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- PDB-5e2e: Crystal Structure of Beta-lactamase Precursor BlaA from Yersinia ... -

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Basic information

Entry
Database: PDB / ID: 5e2e
TitleCrystal Structure of Beta-lactamase Precursor BlaA from Yersinia enterocolitica
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
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 speciesYersinia enterocolitica serotype O:8 / biotype 1B
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKim, Y. / Joachimiak, G. / Endres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Crystal Structure of Beta-lactamase Precursor BlaA from Yersinia enterocolitica
Authors: Kim, Y. / Joachimiak, G. / Endres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionOct 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)58,2882
Polymers58,2882
Non-polymers00
Water4,468248
1
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)29,1441
Polymers29,1441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)29,1441
Polymers29,1441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.116, 93.513, 122.219
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: 29144.145 Da / Num. of mol.: 2 / Fragment: UNP residues 28-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081) (bacteria)
Strain: NCTC 13174 / 8081 / Gene: blaA, YE2019 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1JML9, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1 M CHES:NaOH pH 9.5, 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.9→30.72 Å / Num. obs: 38874 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 20.2 Å2 / Rsym value: 0.073 / Net I/σ(I): 16.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 1.75 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.10PRE-2104refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→30.72 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.55 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1799 4.82 %Random selection
Rwork0.197 ---
obs0.199 37357 96.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→30.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3942 0 0 248 4190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074013
X-RAY DIFFRACTIONf_angle_d0.9065454
X-RAY DIFFRACTIONf_dihedral_angle_d13.5382437
X-RAY DIFFRACTIONf_chiral_restr0.05632
X-RAY DIFFRACTIONf_plane_restr0.005710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9005-1.95190.3159970.2691918X-RAY DIFFRACTION69
1.9519-2.00930.3121120.24232418X-RAY DIFFRACTION86
2.0093-2.07420.29371430.23542691X-RAY DIFFRACTION97
2.0742-2.14830.28041440.22252776X-RAY DIFFRACTION99
2.1483-2.23430.27691570.22092827X-RAY DIFFRACTION100
2.2343-2.33590.26251520.20692806X-RAY DIFFRACTION100
2.3359-2.4590.23391540.20712805X-RAY DIFFRACTION100
2.459-2.6130.25621530.19622804X-RAY DIFFRACTION100
2.613-2.81470.25081400.20512849X-RAY DIFFRACTION100
2.8147-3.09770.26641430.20432839X-RAY DIFFRACTION100
3.0977-3.54530.24461310.19322899X-RAY DIFFRACTION100
3.5453-4.46450.19961390.16442906X-RAY DIFFRACTION100
4.4645-30.71970.19521340.17383020X-RAY DIFFRACTION98
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)
11.48-0.1996-0.16411.59560.49791.69730.0223-0.59930.12790.55210.0607-0.0984-0.0120.5297-0.00460.3312-0.05510.01860.3414-0.03850.09132.7165-27.402550.7414
21.9843-1.0430.14071.72430.41062.1774-0.14920.0679-0.09410.0499-0.03640.1730.60740.40270.16360.19930.08540.02170.16890.0090.17483.3081-43.835230.3401
30.62940.0562-0.21242.10690.84022.38870.037-0.2258-0.1330.41670.1427-0.19480.36630.7331-0.09120.22620.0712-0.03360.35580.0030.14183.2126-33.262346.4632
40.69950.00090.54180.54160.04671.45730.1513-0.35760.0360.06790.206-0.242-0.04150.33040.50170.3597-0.2918-0.03250.7613-0.23680.27611.9034-19.960347.3349
51.50080.0276-0.18632.1817-0.69820.82830.2241-0.8249-0.35480.47230.016-0.12560.098-0.04840.0440.2288-0.1041-0.06910.28070.10080.211618.3967-72.700348.9904
60.36580.58710.54571.85280.42451.1036-0.0414-0.00990.2945-0.1048-0.0035-0.0149-0.37570.15580.03770.2245-0.06450.08440.09160.01820.46822.483-48.027930.3898
71.2285-0.36650.61181.2765-0.10540.81840.05940.07880.2689-0.2066-0.1749-0.1788-0.02420.0867-0.06320.1334-0.02730.06260.0708-0.07510.18419.6991-58.826331.196
81.99110.22870.06611.4407-0.1870.61350.1923-0.7423-0.13530.0786-0.1796-0.3202-0.01740.0807-0.24760.1183-0.0427-0.00310.1939-0.16740.122422.9787-65.319743.4906
91.93130.25281.32530.8087-0.12862.01170.1862-0.8801-0.35510.10360.02640.1136-0.0367-0.4760.19920.1201-0.07160.0020.27240.00910.1139.7268-68.737946.7127
102.48320.26450.30491.72960.15022.42380.2768-0.5934-0.5980.06260.0869-0.07420.2439-0.22650.19030.2081-0.1171-0.08240.27370.10560.28059.0305-79.420745.717
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 6 THROUGH 63 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 64 THROUGH 119 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 120 THROUGH 242 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 243 THROUGH 265 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 6 THROUGH 62 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 63 THROUGH 75 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 76 THROUGH 132 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 133 THROUGH 189 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 190 THROUGH 242 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 243 THROUGH 265 )

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