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- PDB-5nde: Crystal structure of metallo-beta-lactamase SPM-1 in space group P4222 -

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Basic information

Entry
Database: PDB / ID: 5nde
TitleCrystal structure of metallo-beta-lactamase SPM-1 in space group P4222
ComponentsBeta-lactamase IMP-1
KeywordsHYDROLASE / lactamase / inhibitor / cyclobutanone
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 2. / Beta-lactamase, class-B, conserved site / : / Metallo-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
Similarity search - Domain/homology
Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHinchliffe, P. / Spencer, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1100135 United Kingdom
CitationJournal: Chemistry / Year: 2018
Title: Cyclobutanone Mimics of Intermediates in Metallo-beta-Lactamase Catalysis.
Authors: Abboud, M.I. / Kosmopoulou, M. / Krismanich, A.P. / Johnson, J.W. / Hinchliffe, P. / Brem, J. / Claridge, T.D.W. / Spencer, J. / Schofield, C.J. / Dmitrienko, G.I.
History
DepositionMar 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase IMP-1
B: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,16219
Polymers55,8542
Non-polymers1,30817
Water9,098505
1
A: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,91614
Polymers27,9271
Non-polymers98913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2465
Polymers27,9271
Non-polymers3194
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.740, 130.740, 100.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11B-749-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase IMP-1 / Beta-lactamase SPM-1 / Metallo-b-lactamase / Metallo-beta-lactamase blaSPM-1 / SPM-1


Mass: 27927.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: spm-1, bla SPM-1, blaSPM-1, CCBH4851_00081, ICEPaeSP_00028
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q8G9Q0, beta-lactamase

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Non-polymers , 5 types, 522 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / 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

Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 1.0 M lithium sulfate, 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.7→36.261 Å / Num. obs: 96075 / % possible obs: 100 % / Redundancy: 20.8 % / CC1/2: 1 / Rpim(I) all: 0.029 / Net I/σ(I): 21.3
Reflection shellResolution: 1.7→1.94 Å / Redundancy: 21.3 % / Mean I/σ(I) obs: 2.4 / CC1/2: 0.69 / Rpim(I) all: 0.477 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BP0

4bp0


Resolution: 1.7→36.261 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.25
RfactorNum. reflection% reflection
Rfree0.1725 4772 4.97 %
Rwork0.1619 --
obs0.1624 96042 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→36.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3869 0 58 505 4432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074017
X-RAY DIFFRACTIONf_angle_d1.0795422
X-RAY DIFFRACTIONf_dihedral_angle_d12.6041504
X-RAY DIFFRACTIONf_chiral_restr0.049592
X-RAY DIFFRACTIONf_plane_restr0.006687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.30271710.27272992X-RAY DIFFRACTION100
1.7193-1.73960.28261590.25543004X-RAY DIFFRACTION100
1.7396-1.76080.22181690.24862968X-RAY DIFFRACTION100
1.7608-1.78310.24511700.23042990X-RAY DIFFRACTION100
1.7831-1.80650.24631480.22513000X-RAY DIFFRACTION100
1.8065-1.83130.2321480.20943030X-RAY DIFFRACTION100
1.8313-1.85740.20981620.19982984X-RAY DIFFRACTION100
1.8574-1.88520.23151580.19183021X-RAY DIFFRACTION100
1.8852-1.91460.21561740.18072973X-RAY DIFFRACTION100
1.9146-1.9460.16411490.17253043X-RAY DIFFRACTION100
1.946-1.97960.21241380.16693028X-RAY DIFFRACTION100
1.9796-2.01550.17331730.15953004X-RAY DIFFRACTION100
2.0155-2.05430.17411750.15582988X-RAY DIFFRACTION100
2.0543-2.09620.16981640.15623009X-RAY DIFFRACTION100
2.0962-2.14180.16231680.15043028X-RAY DIFFRACTION100
2.1418-2.19160.15741430.15613039X-RAY DIFFRACTION100
2.1916-2.24640.16191650.15163014X-RAY DIFFRACTION100
2.2464-2.30720.19721430.15953036X-RAY DIFFRACTION100
2.3072-2.3750.17911610.15943033X-RAY DIFFRACTION100
2.375-2.45170.1751680.16063027X-RAY DIFFRACTION100
2.4517-2.53930.18941560.15393045X-RAY DIFFRACTION100
2.5393-2.64090.17391720.15913023X-RAY DIFFRACTION100
2.6409-2.76110.1621670.16033042X-RAY DIFFRACTION100
2.7611-2.90660.17831650.16383058X-RAY DIFFRACTION100
2.9066-3.08860.1851190.16363106X-RAY DIFFRACTION100
3.0886-3.32690.16861500.16053083X-RAY DIFFRACTION100
3.3269-3.66140.16151650.14743096X-RAY DIFFRACTION100
3.6614-4.19060.14721630.13823112X-RAY DIFFRACTION100
4.1906-5.27710.13061600.13283144X-RAY DIFFRACTION100
5.2771-36.2690.16721490.18073350X-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)
11.7111-0.38930.23892.7682-0.74331.33890.12940.1371-0.1799-0.2302-0.1651-0.19080.14670.13570.02840.15880.07710.00020.25230.02530.167247.639714.3951-24.3668
20.73550.50860.4065.26650.0131.9587-0.0095-0.8842-0.11021.2545-0.2971-0.5459-0.48380.24850.26190.5491-0.0283-0.26210.65760.11980.56759.594114.0506-7.885
31.0813-0.54170.11781.5554-0.59191.21860.04050.05330.0269-0.0232-0.03110.0214-0.0921-0.0199-0.00280.15910.0483-0.01590.2230.02650.170338.94524.9059-19.863
41.5138-0.58010.08131.1897-0.38262.3617-0.0414-0.2669-0.24020.02240.10240.30460.0277-0.1385-0.07310.20130.0384-0.00870.28440.07820.260929.919120.0748-11.5963
52.5044-0.26160.39092.4705-0.18571.6886-0.0157-0.0491-0.1868-0.0610.1091-0.1085-0.01810.053-0.10610.1432-0.00820.02240.1795-0.01240.165748.3916.476819.0577
61.3756-0.21340.18020.763-0.59253.037-0.04890.01350.30880.03420.0421-0.0645-0.5690.20610.01230.2668-0.0466-0.01740.1825-0.01290.228347.750433.246711.9682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 34 through 142 )
2X-RAY DIFFRACTION2chain 'A' and (resid 143 through 162 )
3X-RAY DIFFRACTION3chain 'A' and (resid 163 through 250 )
4X-RAY DIFFRACTION4chain 'A' and (resid 251 through 316 )
5X-RAY DIFFRACTION5chain 'B' and (resid 32 through 178 )
6X-RAY DIFFRACTION6chain 'B' and (resid 179 through 317 )

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