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- PDB-5hw5: Crystal structure of TEM1 beta-lactamase in the presence of 2.0 M... -

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Basic information

Entry
Database: PDB / ID: 5hw5
TitleCrystal structure of TEM1 beta-lactamase in the presence of 2.0 MPa xenon
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE / xenon
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
XENON / Beta-lactamase TEM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 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: To Be Published
Title: Structure of TEM1 beta-lactamase
Authors: Roose, B.W. / Wang, Y. / 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 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)117,35417
Polymers115,6484
Non-polymers1,70713
Water15,475859
1
A: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3064
Polymers28,9121
Non-polymers3943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4375
Polymers28,9121
Non-polymers5254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3064
Polymers28,9121
Non-polymers3943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3064
Polymers28,9121
Non-polymers3943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.440, 84.620, 96.011
Angle α, β, γ (deg.)90.000, 90.580, 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: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Xe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 859 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
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: SSRL / Beamline: BL14-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.14
ReflectionResolution: 1.41→51.38 Å / Num. obs: 180127 / % possible obs: 97.2 % / Redundancy: 3.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.096 / Net I/σ(I): 6
Reflection shellResolution: 1.41→1.43 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 1.5 / % possible all: 95.3

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimless0.5.4data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HVI

5hvi


Resolution: 1.41→34.661 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.85
RfactorNum. reflection% reflection
Rfree0.221 18166 5.1 %
Rwork0.1843 --
obs0.1859 180094 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.4 Å2 / Biso mean: 12.4313 Å2 / Biso min: 4.13 Å2
Refinement stepCycle: final / Resolution: 1.41→34.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8023 0 12 859 8894
Biso mean--16.71 22.47 -
Num. residues----1052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098214
X-RAY DIFFRACTIONf_angle_d1.23911151
X-RAY DIFFRACTIONf_chiral_restr0.0521295
X-RAY DIFFRACTIONf_plane_restr0.0061455
X-RAY DIFFRACTIONf_dihedral_angle_d12.5393063
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 (%)
1.41-1.43430.32718830.2869165481743190
1.4343-1.46040.286110470.2778163921743990
1.4604-1.48840.26828780.2622166481752691
1.4884-1.51880.27449190.2465165601747991
1.5188-1.55180.26248610.245169101777191
1.5518-1.58780.27359060.2347165951750191
1.5878-1.62750.24868820.2246167841766691
1.6275-1.67150.24288100.2177167911760192
1.6715-1.72060.26018110.2158169241773592
1.7206-1.7760.21818860.2067169521783892
1.776-1.83940.22989010.1992168981779992
1.8394-1.91290.22038330.1837169461777993
1.9129-1.99980.20948790.1828171281800793
1.9998-2.1050.21388780.1805170041788293
2.105-2.23650.21378670.1717171341800193
2.2365-2.40860.22159380.1696170891802793
2.4086-2.64980.20267740.1625172581803294
2.6498-3.03060.20719130.1574172461815994
3.0306-3.80840.17878370.1393173241816195
3.8084-15.25390.19849000.1561173461824695

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