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- PDB-6izd: Crystal structure of the chromosome-encoded beta-lactamase mutant... -

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Basic information

Entry
Database: PDB / ID: 6izd
TitleCrystal structure of the chromosome-encoded beta-lactamase mutant R168H/M221I of Vibrio parahaemolyticus
ComponentsBeta-lactamase
KeywordsHYDROLASE / Vibrio / beta-lactamase
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMa, Q. / Li, P.
Funding support China, 2items
OrganizationGrant numberCountry
1000 talent program China
Chinese Academy of Sciences100 talent program China
CitationJournal: Biochimie / Year: 2020
Title: Structural analysis of the CARB beta-lactamase from Vibrio parahaemolyticus facilitates application of the beta-lactam/ beta-lactamase inhibitor therapy.
Authors: Li, P. / Liu, C. / Li, B. / Ma, Q.
History
DepositionDec 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_mutation / _entity_src_gen.pdbx_gene_src_gene ..._entity.pdbx_mutation / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.2Sep 22, 2021Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Revision 1.3Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2403
Polymers30,0561
Non-polymers1842
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-2 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.598, 60.425, 101.616
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase


Mass: 30056.008 Da / Num. of mol.: 1 / Mutation: R168H, M221I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: BS585_07485, CGJ02_01605 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3E1IK87, beta-lactamase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.84 Å3/Da / Density % sol: 56.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10 mg/ml protein in 10 mM HEPES pH 7.5, 150 mM NaCl, 1 mM DTT was mixed with 2 M Ammonium sulfate, 0.1 M sodium citrate/ Citric acid pH 5.0 in 1:1 volume ratio

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
ReflectionResolution: 1.599→60.423 Å / Num. obs: 46039 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 26.05 Å2 / CC1/2: 1 / Rpim(I) all: 0.019 / Rrim(I) all: 0.068 / Rsym value: 0.065 / Net I/σ(I): 21.3
Reflection shellResolution: 1.599→1.605 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 445 / CC1/2: 0.812 / Rpim(I) all: 0.27 / Rrim(I) all: 0.954 / Rsym value: 0.914 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
autoPROC1.0.4data scaling
MOLREP11.4.05phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G68

1g68


Resolution: 1.6→23.43 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.953 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.079 / SU Rfree Blow DPI: 0.076 / SU Rfree Cruickshank DPI: 0.073
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2260 4.92 %RANDOM
Rwork0.188 ---
obs0.189 45908 100 %-
Displacement parametersBiso mean: 30.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.3674 Å20 Å20 Å2
2---3.5145 Å20 Å2
3---3.1471 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: 1 / Resolution: 1.6→23.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 12 236 2291
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012102HARMONIC2
X-RAY DIFFRACTIONt_angle_deg12847HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d765SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes301HARMONIC5
X-RAY DIFFRACTIONt_it2102HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion16.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion286SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2703SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.64 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 159 4.71 %
Rwork0.214 3216 -
all0.216 3375 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -6.2053 Å / Origin y: 17.5942 Å / Origin z: -12.6628 Å
111213212223313233
T-0.0923 Å2-0.028 Å2-0.0069 Å2--0.0574 Å2-0.0071 Å2---0.0926 Å2
L1.2694 °2-0.0643 °2-0.4282 °2-0.8348 °2-0.7619 °2--1.6646 °2
S-0.1261 Å °0.226 Å °-0.0048 Å °-0.0059 Å °0.0313 Å °-0.0325 Å °-0.0443 Å °-0.1047 Å °0.0948 Å °
Refinement TLS groupSelection details: { A|* }

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