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- PDB-5fqb: Crystal Structure of Bacillus cereus Metallo-Beta-Lactamase with 2C -

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Basic information

Entry
Database: PDB / ID: 5fqb
TitleCrystal Structure of Bacillus cereus Metallo-Beta-Lactamase with 2C
ComponentsBETA-LACTAMASE 2
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE / LACTAMASE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
: / Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase ...: / Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-OK3 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesBACILLUS CEREUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsCahill, S.T. / Brem, J. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis of metallo-beta-lactamase, serine-beta-lactamase and penicillin-binding protein inhibition by cyclic boronates.
Authors: Brem, J. / Cain, R. / Cahill, S. / McDonough, M.A. / Clifton, I.J. / Jimenez-Castellanos, J.C. / Avison, M.B. / Spencer, J. / Fishwick, C.W. / Schofield, C.J.
History
DepositionDec 8, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 2.0Oct 30, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Non-polymer description / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / exptl_crystal_grow / pdbx_database_status / pdbx_entity_nonpoly
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _entity.pdbx_description / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-LACTAMASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6726
Polymers24,9961
Non-polymers6765
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.147, 61.117, 69.390
Angle α, β, γ (deg.)90.00, 93.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein BETA-LACTAMASE 2 / BETA-LACTAMASE II / CEPHALOSPORINASE / PENICILLINASE / METALLO-BETA-LACTAMASE II


Mass: 24995.533 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 31-257
Source method: isolated from a genetically manipulated source
Details: (R)-3-(4-(AMINOMETHYL)BENZAMIDO)-8-CARBOXY-2,2-DIHYDROXY-3,4-DIHYDRO-2H-BENZO(E)(1,2)OXABORININ-2-UIDE BOUND AT ACTIVE SITE
Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P04190, beta-lactamase

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Non-polymers , 5 types, 194 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-OK3 / (4~{R})-4-[[4-(aminomethyl)phenyl]carbonylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid


Mass: 357.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18BN2O6
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 45.35 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M AMMONIUM SULFATE, 0.1 M BIS TRIS, 25 % W/V PEG 3350 PH 5.5, 1 MM TCEP.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 21, 2015 / Details: OSMIC HF MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→21.64 Å / Num. obs: 17335 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 20.71 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.77
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 5.2 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C09

4c09


Resolution: 1.899→21.642 Å / SU ML: 0.14 / σ(F): 1.35 / Phase error: 17.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1807 1740 10.04 %
Rwork0.1403 --
obs0.1444 17332 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.8 Å2
Refinement stepCycle: LAST / Resolution: 1.899→21.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1659 0 39 189 1887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011754
X-RAY DIFFRACTIONf_angle_d1.2452393
X-RAY DIFFRACTIONf_dihedral_angle_d14.134630
X-RAY DIFFRACTIONf_chiral_restr0.048283
X-RAY DIFFRACTIONf_plane_restr0.006301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8986-1.95440.20781420.15781237X-RAY DIFFRACTION95
1.9544-2.01740.20141360.15031304X-RAY DIFFRACTION97
2.0174-2.08950.19581480.14081253X-RAY DIFFRACTION97
2.0895-2.17310.20881330.13191287X-RAY DIFFRACTION98
2.1731-2.27190.18641510.13711291X-RAY DIFFRACTION98
2.2719-2.39150.17561410.13181312X-RAY DIFFRACTION98
2.3915-2.54110.19071500.141292X-RAY DIFFRACTION99
2.5411-2.7370.21231470.15311296X-RAY DIFFRACTION99
2.737-3.01180.19181530.1631293X-RAY DIFFRACTION99
3.0118-3.44610.20321450.1411333X-RAY DIFFRACTION100
3.4461-4.33590.1541450.12111338X-RAY DIFFRACTION100
4.3359-21.64380.14891490.14331356X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.1562-0.1509-0.95164.3810.56275.17390.03060.51280.4231-0.2833-0.1264-0.6248-0.69670.99520.02550.233-0.0729-0.01650.41950.09490.220868.63884.519110.0623
21.48120.0775-0.69852.4842-0.79257.3144-0.02330.14010.1518-0.1052-0.0775-0.0087-0.44870.42760.09360.1096-0.0114-0.03630.17270.01730.135359.15053.56718.1147
33.4475-0.52741.79262.4082-3.48739.1112-0.1770.16790.2057-0.0055-0.0453-0.0211-0.4395-0.17510.12470.150.0143-0.00970.1393-0.03130.128951.88483.646912.9193
43.1738-0.39510.73821.590.4154.0554-0.01270.0179-0.08250.0599-0.0085-0.02160.14590.15830.02520.111-0.00370.0240.07960.02270.117760.8726-4.662224.2413
54.5468-0.6633-0.39873.06791.02185.9757-0.08090.10060.12450.06190.171-0.17230.1260.813-0.05880.1007-0.0176-0.02740.2564-0.0070.160573.3367-1.339228.6781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 36 THROUGH 79 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 80 THROUGH 121 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 122 THROUGH 142 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 143 THROUGH 264 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 265 THROUGH 294 )

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