HEADER HYDROLASE 24-MAY-24 9BZR TITLE STRUCTURE OF CLASS A BETA-LACTAMASE FROM BORDETELLA BRONCHISEPTICA TITLE 2 RB50 IN A COMPLEX WITH CLAVULONATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLASS A BETA-LACTAMASE, PENP SUPERFAMILY; COMPND 3 CHAIN: A; COMPND 4 EC: 3.5.2.6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BORDETELLA BRONCHISEPTICA RB50; SOURCE 3 ORGANISM_TAXID: 257310; SOURCE 4 GENE: BB2049; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: GOLD; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: P53 KEYWDS LACTAMASE, SERINE HYDROLASE, PENP, CSBID, CENTER FOR STRUCTURAL KEYWDS 2 BIOLOGY OF INFECTIOUS DISEASES, CLAVULONATE, STRUCTURAL GENOMICS, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.MALTSEVA,Y.KIM,M.ENDRES,A.JOACHIMIAK,CENTER FOR STRUCTURAL BIOLOGY AUTHOR 2 OF INFECTIOUS DISEASES (CSBID) REVDAT 2 16-OCT-24 9BZR 1 REMARK REVDAT 1 12-JUN-24 9BZR 0 JRNL AUTH N.MALTSEVA,Y.KIM,M.ENDRES,A.JOACHIMIAK JRNL TITL STRUCTURE OF CLASS A BETA-LACTAMASE FROM BORDETELLA JRNL TITL 2 BRONCHISEPTICA RB50 IN A COMPLEX WITH CLAVULONATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.310 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 41485 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 2037 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 35.5400 - 3.4400 0.98 2817 140 0.1484 0.1839 REMARK 3 2 3.4400 - 2.7300 0.99 2782 116 0.1755 0.2175 REMARK 3 3 2.7300 - 2.3800 0.99 2730 124 0.1738 0.2340 REMARK 3 4 2.3800 - 2.1700 0.99 2729 130 0.1435 0.1927 REMARK 3 5 2.1700 - 2.0100 0.99 2750 124 0.1335 0.1731 REMARK 3 6 2.0100 - 1.8900 0.98 2703 135 0.1490 0.1844 REMARK 3 7 1.8900 - 1.8000 0.99 2674 145 0.1452 0.2019 REMARK 3 8 1.8000 - 1.7200 0.98 2655 168 0.1564 0.2257 REMARK 3 9 1.7200 - 1.6500 0.97 2644 160 0.1693 0.2216 REMARK 3 10 1.6500 - 1.6000 0.97 2658 126 0.1816 0.2717 REMARK 3 11 1.6000 - 1.5500 0.93 2523 151 0.1915 0.2205 REMARK 3 12 1.5500 - 1.5000 0.95 2598 136 0.2082 0.2454 REMARK 3 13 1.5000 - 1.4600 0.95 2592 143 0.2169 0.2784 REMARK 3 14 1.4600 - 1.4300 0.92 2475 140 0.2548 0.3427 REMARK 3 15 1.4300 - 1.4000 0.77 2118 99 0.2731 0.3188 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) : 0.151 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.628 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.85 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 : 0.004 2172 REMARK 3 ANGLE : 0.758 2951 REMARK 3 CHIRALITY : 0.064 328 REMARK 3 PLANARITY : 0.009 405 REMARK 3 DIHEDRAL : 13.076 810 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 9BZR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1000284463. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-18 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 : APS 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) : 0.97926 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 X 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41957 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 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 (%) : 97.5 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.14800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2000 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 : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.74100 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 (%): 35.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.9 M SODIUM MALONATE PH 5.