HEADER HYDROLASE 18-DEC-23 8RII TITLE STRUCTURE OF E166A BLAC FROM MYCOBACTERIUM TUBERCULOSIS AT PH 6.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AMBLER CLASS A BETA-LACTAMASE; COMPND 5 EC: 3.5.2.6; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: BLAC, BLAA, RV2068C, MTCY49.07C; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS BETA-LACTAMASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.SUN,S.BRUENLE,M.UBBINK REVDAT 2 09-OCT-24 8RII 1 REMARK REVDAT 1 28-AUG-24 8RII 0 JRNL AUTH J.SUN,A.L.BOYLE,S.BRUNLE,M.UBBINK JRNL TITL A LOW-BARRIER PROTON SHARED BETWEEN TWO ASPARTATES ACTS AS A JRNL TITL 2 CONFORMATIONAL SWITCH THAT CHANGES THE SUBSTRATE SPECIFICITY JRNL TITL 3 OF THE BETA-LACTAMASE BLAC. JRNL REF INT.J.BIOL.MACROMOL. V. 278 34665 2024 JRNL REFN ISSN 0141-8130 JRNL PMID 39134195 JRNL DOI 10.1016/J.IJBIOMAC.2024.134665 REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 10932 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.273 REMARK 3 R VALUE (WORKING SET) : 0.271 REMARK 3 FREE R VALUE : 0.318 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.650 REMARK 3 FREE R VALUE TEST SET COUNT : 508 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 40.0000 - 3.6500 0.99 2684 159 0.2497 0.2771 REMARK 3 2 3.6500 - 2.9000 0.99 2613 110 0.2664 0.3017 REMARK 3 3 2.9000 - 2.5300 1.00 2584 116 0.3047 0.3786 REMARK 3 4 2.5300 - 2.3000 1.00 2543 123 0.3035 0.4198 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) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.970 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 : 0.003 NULL REMARK 3 ANGLE : 0.689 NULL REMARK 3 CHIRALITY : 0.042 319 REMARK 3 PLANARITY : 0.005 367 REMARK 3 DIHEDRAL : 5.407 293 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 8RII COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1292135428. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10949 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MB1 6.5 PH (BUFFER) 34.643 %W/V REMARK 280 M1K3350 (PRECIPITANT) 0.08 M ALCOHOLS (COMPLEX INGREDIENT), REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 26.92500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.00500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.34000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.00500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.92500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.34000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS A 219 CA - CB - CG ANGL. DEV. = 13.8 DEGREES 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 CYS A 69 -144.83 47.76 REMARK 500 ARG A 220 -122.52 -121.55 REMARK 500 ARG A 267 61.08 -114.89 REMARK 500 REMARK 500 REMARK: NULL DBREF 8RII A 29 293 UNP P9WKD3 BLAC_MYCTU 43 307 SEQADV 8RII ALA A 166 UNP P9WKD3 GLU 182 ENGINEERED MUTATION SEQRES 1 A 265 ASP LEU ALA ASP ARG PHE ALA GLU LEU GLU ARG ARG TYR SEQRES 2 A 265 ASP ALA ARG LEU GLY VAL TYR VAL PRO ALA THR GLY THR SEQRES 3 A 265 THR ALA ALA ILE GLU TYR ARG ALA ASP GLU ARG PHE ALA SEQRES 4 A 265 PHE CYS SER THR PHE LYS ALA PRO LEU VAL ALA ALA VAL SEQRES 5 A 265 LEU HIS GLN ASN PRO LEU THR HIS LEU ASP LYS LEU ILE SEQRES 6 A 265 THR TYR THR SER ASP ASP ILE ARG SER ILE SER PRO VAL SEQRES 7 A 265 ALA GLN GLN HIS VAL GLN THR GLY MET THR ILE GLY GLN SEQRES 8 A 265 LEU CYS ASP ALA ALA ILE ARG TYR SER ASP GLY THR ALA SEQRES 9 A 265 ALA ASN LEU LEU LEU ALA ASP LEU GLY GLY PRO GLY GLY SEQRES 10 A 265 GLY THR ALA ALA PHE THR GLY TYR LEU ARG SER LEU GLY SEQRES 11 A 265 ASP THR VAL SER ARG LEU ASP ALA GLU ALA PRO GLU LEU SEQRES 12 A 265 ASN ARG ASP PRO PRO GLY ASP GLU ARG ASP THR THR THR SEQRES 13 A 265 PRO HIS ALA ILE ALA LEU VAL LEU GLN GLN LEU VAL LEU SEQRES 14 A 265 GLY ASN ALA LEU PRO PRO ASP LYS ARG ALA LEU LEU THR SEQRES 15 A 265 ASP TRP MET ALA ARG ASN THR THR GLY ALA LYS ARG ILE SEQRES 16 A 265 ARG ALA GLY PHE PRO ALA ASP TRP LYS VAL ILE ASP LYS SEQRES 17 A 265 THR GLY THR GLY ASP TYR GLY ARG ALA ASN ASP ILE ALA SEQRES 18 A 265 VAL VAL TRP SER PRO THR GLY VAL PRO TYR VAL VAL ALA SEQRES 19 A 265 VAL MET SER ASP ARG ALA GLY GLY GLY TYR ASP ALA GLU SEQRES 20 A 265 PRO ARG GLU ALA LEU LEU ALA GLU ALA ALA THR CYS VAL SEQRES 21 A 265 ALA GLY VAL LEU ALA FORMUL 2 HOH *80(H2 O) HELIX 1 AA1 ASP A 29 ASP A 42 1 14 HELIX 2 AA2 CYS A 69 THR A 71 5 3 HELIX 3 AA3 PHE A 72 ASN A 86 1 13 HELIX 4 AA4 PRO A 87 ASP A 92 5 6 HELIX 5 AA5 THR A 98 ILE A 102 5 5 HELIX 6 AA6 VAL A 108 HIS A 112 5 5 HELIX 7 AA7 ILE A 119 TYR A 129 1 11 HELIX 8 AA8 ASP A 131 GLY A 144 1 14 HELIX 9 AA9 GLY A 145B LEU A 155 1 13 HELIX 10 AB1 PRO A 167 ARG A 171 5 5 HELIX 11 AB2 THR A 182 LEU A 195 1 14 HELIX 12 AB3 PRO A 200 ARG A 213 1 14 HELIX 13 AB4 ARG A 220 PHE A 225 5 6 HELIX 14 AB5 ARG A 267 GLY A 271 5 5 HELIX 15 AB6 ARG A 277 ALA A 293 1 17 SHEET 1 AA1 5 ILE A 58 TYR A 60 0 SHEET 2 AA1 5 ARG A 44 VAL A 49 -1 N VAL A 49 O ILE A 58 SHEET 3 AA1 5 PRO A 258 ASP A 266 -1 O MET A 264 N GLY A 46 SHEET 4 AA1 5 ARG A 243 TRP A 251 -1 N ALA A 248 O VAL A 261 SHEET 5 AA1 5 LYS A 230 GLY A 238 -1 N GLY A 236 O ASN A 245 SHEET 1 AA2 2 PHE A 66 ALA A 67 0 SHEET 2 AA2 2 THR A 180 THR A 181 -1 O THR A 181 N PHE A 66 SHEET 1 AA3 2 LEU A 94 ILE A 95 0 SHEET 2 AA3 2 MET A 117 THR A 118 -1 O MET A 117 N ILE A 95 CISPEP 1 ALA A 166 PRO A 167 0 2.72 CRYST1 53.850 54.680 80.010 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 0.018570 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018288 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012498 0.00000