1; COMPND 2 MOLECULE: AAC 3-VI PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AAC-VIA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTER CLOACAE; SOURCE 3 ORGANISM_TAXID: 550; SOURCE 4 GENE: AAC 3-VI; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ACETYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.J.CUNEO,P.KUMAR,E.H.SERPERSU REVDAT 3 04-OCT-23 6BC5 1 REMARK REVDAT 2 12-SEP-18 6BC5 1 JRNL REVDAT 1 28-FEB-18 6BC5 0 JRNL AUTH P.KUMAR,E.H.SERPERSU,M.J.CUNEO JRNL TITL A LOW-BARRIER HYDROGEN BOND MEDIATES ANTIBIOTIC RESISTANCE JRNL TITL 2 IN A NONCANONICAL CATALYTIC TRIAD. JRNL REF SCI ADV V. 4 S8667 2018 JRNL REFN ESSN 2375-2548 JRNL PMID 29632894 JRNL DOI 10.1126/SCIADV.AAS8667 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 14074 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 688 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 39.0401 - 3.7584 0.99 2825 135 0.1519 0.1865 REMARK 3 2 3.7584 - 2.9835 0.98 2753 142 0.1802 0.2104 REMARK 3 3 2.9835 - 2.6065 0.97 2695 146 0.2014 0.2284 REMARK 3 4 2.6065 - 2.3682 0.96 2688 123 0.2042 0.2533 REMARK 3 5 2.3682 - 2.1985 0.87 2425 142 0.2049 0.2575 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.47 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 2152 REMARK 3 ANGLE : 0.583 2953 REMARK 3 CHIRALITY : 0.043 315 REMARK 3 PLANARITY : 0.004 387 REMARK 3 DIHEDRAL : 5.508 1708 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 6BC5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1000230659. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14077 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.48400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PDB ENTRY 6BC6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, PH 5.6, 0.2 M REMARK 280 AMMONIUM ACETATE, 10% GLYCEROL, 17-25% PEG4000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.75933 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.51867 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 41.63900 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 69.39833 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 13.87967 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 TOTAL BURIED SURFACE AREA: 1070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 ASP A 3 REMARK 465 PRO A 4 REMARK 465 ARG A 5 REMARK 465 LYS A 6 REMARK 465 ASN A 7 REMARK 465 GLY A 8 REMARK 465 ASP A 9 REMARK 465 LEU A 10 REMARK 465 HIS A 11 REMARK 465 GLU A 12 REMARK 465 PRO A 13 REMARK 465 ALA A 14 REMARK 465 THR A 15 REMARK 465 ALA A 16 REMARK 465 PRO A 17 REMARK 465 ALA A 18 REMARK 465 PRO A 287 REMARK 465 ALA A 288 REMARK 465 ALA A 289 REMARK 465 ALA A 290 REMARK 465 ALA A 291 REMARK 465 LEU A 292 REMARK 465 LYS A 293 REMARK 465 PRO A 294 REMARK 465 LYS A 295 REMARK 465 GLN A 296 REMARK 465 ARG A 297 REMARK 465 ARG A 298 REMARK 465 ASP A 299 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 NH2 ARG A 201 OD2 ASP A 224 1.50 REMARK 500 NH2 ARG A 201 O HOH A 401 1.99 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 SER A 79 -145.79 57.72 REMARK 500 PRO A 84 43.20 -80.91 REMARK 500 ALA A 184 67.99 -103.