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- PDB-5i63: Crystal structure of TEM1 beta-lactamase mutant I263N in the pres... -

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Basic information

Entry
Database: PDB / ID: 5i63
TitleCrystal structure of TEM1 beta-lactamase mutant I263N in the presence of 1.2 MPa xenon
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE / xenon
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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: 1.95 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
DepositionFeb 15, 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 1.5Nov 13, 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)116,70212
Polymers115,6514
Non-polymers1,0508
Water10,953608
1
A: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1753
Polymers28,9131
Non-polymers2632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1753
Polymers28,9131
Non-polymers2632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1753
Polymers28,9131
Non-polymers2632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1753
Polymers28,9131
Non-polymers2632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.070, 84.200, 96.220
Angle α, β, γ (deg.)90.000, 89.970, 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: 28912.846 Da / Num. of mol.: 4 / Mutation: M180T, I259N
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.: 8 / Source method: obtained synthetically / Formula: Xe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / 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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium formate (pH 7.0), 20% (w/v) PEG 3350 / PH range: 7.0 - 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.181 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.181 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.38
ReflectionResolution: 1.95→63.36 Å / Num. obs: 68222 / % possible obs: 97.8 % / Redundancy: 3.8 % / CC1/2: 0.985 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.091 / Rrim(I) all: 0.177 / Net I/σ(I): 7.2 / Num. measured all: 258898 / Scaling rejects: 595
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.95-23.80.587196.3
9.15-63.363.60.059198.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimless0.5.17data scaling
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HVI

5hvi


Resolution: 1.95→60.07 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 34.73
RfactorNum. reflection% reflection
Rfree0.2224 6830 5.14 %
Rwork0.1844 --
obs0.1873 68198 96.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.1 Å2 / Biso mean: 12.9396 Å2 / Biso min: 1.57 Å2
Refinement stepCycle: final / Resolution: 1.95→60.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7984 0 8 608 8600
Biso mean--21.69 21.42 -
Num. residues----1052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058141
X-RAY DIFFRACTIONf_angle_d0.84911051
X-RAY DIFFRACTIONf_chiral_restr0.0491286
X-RAY DIFFRACTIONf_plane_restr0.0041441
X-RAY DIFFRACTIONf_dihedral_angle_d13.0313013
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 (%)
1.9504-1.98410.26243220.22776106642890
1.9841-2.02010.25283290.22376274660390
2.0201-2.0590.2863230.22166173649690
2.059-2.1010.27973370.21716240657790
2.101-2.14670.23993250.20336244656991
2.1467-2.19660.23573110.19846215652691
2.1966-2.25160.24873250.20416302662791
2.2516-2.31240.24873350.19846251658691
2.3124-2.38050.25083150.26253656892
2.3805-2.45730.23963310.20036318664992
2.4573-2.54510.22393200.19396330665092
2.5451-2.6470.23453360.18516299663592
2.647-2.76740.21523520.20236373672592
2.7674-2.91330.23313330.19166311664492
2.9133-3.09570.2183370.18936300663793
3.0957-3.33460.21873450.17616468681393
3.3346-3.66990.17283440.15766370671493
3.6699-4.20030.19873310.15176419675094
4.2003-5.28960.18563440.14356423676794
5.2896-37.56770.1863420.18396472681494

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