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- PDB-6nj1: Crystal structure of class A beta-lactamase from Clostridium kluy... -

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Basic information

Entry
Database: PDB / ID: 6nj1
TitleCrystal structure of class A beta-lactamase from Clostridium kluyveri DSM 555
ComponentsBeta-lactamase
KeywordsHYDROLASE / antibiotic resistance / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesClostridium kluyveri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.399 Å
AuthorsMichalska, K. / Welk, L. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal structure of class A beta-lactamase from Clostridium kluyveri DSM 555
Authors: Michalska, K. / Welk, L. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1416
Polymers30,9631
Non-polymers1775
Water3,873215
1
A: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,28112
Polymers61,9272
Non-polymers35510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+5/31
Buried area1970 Å2
ΔGint-101 kcal/mol
Surface area22770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.878, 66.878, 119.795
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-402-

CL

21A-534-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 30963.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium kluyveri (strain ATCC 8527 / DSM 555 / NCIMB 10680) (bacteria)
Strain: ATCC 8527 / DSM 555 / NCIMB 10680 / Gene: bla, CKL_2902 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5N1B8, beta-lactamase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1 M LiCl, 0.1 M sodium citrate pH 4.0, 20% PEG6000, cryo 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 9, 2018 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 118279 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 24.627
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.676 / Mean I/σ(I) obs: 1.332 / Num. unique obs: 3040 / CC1/2: 0.709 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2947: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.399→29.197 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0.23 / Phase error: 14.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1512 5758 4.87 %
Rwork0.1235 --
obs0.1249 118223 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.399→29.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 5 215 2231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122085
X-RAY DIFFRACTIONf_angle_d1.222832
X-RAY DIFFRACTIONf_dihedral_angle_d16.091776
X-RAY DIFFRACTIONf_chiral_restr0.092324
X-RAY DIFFRACTIONf_plane_restr0.008369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.399-1.41490.26221860.23333722X-RAY DIFFRACTION98
1.4149-1.43150.25051970.21033700X-RAY DIFFRACTION100
1.4315-1.4490.22791770.213780X-RAY DIFFRACTION100
1.449-1.46730.25461710.19163719X-RAY DIFFRACTION100
1.4673-1.48660.22271750.18853868X-RAY DIFFRACTION100
1.4866-1.5070.21671750.1733707X-RAY DIFFRACTION100
1.507-1.52850.19312150.15733760X-RAY DIFFRACTION100
1.5285-1.55130.19641700.14653753X-RAY DIFFRACTION100
1.5513-1.57560.19932090.14823734X-RAY DIFFRACTION100
1.5756-1.60140.17142080.13243751X-RAY DIFFRACTION100
1.6014-1.6290.17561850.12443766X-RAY DIFFRACTION100
1.629-1.65860.1581800.11673709X-RAY DIFFRACTION100
1.6586-1.69050.15751980.113766X-RAY DIFFRACTION100
1.6905-1.7250.13481740.10493801X-RAY DIFFRACTION100
1.725-1.76250.15372180.10813736X-RAY DIFFRACTION100
1.7625-1.80350.15671740.10323746X-RAY DIFFRACTION100
1.8035-1.84860.13841900.1053746X-RAY DIFFRACTION100
1.8486-1.89860.15061580.09763809X-RAY DIFFRACTION100
1.8986-1.95450.12692230.09693689X-RAY DIFFRACTION100
1.9545-2.01750.1181840.0993790X-RAY DIFFRACTION100
2.0175-2.08960.13152060.09983731X-RAY DIFFRACTION100
2.0896-2.17330.13271890.10593753X-RAY DIFFRACTION100
2.1733-2.27210.14051980.10763739X-RAY DIFFRACTION100
2.2721-2.39190.14932420.11123712X-RAY DIFFRACTION100
2.3919-2.54170.13792380.11123710X-RAY DIFFRACTION100
2.5417-2.73780.13731560.12083772X-RAY DIFFRACTION100
2.7378-3.0130.15671660.12983763X-RAY DIFFRACTION100
3.013-3.44840.15522100.13453754X-RAY DIFFRACTION100
3.4484-4.34240.13741880.1133720X-RAY DIFFRACTION100
4.3424-29.20360.16231980.14583759X-RAY DIFFRACTION100

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