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue COA A 301 DBREF 6BC5 A 1 299 UNP Q47030 Q47030_ENTCL 1 299 SEQADV 6BC5 GLY A -2 UNP Q47030 EXPRESSION TAG SEQADV 6BC5 SER A -1 UNP Q47030 EXPRESSION TAG SEQADV 6BC5 HIS A 0 UNP Q47030 EXPRESSION TAG SEQRES 1 A 302 GLY SER HIS MET THR ASP PRO ARG LYS ASN GLY ASP LEU SEQRES 2 A 302 HIS GLU PRO ALA THR ALA PRO ALA THR PRO TRP SER LYS SEQRES 3 A 302 SER GLU LEU VAL ARG GLN LEU ARG ASP LEU GLY VAL ARG SEQRES 4 A 302 SER GLY ASP MET VAL MET PRO HIS VAL SER LEU ARG ALA SEQRES 5 A 302 VAL GLY PRO LEU ALA ASP GLY PRO GLN THR LEU VAL ASP SEQRES 6 A 302 ALA LEU ILE GLU ALA VAL GLY PRO THR GLY ASN ILE LEU SEQRES 7 A 302 ALA PHE VAL SER TRP ARG ASP SER PRO TYR GLU GLN THR SEQRES 8 A 302 LEU GLY HIS ASP ALA PRO PRO ALA ALA ILE ALA GLN SER SEQRES 9 A 302 TRP PRO ALA PHE ASP PRO ASP HIS ALA PRO ALA TYR PRO SEQRES 10 A 302 GLY PHE GLY ALA ILE ASN GLU PHE ILE ARG THR TYR PRO SEQRES 11 A 302 GLY CYS ARG ARG THR ALA HIS PRO ASP ALA SER MET ALA SEQRES 12 A 302 ALA ILE GLY PRO ASP ALA ALA TRP LEU VAL ALA PRO HIS SEQRES 13 A 302 GLU MET GLY ALA ALA TYR GLY PRO ARG SER PRO ILE ALA SEQRES 14 A 302 ARG PHE LEU ALA HIS ALA GLY LYS ILE LEU SER ILE GLY SEQRES 15 A 302 ALA GLY PRO ASP ALA VAL THR ALA LEU HIS TYR ALA GLU SEQRES 16 A 302 ALA VAL ALA ARG ILE GLU GLY LYS ARG ARG VAL THR TYR SEQRES 17 A 302 SER MET PRO LEU LEU ARG GLU GLY LYS ARG VAL TRP VAL SEQRES 18 A 302 THR THR SER ASP TRP ASP SER ASN GLY ILE LEU ASP GLU SEQRES 19 A 302 TYR ALA ALA PRO ASP GLY PRO ASP ALA VAL GLU ARG ILE SEQRES 20 A 302 ALA ARG ASP TYR LEU ALA ARG THR ARG VAL ALA GLN GLY SEQRES 21 A 302 PRO VAL GLY GLY ALA GLN SER ARG LEU ILE ASP ALA ALA SEQRES 22 A 302 ASP ILE VAL SER PHE GLY ILE GLU TRP LEU GLU ALA ARG SEQRES 23 A 302 HIS ALA ALA PRO ALA ALA ALA ALA LEU LYS PRO LYS GLN SEQRES 24 A 302 ARG ARG ASP HET COA A 301 48 HETNAM COA COENZYME A FORMUL 2 COA C21 H36 N7 O16 P3 S FORMUL 3 HOH *129(H2 O) HELIX 1 AA1 SER A 22 GLY A 34 1 13 HELIX 2 AA2 SER A 46 GLY A 51 1 6 HELIX 3 AA3 GLY A 56 GLY A 69 1 14 HELIX 4 AA4 PRO A 84 LEU A 89 1 6 HELIX 5 AA5 PRO A 95 TRP A 102 1 8 HELIX 6 AA6 TYR A 113 GLY A 117 5 5 HELIX 7 AA7 ALA A 118 THR A 125 1 8 HELIX 8 AA8 ASP A 145 ALA A 151 1 7 HELIX 9 AA9 SER A 163 ALA A 170 1 8 HELIX 10 AB1 ALA A 187 ALA A 195 1 9 HELIX 11 AB2 LEU A 229 ALA A 233 5 5 HELIX 12 AB3 ASP A 239 THR A 252 1 14 HELIX 13 AB4 ALA A 269 HIS A 284 1 16 SHEET 1 AA1 7 ARG A 130 ARG A 131 0 SHEET 2 AA1 7 MET A 139 ILE A 142 -1 O ALA A 141 N ARG A 130 SHEET 3 AA1 7 ASN A 73 PHE A 77 -1 N ALA A 76 O ALA A 140 SHEET 4 AA1 7 MET A 40 VAL A 45 1 N VAL A 41 O ASN A 73 SHEET 5 AA1 7 LYS A 174 ILE A 178 1 O ILE A 178 N HIS A 44 SHEET 6 AA1 7 ALA A 262 ASP A 268 -1 O ILE A 267 N ILE A 175 SHEET 7 AA1 7 ALA A 255 VAL A 259 -1 N GLY A 257 O SER A 264 SHEET 1 AA2 2 ARG A 202 ARG A 211 0 SHEET 2 AA2 2 LYS A 214 TRP A 223 -1 O VAL A 216 N LEU A 209 CISPEP 1 ALA A 151 PRO A 152 0 -0.49 CISPEP 2 ASP A 236 GLY A 237 0 -7.28 SITE 1 AC1 16 ARG A 28 HIS A 44 VAL A 45 SER A 46 SITE 2 AC1 16 LEU A 47 ARG A 48 PHE A 116 GLY A 117 SITE 3 AC1 16 ALA A 118 PHE A 122 ALA A 184 THR A 186 SITE 4 AC1 16 HIS A 189 HOH A 446 HOH A 490 HOH A 502 CRYST1 78.068 78.068 83.278 90.00 90.00 120.00 P 61 6 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 0.012809 0.007395 0.000000 0.00000 SCALE2 0.000000 0.014791 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012008 0.00000