HEADER HYDROLASE 29-AUG-25 9WIP TITLE CRYSTAL STRUCTURE OF ADC-227 IN THE FREE FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.2.6; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: GENBANK:MN603401.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACINETOBACTER BAUMANNII; SOURCE 3 ORGANISM_TAXID: 470; SOURCE 4 GENE: AMPC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETE-LACATMASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.KAWAI,Y.DOI REVDAT 1 25-MAR-26 9WIP 0 JRNL AUTH A.KAWAI,Y.DOI JRNL TITL STABLE CEFIDEROCOL RESISTANCE MEDIATED BY A VALINE JRNL TITL 2 SUBSTITUTION AT POSITION 293 COMBINED WITH AN ALANINE JRNL TITL 3 DUPLICATION IN THE OMEGA LOOP OF ADC BETA-LACTAMASE IN JRNL TITL 4 ACINETOBACTER BAUMANNII JRNL REF MBIO 2026 JRNL REFN ESSN 2150-7511 JRNL DOI 10.1128/MBIO.03518-25 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.20.1 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 24400 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1220 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 2.0200 - 1.9500 0.96 2564 129 0.2980 0.3550 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 9WIP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1300063104. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24405 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 48.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 19.30 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.98900 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: MOLREP REMARK 200 STARTING MODEL: 4QD4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, AND 0.1 M HEPES-NAOH, PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 32.61067 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 65.22133 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 65.22133 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 32.61067 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: 160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 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 MET A -2 REMARK 465 ALA A -1 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 GLU A 21 CG CD OE1 OE2 REMARK 470 GLN A 49 CG CD OE1 NE2 REMARK 470 ASP A 123 CG OD1 OD2 REMARK 470 ARG A 214 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 345 CG CD OE1 OE2 REMARK 470 LYS A 359 CG CD CE NZ 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 116 57.60 -163.99 REMARK 500 LYS A 141 -138.07 -94.96 REMARK 500 LYS A 141 -137.69 -94.96 REMARK 500 THR A 177 -57.19 -120.89 REMARK 500 ASN A 204 -162.59 -79.73 REMARK 500 TYR A 223 35.84 -159.82 REMARK 500 VAL A 263 -65.71 -97.24 REMARK 500 ASN A 264 -116.54 -145.33 REMARK 500 ALA A 269 -169.23 -101.40 REMARK 500 THR A 317 -165.51 -119.03 REMARK 500 LYS A 359 99.55 -60.61 REMARK 500 REMARK 500 REMARK: NULL DBREF 9WIP A -2 360 PDB 9WIP 9WIP -2 360 SEQRES 1 A 363 MET ALA GLY ASN THR PRO LYS ASP GLN GLU ILE LYS LYS SEQRES 2 A 363 LEU VAL ASP GLN ASN PHE LYS PRO LEU LEU GLU LYS TYR SEQRES 3 A 363 ASP VAL PRO GLY MET ALA VAL GLY VAL ILE GLN ASN ASN SEQRES 4 A 363 LYS LYS TYR GLU MET TYR TYR GLY LEU GLN SER VAL GLN SEQRES 5 A 363 ASP LYS LYS ALA VAL ASN SER SER THR ILE PHE GLU LEU SEQRES 6 A 363 GLY SER VAL SER LYS LEU PHE THR ALA THR ALA GLY GLY SEQRES 7 A 363 TYR ALA LYS ASN LYS GLY LYS ILE SER PHE ASP ASP THR SEQRES 8 A 363 PRO GLY LYS TYR TRP LYS GLU LEU LYS ASN THR PRO ILE SEQRES 9 A 363 ASP GLN VAL ASN LEU LEU GLN LEU ALA THR TYR THR SER SEQRES 10 A 363 GLY ASN LEU ALA LEU GLN PHE PRO ASP GLU VAL LYS THR SEQRES 11 A 