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- PDB-5ls3: Crystal structure of metallo-beta-lactamase SPM-1 with Y58C mutation -

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Basic information

Entry
Database: PDB / ID: 5ls3
TitleCrystal structure of metallo-beta-lactamase SPM-1 with Y58C mutation
ComponentsBeta-lactamase IMP-1
KeywordsHYDROLASE / metallo-beta-lactamase / carbapenemase
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: 1.754 Å
AuthorsHinchliffe, P. / Spencer, J.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1100135 United Kingdom
ational Institute of Allergy and Infectious Diseases of the U.S. National Institutes of HealthR01AI100560 United States
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: (19) F-NMR Reveals the Role of Mobile Loops in Product and Inhibitor Binding by the Sao Paulo Metallo-beta-Lactamase.
Authors: Abboud, M.I. / Hinchliffe, P. / Brem, J. / Macsics, R. / Pfeffer, I. / Makena, A. / Umland, K.D. / Rydzik, A.M. / Li, G.B. / Spencer, J. / Claridge, T.D. / Schofield, C.J.
History
DepositionAug 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Jul 12, 2017Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,0617
Polymers55,7342
Non-polymers3275
Water6,738374
1
B: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0634
Polymers27,8671
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Beta-lactamase IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9983
Polymers27,8671
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.886, 59.886, 276.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-548-

HOH

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Components

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


Mass: 27867.148 Da / Num. of mol.: 2 / Mutation: Y58C
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
Plasmid: pOPIN-F / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q8G9Q0, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M mixture of HEPES and MOPS pH7.5, 0.03 M NaF, 0.03 M NaI, 0.03 M NaB, 12% PEG3350, 12% PEG1000, 12% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.75→29.263 Å / Num. obs: 50459 / % possible obs: 97.9 % / Redundancy: 25 % / CC1/2: 1 / Rpim(I) all: 0.02 / Net I/σ(I): 32.2
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 24.1 % / Mean I/σ(I) obs: 5.1 / CC1/2: 0.895 / Rpim(I) all: 0.205 / % possible all: 86.8

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Processing

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

4bp0


Resolution: 1.754→29.263 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.184 2485 4.93 %
Rwork0.1659 --
obs0.1668 50435 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.754→29.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3803 0 5 374 4182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073900
X-RAY DIFFRACTIONf_angle_d1.1595267
X-RAY DIFFRACTIONf_dihedral_angle_d12.3621463
X-RAY DIFFRACTIONf_chiral_restr0.051583
X-RAY DIFFRACTIONf_plane_restr0.006672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.754-1.78770.27511230.22062257X-RAY DIFFRACTION85
1.7877-1.82420.2051350.19492600X-RAY DIFFRACTION97
1.8242-1.86390.23671330.18312590X-RAY DIFFRACTION97
1.8639-1.90720.211440.1862592X-RAY DIFFRACTION97
1.9072-1.95490.24021350.18492608X-RAY DIFFRACTION97
1.9549-2.00780.20191360.17762636X-RAY DIFFRACTION97
2.0078-2.06680.18051390.16862656X-RAY DIFFRACTION98
2.0668-2.13350.21491420.16912621X-RAY DIFFRACTION98
2.1335-2.20970.19731440.1682609X-RAY DIFFRACTION98
2.2097-2.29820.20221280.17182690X-RAY DIFFRACTION98
2.2982-2.40270.21731320.16922661X-RAY DIFFRACTION98
2.4027-2.52930.20511400.17362680X-RAY DIFFRACTION98
2.5293-2.68770.2191270.16772698X-RAY DIFFRACTION98
2.6877-2.89510.20331360.17522704X-RAY DIFFRACTION98
2.8951-3.18610.19211230.17012754X-RAY DIFFRACTION99
3.1861-3.64640.17421480.15292757X-RAY DIFFRACTION99
3.6464-4.59120.13321640.14472826X-RAY DIFFRACTION99
4.5912-29.26670.16861560.1663011X-RAY DIFFRACTION99
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)
12.56990.74460.7752.72540.44583.0066-0.0015-0.18480.21820.218-0.0070.1027-0.3029-0.1218-0.00240.2020.02830.02690.11550.01240.1591-11.113232.5646-16.2761
22.4042.64692.30644.69823.98323.43430.6828-0.8214-0.06451.3656-0.60341.00911.0816-1.6301-0.06960.6918-0.08620.21850.79960.03570.6949-29.854826.6061-10.6624
31.99580.1460.76642.7253-0.80852.86860.1336-0.0043-0.21110.09590.021-0.16750.16220.1378-0.12660.16050.0184-0.01010.1142-0.02980.1634-4.970719.3025-18.5188
45.78444.1445-0.30147.04671.09655.6630.1058-0.1957-0.66230.27550.13810.46760.8021-0.2672-0.22920.4338-0.0021-0.16320.190.06740.4366-5.71066.4404-8.1271
51.6416-0.3180.29452.542-0.50423.3894-0.02940.0440.1680.0138-0.0361-0.0133-0.51180.00310.05250.2203-0.00830.00580.1451-0.01320.1711-1.692328.938619.3122
64.6348-3.63252.27617.4027-4.91928.94280.02461.73060.108-1.9216-0.3446-0.80.97870.67240.23890.7473-0.11390.20460.83050.01490.62812.754227.0266.8795
72.0020.50710.01182.40280.51673.2182-0.118-0.0232-0.09270.0002-0.00490.09370.0033-0.16930.13240.13530.02260.02870.1390.02650.176-6.932115.392319.9453
88.7317-6.0071-6.78764.49215.66348.029-0.20630.5546-0.7620.0456-0.28050.39410.574-0.41970.48370.2788-0.08180.03960.2799-0.05660.39-9.17124.15497.5479
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 31 through 142 )
2X-RAY DIFFRACTION2chain 'B' and (resid 143 through 163 )
3X-RAY DIFFRACTION3chain 'B' and (resid 164 through 291 )
4X-RAY DIFFRACTION4chain 'B' and (resid 292 through 310 )
5X-RAY DIFFRACTION5chain 'A' and (resid 32 through 142 )
6X-RAY DIFFRACTION6chain 'A' and (resid 143 through 163 )
7X-RAY DIFFRACTION7chain 'A' and (resid 164 through 291 )
8X-RAY DIFFRACTION8chain 'A' and (resid 292 through 311 )

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