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- PDB-5hvi: Crystal structure of TEM1 beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 5hvi
TitleCrystal structure of TEM1 beta-lactamase
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE
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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsRoose, B.W. / Dmochowski, I.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM097478 United States
Department of Defense Lung Cancer Research ProgramW81XWH-14-1-0424 United States
CitationJournal: Chemphyschem / Year: 2018
Title: A Structural Basis for129Xe Hyper-CEST Signal in TEM-1 beta-Lactamase.
Authors: Roose, B.W. / Zemerov, S.D. / Wang, Y. / Kasimova, M.A. / Carnevale, V. / Dmochowski, I.J.
History
DepositionJan 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase TEM
B: Beta-lactamase TEM
C: Beta-lactamase TEM
D: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)115,6484
Polymers115,6484
Non-polymers00
Water17,421967
1
A: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)28,9121
Polymers28,9121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)28,9121
Polymers28,9121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)28,9121
Polymers28,9121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)28,9121
Polymers28,9121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.663, 84.156, 95.703
Angle α, β, γ (deg.)90.000, 90.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-lactamase TEM / IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 ...IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 / TEM-8/CAZ-2


Mass: 28911.904 Da / Num. of mol.: 4 / Mutation: M180T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6 / Plasmid: pJ411 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62593, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 967 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 2% (v/v) tacsimate (pH 6.0), 0.1 M Bis-Tris (pH 6.5), 20% (w/v) PEG 3350
PH range: 6.0 - 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.02
ReflectionResolution: 1.64→63.2 Å / Num. obs: 113836 / % possible obs: 96.9 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.037 / Net I/σ(I): 15.1 / Num. measured all: 409738 / Scaling rejects: 276
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3.4 / % possible all: 89.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
Aimless0.5.1data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BTL

1btl


Resolution: 1.64→63.198 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.83
RfactorNum. reflection% reflection
Rfree0.2065 11493 5.36 %
Rwork0.1673 --
obs0.1693 113804 92.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 50.22 Å2 / Biso mean: 12.2983 Å2 / Biso min: 3.87 Å2
Refinement stepCycle: final / Resolution: 1.64→63.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8054 0 0 967 9021
Biso mean---22.32 -
Num. residues----1052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088227
X-RAY DIFFRACTIONf_angle_d1.13211164
X-RAY DIFFRACTIONf_chiral_restr0.0441293
X-RAY DIFFRACTIONf_plane_restr0.0051459
X-RAY DIFFRACTIONf_dihedral_angle_d12.9843072
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6401-1.66840.27415440.21488972951678
1.6684-1.69870.26934790.2134102731075288
1.6987-1.73130.26575140.205101131062787
1.7313-1.76660.24795800.207199851056587
1.7666-1.8050.21574880.1979101301061887
1.805-1.8470.23134810.1939100201050186
1.847-1.89310.23485230.185698531037685
1.8931-1.94430.19955220.178898511037385
1.9443-2.00140.22875050.174299341043986
2.0014-2.06590.2015350.172999861052186
2.0659-2.13960.19275380.1654101321067087
2.1396-2.22520.20485550.1587103771093290
2.2252-2.32630.1884700.161104701094091
2.3263-2.44860.20156560.1627104581111490
2.4486-2.60170.19925910.1572104581104991
2.6017-2.80190.22855590.1619105861114591
2.8019-3.08260.18925950.1633105401113591
3.0826-3.5260.18486390.1455102821092189
3.526-4.4320.18545130.132102621077589
4.432-18.34560.1954730.171105971107091

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