363 ASP GLN GLN VAL LEU THR PHE PHE LYS ASP TRP LYS PRO SEQRES 12 A 363 LYS ASN SER ILE GLY GLU TYR ARG GLN TYR SER ASN PRO SEQRES 13 A 363 SER ILE GLY LEU PHE GLY LYS VAL VAL ALA LEU SER MET SEQRES 14 A 363 ASN LYS PRO PHE ASP GLN VAL LEU GLU LYS THR ILE PHE SEQRES 15 A 363 PRO ALA LEU GLY LEU LYS HIS SER TYR VAL ASN VAL PRO SEQRES 16 A 363 LYS THR GLN MET GLN ASN TYR ALA PHE GLY TYR ASN GLN SEQRES 17 A 363 GLU ASN GLN PRO ILE ARG VAL ASN ARG GLY PRO LEU ASP SEQRES 18 A 363 ALA ALA PRO ALA TYR GLY VAL LYS SER THR LEU PRO ASP SEQRES 19 A 363 MET LEU LYS PHE ILE HIS ALA ASN LEU ASN PRO GLN LYS SEQRES 20 A 363 TYR PRO THR ASP ILE GLN ARG ALA ILE ASN GLU THR HIS SEQRES 21 A 363 GLN GLY ARG TYR GLN VAL ASN THR MET TYR GLN ALA LEU SEQRES 22 A 363 GLY TRP GLU GLU PHE SER TYR PRO ALA THR LEU GLN THR SEQRES 23 A 363 LEU LEU ASP SER ASN SER GLU GLN ILE TRP MET LYS PRO SEQRES 24 A 363 ASN LYS VAL THR ALA ILE SER LYS GLU PRO SER VAL LYS SEQRES 25 A 363 MET TYR HIS LYS THR GLY SER THR THR GLY PHE GLY THR SEQRES 26 A 363 TYR VAL VAL PHE ILE PRO LYS GLU ASN ILE GLY LEU VAL SEQRES 27 A 363 MET LEU THR ASN LYS ARG ILE PRO ASN GLU GLU ARG ILE SEQRES 28 A 363 LYS ALA ALA TYR ALA VAL LEU ASN ALA ILE LYS GLU HET EPE A 401 15 HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 2 EPE C8 H18 N2 O4 S FORMUL 3 HOH *158(H2 O) HELIX 1 AA1 THR A 2 PHE A 16 1 15 HELIX 2 AA2 PHE A 16 ASP A 24 1 9 HELIX 3 AA3 GLY A 63 VAL A 65 5 3 HELIX 4 AA4 SER A 66 LYS A 80 1 15 HELIX 5 AA5 THR A 88 TYR A 92 5 5 HELIX 6 AA6 TRP A 93 LYS A 97 5 5 HELIX 7 AA7 THR A 99 VAL A 104 5 6 HELIX 8 AA8 ASN A 105 THR A 111 1 7 HELIX 9 AA9 THR A 127 ASP A 137 1 11 HELIX 10 AB1 SER A 151 MET A 166 1 16 HELIX 11 AB2 PRO A 169 THR A 177 1 9 HELIX 12 AB3 THR A 177 GLY A 183 1 7 HELIX 13 AB4 PRO A 192 TYR A 199 5 8 HELIX 14 AB5 PRO A 216 ASP A 218 5 3 HELIX 15 AB6 ALA A 219 GLY A 224 1 6 HELIX 16 AB7 THR A 228 ASN A 241 1 14 HELIX 17 AB8 PRO A 242 TYR A 245 5 4 HELIX 18 AB9 PRO A 246 HIS A 257 1 12 HELIX 19 AC1 THR A 280 SER A 287 1 8 HELIX 20 AC2 SER A 289 MET A 294 1 6 HELIX 21 AC3 PRO A 343 LYS A 359 1 17 SHEET 1 AA1 9 LYS A 52 ALA A 53 0 SHEET 2 AA1 9 LYS A 37 SER A 47 -1 N GLN A 46 O LYS A 52 SHEET 3 AA1 9 GLY A 27 GLN A 34 -1 N MET A 28 O TYR A 43 SHEET 4 AA1 9 ILE A 332 THR A 338 -1 O LEU A 337 N ALA A 29 SHEET 5 AA1 9 GLY A 321 ILE A 327 -1 N ILE A 327 O ILE A 332 SHEET 6 AA1 9 LYS A 309 SER A 316 -1 N GLY A 315 O THR A 322 SHEET 7 AA1 9 GLU A 273 SER A 276 -1 N PHE A 275 O MET A 310 SHEET 8 AA1 9 MET A 266 GLN A 268 -1 N TYR A 267 O GLU A 274 SHEET 9 AA1 9 TYR A 261 GLN A 262 -1 N TYR A 261 O GLN A 268 SHEET 1 AA2 2 PHE A 60 GLU A 61 0 SHEET 2 AA2 2 LYS A 226 SER A 227 -1 O SER A 227 N PHE A 60 SHEET 1 AA3 2 TYR A 147 ARG A 148 0 SHEET 2 AA3 2 ASN A 297 LYS A 298 -1 O ASN A 297 N ARG A 148 SHEET 1 AA4 2 GLY A 202 TYR A 203 0 SHEET 2 AA4 2 PRO A 209 ILE A 210 -1 O ILE A 210 N GLY A 202 CISPEP 1 TYR A 277 PRO A 278 0 2.67 CRYST1 76.008 76.008 97.832 90.00 90.00 120.00 P 31 2 1 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 0.013157 0.007596 0.000000 0.00000 SCALE2 0.000000 0.015192 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010222 0.00000 CONECT 2864 2865 2869 2873 CONECT 2865 2864 2866 CONECT 2866 2865 2867 CONECT 2867 2866 2868 2870 CONECT 2868 2867 2869 CONECT 2869 2864 2868 CONECT 2870 2867 2871 CONECT 2871 2870 2872 CONECT 2872 2871 CONECT 2873 2864 2874 CONECT 2874 2873 2875 CONECT 2875 2874 2876 2877 2878 CONECT 2876 2875 CONECT 2877 2875 CONECT 2878 2875 MASTER 249 0 1 21 15 0 0 6 3027 1 15 28 END