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- PDB-6n9k: Beta-lactamase from Escherichia coli str. Sakai -

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Basic information

Entry
Database: PDB / ID: 6n9k
TitleBeta-lactamase from Escherichia coli str. Sakai
ComponentsBeta-lactamase
KeywordsLIGASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsOsipiuk, J. / Wu, R. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: to be published
Title: Beta-lactamase from Escherichia coli str. Sakai
Authors: Osipiuk, J. / Wu, R. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Other
Category: pdbx_SG_project / pdbx_audit_support / pdbx_database_status
Item: _pdbx_audit_support.funding_organization / _pdbx_database_status.SG_entry
Revision 1.2Oct 11, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,32910
Polymers79,7042
Non-polymers6258
Water11,367631
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1655
Polymers39,8521
Non-polymers3124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1655
Polymers39,8521
Non-polymers3124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.929, 127.929, 93.020
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Beta-lactamase /


Mass: 39852.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Strain: Sakai / Gene: ampC, ECpv15279_5067, ECs_5131 / Plasmid: pMCSG53
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8XDQ2, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 631 / 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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2 M Lithium Sulfate, 30% PEG 8000, 0.1 M Sodium Acetate:Acetic Acid buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→47.64 Å / Num. obs: 112960 / % possible obs: 99.7 % / Redundancy: 9 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.021 / Rrim(I) all: 0.066 / Χ2: 1.223 / Net I/av σ(I): 34.3 / Net I/σ(I): 13.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.54 / Num. unique obs: 5360 / CC1/2: 0.687 / Rpim(I) all: 0.337 / Rrim(I) all: 0.701 / Χ2: 0.619 / % possible all: 95.2

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Processing

Software
NameVersionClassification
HKL-3000data reduction
REFMAC5.8.0232refinement
PDB_EXTRACT3.24data extraction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GGW

5ggw


Resolution: 1.6→47.64 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.437 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.063
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1557 5620 5 %RANDOM
Rwork0.1375 ---
obs0.1384 107309 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 73.31 Å2 / Biso mean: 20.122 Å2 / Biso min: 11.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å2-0 Å2
2--0.03 Å20 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 1.6→47.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5602 0 38 631 6271
Biso mean--40.89 35.45 -
Num. residues----717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136236
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175831
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.6498586
X-RAY DIFFRACTIONr_angle_other_deg1.4971.57313681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6015846
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36423.624298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.188151070
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6951526
X-RAY DIFFRACTIONr_chiral_restr0.0890.2825
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027049
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021253
LS refinement shellResolution: 1.602→1.644 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 395 -
Rwork0.24 7552 -
all-7947 -
obs--95.46 %
Refinement TLS params.

S11: 0.0162 Å ° / T33: 0.0017 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)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)Origin x (Å)Origin y (Å)Origin z (Å)
10.6829-0.0544-0.05810.24960.00730.03090.0160.012-0.0048-0.00970.0080.0197-0.008-0.00640.01860.0006-0.00410.03650.0024-0.466245.85846.055
20.69720.0733-0.06350.2241-0.05220.095-0.00840.01310.0035-0.0162-0.01470.02460.011400.013-0.002-0.00150.03390.0016-1.119945.89610.2322
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 504
2X-RAY DIFFRACTION2B21 - 504

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