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- PDB-6dn4: Cronobacter sakazakii (Enterobacter sakazakii) Metallo-beta-lacta... -

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Basic information

Entry
Database: PDB / ID: 6dn4
TitleCronobacter sakazakii (Enterobacter sakazakii) Metallo-beta-lactamse HARLDQ motif
ComponentsBeta-lactamase
KeywordsMETAL BINDING PROTEIN / Metallo-beta-lactamse
Function / homologyMetallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta / Beta-lactamase
Function and homology information
Biological speciesCronobacter sakazakii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsMonteiro Pedroso, M. / Waite, D. / Natasa, M. / McGeary, R. / Guddat, L. / Hugenholtz, P. / Schenk, G.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP108477 Australia
Australian Research Council (ARC)DP150104358 Australia
Australian Research Council (ARC)T120100694 Australia
CitationJournal: Protein Cell / Year: 2020
Title: Broad spectrum antibiotic-degrading metallo-beta-lactamases are phylogenetically diverse
Authors: Monteiro Pedroso, M. / Waite, D. / Melse, O. / Wilson, L. / Natasa, M. / McGeary, R. / Antes, I. / Guddat, L. / Hugenholtz, P. / Schenk, G.
History
DepositionJun 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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


Theoretical massNumber of molelcules
Total (without water)32,0751
Polymers32,0751
Non-polymers00
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.580, 84.580, 74.982
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Beta-lactamase


Mass: 32074.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cronobacter sakazakii (bacteria) / Gene: CSK29544_03680 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0F6VWC7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.49 M NaH2PO4 0.91 M K2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.71073 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 20, 2016
RadiationMonochromator: MX2 Beamline Australian Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71073 Å / Relative weight: 1
ReflectionResolution: 1.99→42.29 Å / Num. obs: 18134 / % possible obs: 99.7 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.053 / Net I/σ(I): 12
Reflection shellResolution: 1.99→2.0436 Å / Num. unique obs: 18134 / % possible all: 99.69

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
Blu-Icedata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SML

1sml


Resolution: 1.99→42.29 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1827 1807 9.96 %
Rwork0.1436 --
obs0.1476 18134 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→42.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2109 0 0 347 2456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042167
X-RAY DIFFRACTIONf_angle_d0.5992950
X-RAY DIFFRACTIONf_dihedral_angle_d13.9281295
X-RAY DIFFRACTIONf_chiral_restr0.045318
X-RAY DIFFRACTIONf_plane_restr0.005393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9898-2.04360.23861270.18341208X-RAY DIFFRACTION98
2.0436-2.10370.17761400.16411274X-RAY DIFFRACTION99
2.1037-2.17160.20781370.14451247X-RAY DIFFRACTION100
2.1716-2.24920.19491400.13631241X-RAY DIFFRACTION100
2.2492-2.33920.15441410.13771257X-RAY DIFFRACTION100
2.3392-2.44570.18961410.14071245X-RAY DIFFRACTION100
2.4457-2.57460.17731400.1441266X-RAY DIFFRACTION100
2.5746-2.73590.19481420.14761247X-RAY DIFFRACTION100
2.7359-2.94710.20971420.15341254X-RAY DIFFRACTION100
2.9471-3.24360.18541380.13971261X-RAY DIFFRACTION100
3.2436-3.71270.17351430.12791264X-RAY DIFFRACTION100
3.7127-4.67660.15051380.12091268X-RAY DIFFRACTION100
4.6766-42.29950.18481380.1671295X-RAY DIFFRACTION100
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)
10.79310.03020.78220.3977-0.48172.76580.05810.0702-0.0362-0.00350.03720.04720.0853-0.0561-0.0810.06550.01140.01120.06680.00450.081916.785520.3032-12.3197
20.7359-0.12170.22320.3490.02341.3687-0.002-0.02820.02540.00150.02250.0851-0.0691-0.1245-0.03080.07680.02110.0260.08770.01110.08899.328628.7024-10.0225
31.301-0.21550.76480.8171-0.29824.1296-0.0389-0.08060.05780.0653-0.0048-0.0107-0.17510.0189-0.00960.10990.01180.02780.0625-0.00360.085321.318633.914-9.1222
40.78150.033-0.33891.1572-0.06861.01750.0440.04890.12650.03090.04980.0974-0.2704-0.19770.05530.13490.03540.03520.0880.05250.101815.161836.2952-29.3443
51.35360.66941.1291.2303-0.00984.7653-0.18560.03830.1935-0.1652-0.0512-0.028-0.52870.0786-0.04870.235-0.02130.04430.0719-0.01110.129522.286442.0585-21.5555
63.8326-1.29220.80664.3697-1.83852.61060.00390.18750.1256-0.21360.13010.0841-0.23430.1939-0.0430.0779-0.01340.03790.08150.0120.0827.938829.8126-12.5231
73.4451-1.3151.03175.0806-1.95474.12510.10550.0313-0.22060.043-0.069-0.16050.02930.3071-0.04020.05080.00980.0260.12520.00650.088235.042420.9328-7.4088
83.3934-0.70583.09312.8786-2.39447.2031-0.0680.2888-0.0879-0.17060.0013-0.0755-0.26170.53990.02870.1212-0.00880.04910.06960.00040.082327.403935.8635-28.9614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 101 )
2X-RAY DIFFRACTION2chain 'A' and (resid 102 through 188 )
3X-RAY DIFFRACTION3chain 'A' and (resid 189 through 212 )
4X-RAY DIFFRACTION4chain 'A' and (resid 213 through 230 )
5X-RAY DIFFRACTION5chain 'A' and (resid 231 through 243 )
6X-RAY DIFFRACTION6chain 'A' and (resid 244 through 259 )
7X-RAY DIFFRACTION7chain 'A' and (resid 260 through 279 )
8X-RAY DIFFRACTION8chain 'A' and (resid 280 through 303 )

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