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 37.62750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.95700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 37.62750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.95700 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 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 SER A 34 REMARK 465 SER A 305 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 OG SER A 80 C6 TEM A 402 2.09 REMARK 500 OG SER A 80 O8 TEM A 402 2.19 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 79 -137.06 46.63 REMARK 500 ARG A 230 -124.58 -103.27 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 615 DISTANCE = 6.22 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9BZN RELATED DB: PDB REMARK 900 RELATED ID: IDP07519 RELATED DB: TARGETTRACK DBREF1 9BZR A 37 305 UNP A0A0H3LUA9_BORBR DBREF2 9BZR A A0A0H3LUA9 37 305 SEQADV 9BZR SER A 34 UNP A0A0H3LUA EXPRESSION TAG SEQADV 9BZR ASN A 35 UNP A0A0H3LUA EXPRESSION TAG SEQADV 9BZR ALA A 36 UNP A0A0H3LUA EXPRESSION TAG SEQRES 1 A 272 SER ASN ALA ALA ALA GLN ALA GLN ARG GLN LEU ALA LEU SEQRES 2 A 272 LEU GLU GLN ARG HIS GLY VAL ARG LEU GLY VAL GLN VAL SEQRES 3 A 272 HIS ASP ARG ASP SER ASP ARG ALA PHE SER HIS ARG ALA SEQRES 4 A 272 ASP GLU ARG PHE PRO MET CYS SER THR PHE LYS LEU LEU SEQRES 5 A 272 ALA ALA GLY ALA VAL LEU ALA ARG ALA ASP ARG GLY ASP SEQRES 6 A 272 ASP SER LEU ARG ARG LEU ILE ARG TYR GLY ALA ALA ASP SEQRES 7 A 272 ILE VAL ALA TYR SER PRO VAL THR GLY PRO ARG GLN ALA SEQRES 8 A 272 GLU GLY MET THR LEU GLU GLN LEU CYS GLU ALA ALA VAL SEQRES 9 A 272 THR ARG SER ASP ASN THR ALA GLY ASN LEU LEU LEU SER SEQRES 10 A 272 THR LEU GLY GLY PRO PRO GLY LEU THR ALA TYR ALA ARG SEQRES 11 A 272 GLY LEU GLY ASP ARG MET THR ARG LEU ASP ARG ILE GLU SEQRES 12 A 272 THR ALA LEU ASN GLU ALA ARG PRO GLY ASP PRO ARG ASP SEQRES 13 A 272 THR THR THR PRO ALA ALA MET ALA GLY ASN LEU GLN ARG SEQRES 14 A 272 LEU LEU LEU GLY ASP ALA LEU GLN SER ALA SER ARG GLN SEQRES 15 A 272 ARG LEU ALA ASP TRP LEU LEU ALA SER GLN THR GLY ASP SEQRES 16 A 272 THR ARG LEU ARG ALA GLY LEU PRO ALA GLY TRP ARG ILE SEQRES 17 A 272 GLY ASP LYS THR GLY ALA GLY GLY HIS GLY THR ASN ASN SEQRES 18 A 272 ASP ILE GLY VAL ILE TRP PRO ARG ASP GLY ALA PRO VAL SEQRES 19 A 272 LEU ILE SER ALA TYR LEU THR GLN SER SER ALA SER ARG SEQRES 20 A 272 GLU ALA GLN ASN ALA VAL LEU ALA GLU VAL GLY ARG ILE SEQRES 21 A 272 ALA ALA HIS ALA VAL ALA ALA TRP ARG LEU GLY SER HET MLA A 401 7 HET TEM A 402 11 HET MLA A 403 7 HET CL A 404 1 HETNAM MLA MALONIC ACID HETNAM TEM N-(2-HYDROXY-4-OXO-BUTYL)-N-(3-OXO-TRANSPROPENYL)AMINE HETNAM CL CHLORIDE ION HETSYN MLA DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; HETSYN 2 MLA METHANEDICARBOXYLIC ACID FORMUL 2 MLA 2(C3 H4 O4) FORMUL 3 TEM C7 H11 N O3 FORMUL 5 CL CL 1- FORMUL 6 HOH *114(H2 O) HELIX 1 AA1 ASN A 35 GLY A 52 1 18 HELIX 2 AA2 THR A 81 ARG A 96 1 16 HELIX 3 AA3 GLY A 108 ILE A 112 5 5 HELIX 4 AA4 LEU A 129 ARG A 139 1 11 HELIX 5 AA5 ASP A 141 LEU A 152 1 12 HELIX 6 AA6 GLY A 154 LEU A 165 1 12 HELIX 7 AA7 THR A 177 GLU A 181 5 5 HELIX 8 AA8 THR A 192 LEU A 205 1 14 HELIX 9 AA9 GLN A 210 SER A 224 1 15 HELIX 10 AB1 ARG A 230 LEU A 235 1 6 HELIX 11 AB2 SER A 279 GLY A 304 1 26 SHEET 1 AA1 5 ALA A 67 HIS A 70 0 SHEET 2 AA1 5 ARG A 54 ASP A 61 -1 N VAL A 57 O HIS A 70 SHEET 3 AA1 5 VAL A 267 THR A 274 -1 O TYR A 272 N GLY A 56 SHEET 4 AA1 5 THR A 252 TRP A 260 -1 N ILE A 259 O VAL A 267 SHEET 5 AA1 5 ARG A 240 GLY A 248 -1 N ARG A 240 O TRP A 260 SHEET 1 AA2 2 PHE A 76 PRO A 77 0 SHEET 2 AA2 2 THR A 190 THR A 191 -1 O THR A 191 N PHE A 76 SHEET 1 AA3 2 LEU A 104 ILE A 105 0 SHEET 2 AA3 2 MET A 127 THR A 128 -1 O MET A 127 N ILE A 105 LINK OG SER A 80 C7 TEM A 402 1555 1555 1.37 CISPEP 1 GLU A 176 THR A 177 0 0.63 CRYST1 75.255 41.914 78.053 90.00 116.96 90.00 C 1 2 1 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 0.013288 0.000000 0.006759 0.00000 SCALE2 0.000000 0.023858 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014374 0.00000