HEADER HYDROLASE 27-NOV-24 9HIT TITLE STRUCTURE OF P167S/D240G BLAC FROM MYCOBACTERIUM TUBERCULOSIS 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: BLAC, BLAA, BQ2027_MB2094C; 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 1 22-OCT-25 9HIT 0 JRNL AUTH J.SUN,M.TIMMER,S.BRUNLE,A.L.BOYLE,M.UBBINK JRNL TITL DIRECTED EVOLUTION OF A BETA-LACTAMASE SAMPLES A WIDE JRNL TITL 2 VARIETY OF CONFORMATIONAL STATES. JRNL REF PROTEIN SCI. V. 34 70322 2025 JRNL REFN ESSN 1469-896X JRNL PMID 41074874 JRNL DOI 10.1002/PRO.70322 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 1.0 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 55067 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 2565 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1989 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 264 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.30000 REMARK 3 B22 (A**2) : -0.39000 REMARK 3 B33 (A**2) : 0.73000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.36000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.051 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.046 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.036 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.001 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 9HIT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1292143381. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-SEP-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 : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55085 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 38.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 1.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 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 (%): 39.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE PH 6.07 1.16 M REMARK 280 TRISODIUM CITRATE (PRECIPITANT), VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 27.22400 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 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 O HOH A 489 O HOH A 580 1.90 REMARK 500 O HOH A 554 O HOH A 612 1.96 REMARK 500 O HOH A 552 O HOH A 656 2.05 REMARK 500 OH TYR A 41 OE2 GLU A 283 2.09 REMARK 500 O HOH A 535 O HOH A 611 2.11 REMARK 500 O HOH A 486 O HOH A 613 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 128 NE - CZ - NH1 ANGL. DEV. = 3.3 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 -145.42 49.32 REMARK 500 SER A 104 -171.18 55.95 REMARK 500 ARG A 220 -120.51 -114.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 39 0.11 SIDE CHAIN REMARK 500 ARG A 103 0.14 SIDE CHAIN REMARK 500 ARG A 267 0.19 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL 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 662 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 663 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH A 664 DISTANCE = 10.56 ANGSTROMS DBREF 9HIT A 28 293 UNP P0A5I7 BLAC_MYCBO 42 307 SEQADV 9HIT SER A 167 UNP P0A5I7 PRO 183 ENGINEERED MUTATION SEQADV 9HIT GLY A 240 UNP P0A5I7 ASP 255 ENGINEERED MUTATION SEQRES 1 A 266 ALA ASP LEU ALA ASP ARG PHE ALA GLU LEU GLU ARG ARG SEQRES 2 A 266 TYR ASP ALA ARG LEU GLY VAL TYR VAL PRO ALA THR GLY SEQRES 3 A 266 THR THR ALA ALA ILE GLU TYR ARG ALA ASP GLU ARG PHE SEQRES 4 A 266 ALA PHE CYS SER THR PHE LYS ALA PRO LEU VAL ALA ALA SEQRES 5 A 266 VAL LEU HIS GLN ASN PRO LEU THR HIS LEU ASP LYS LEU SEQRES 6 A 266 ILE THR TYR THR SER ASP ASP ILE ARG SER ILE SER PRO SEQRES 7 A 266 VAL ALA GLN GLN HIS VAL GLN THR GLY MET THR ILE GLY SEQRES 8 A 266 GLN LEU CYS ASP ALA ALA ILE ARG TYR SER ASP GLY THR SEQRES 9 A 266 ALA ALA ASN LEU LEU LEU ALA ASP LEU GLY GLY PRO GLY SEQRES 10 A 266 GLY GLY THR ALA ALA PHE THR GLY TYR LEU ARG SER LEU SEQRES 11 A 266 GLY ASP THR VAL SER ARG LEU ASP ALA GLU GLU SER GLU SEQRES 12 A 266 LEU ASN ARG ASP PRO PRO GLY ASP GLU ARG ASP THR THR SEQRES 13 A 266 THR PRO HIS ALA ILE ALA LEU VAL LEU GLN GLN LEU VAL SEQRES 14 A 266 LEU GLY ASN ALA LEU PRO PRO ASP LYS ARG ALA LEU LEU SEQRES 15 A 266 THR ASP TRP MET ALA ARG ASN THR THR GLY ALA LYS ARG SEQRES 16 A 266 ILE ARG ALA GLY PHE PRO ALA ASP TRP LYS VAL ILE ASP SEQRES 17 A 266 LYS THR GLY THR GLY GLY TYR GLY ARG ALA ASN ASP ILE SEQRES 18 A 266 ALA VAL VAL TRP SER PRO THR GLY VAL PRO TYR VAL VAL SEQRES 19 A 266 ALA VAL MET SER ASP ARG ALA GLY GLY GLY TYR ASP ALA SEQRES 20 A 266 GLU PRO ARG GLU ALA LEU LEU ALA GLU ALA ALA THR CYS SEQRES 21 A 266 VAL ALA GLY VAL LEU ALA HET CIT A 301 13 HETNAM CIT CITRIC ACID FORMUL 2 CIT C6 H8 O7 FORMUL 3 HOH *264(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 143 1 13 HELIX 9 AA9 PRO A 145 GLY A 145B 5 3 HELIX 10 AB1 GLY A 145C LEU A 155 1 12 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 1 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 47 O TYR A 60 SHEET 3 AA1 5 PRO A 258 ASP A 266 -1 O ASP A 266 N ARG A 44 SHEET 4 AA1 5 ALA A 244 TRP A 251 -1 N VAL A 250 O TYR A 259 SHEET 5 AA1 5 LYS A 230 THR A 237 -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 CRYST1 38.899 54.448 53.943 90.00 92.40 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 0.025708 0.000000 0.001077 0.00000 SCALE2 0.000000 0.018366 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018554 0.00000 CONECT 2049 2050 2051 2052 CONECT 2050 2049 CONECT 2051 2049 CONECT 2052 2049 2053 CONECT 2053 2052 2054 2055 2059 CONECT 2054 2053 CONECT 2055 2053 2056 CONECT 2056 2055 2057 2058 CONECT 2057 2056 CONECT 2058 2056 CONECT 2059 2053 2060 2061 CONECT 2060 2059 CONECT 2061 2059 MASTER 269 0 1 15 9 0 0 6 2266 1 13 21 END