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- PDB-2hp5: Crystal Structure of the OXA-10 W154G mutant at pH 7.0 -

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Basic information

Entry
Database: PDB / ID: 2hp5
TitleCrystal Structure of the OXA-10 W154G mutant at pH 7.0
ComponentsBeta-lactamase PSE-2
KeywordsHYDROLASE / class D beta-lactamase / lysine carboxylation
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Beta-lactamase OXA-10
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKerff, F. / Falzone, C. / Herman, R. / Sauvage, E. / Charlier, P.
CitationJournal: Biochemistry / Year: 2009
Title: Critical role of tryptophan 154 for the activity and stability of class D beta-lactamases.
Authors: Baurin, S. / Vercheval, L. / Bouillenne, F. / Falzone, C. / Brans, A. / Jacquamet, L. / Ferrer, J.L. / Sauvage, E. / Dehareng, D. / Frere, J.M. / Charlier, P. / Galleni, M. / Kerff, F.
History
DepositionJul 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase PSE-2
B: Beta-lactamase PSE-2
C: Beta-lactamase PSE-2
D: Beta-lactamase PSE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,53018
Polymers110,3344
Non-polymers1,19614
Water1,67593
1
A: Beta-lactamase PSE-2
B: Beta-lactamase PSE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7659
Polymers55,1672
Non-polymers5987
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-101 kcal/mol
Surface area21200 Å2
MethodPISA
2
C: Beta-lactamase PSE-2
D: Beta-lactamase PSE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7659
Polymers55,1672
Non-polymers5987
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-106 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.110, 125.400, 92.360
Angle α, β, γ (deg.)90.00, 99.80, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer. There are two dimers in the asymmetric unit: first dimes is assembled from monomers A and B, the other dimer from monomers C and D.

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Components

#1: Protein
Beta-lactamase PSE-2 / Beta lactamase OXA-10


Mass: 27583.381 Da / Num. of mol.: 4 / Mutation: W154G, N-terminal Met added
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pse2, oxa10 / Plasmid: pET22BKanR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Hotstar / References: UniProt: P14489, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 293 K / pH: 7
Details: Ammonium Sulfate 2.2 M, HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 26, 2006
RadiationMonochromator: MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→46.47 Å / Num. obs: 28824 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 45.63 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 11
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 3.1 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K4F

1k4f


Resolution: 2.7→46.47 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.86 / SU B: 40.292 / SU ML: 0.408 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1438 5 %RANDOM
Rwork0.21 ---
obs0.213 27307 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.43 Å2
Baniso -1Baniso -2Baniso -3
1-3.25 Å20 Å24.47 Å2
2---4.25 Å20 Å2
3---2.53 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7475 0 54 93 7622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227669
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0751.95410364
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6355941
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.21625.104337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15151383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4391532
X-RAY DIFFRACTIONr_chiral_restr0.0730.21139
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025663
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.23613
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.25275
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2262
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.60924843
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.56337583
X-RAY DIFFRACTIONr_scbond_it1.46923256
X-RAY DIFFRACTIONr_scangle_it2.15232781
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 106 -
Rwork0.322 2019 -
obs--97.43 %
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)
12.2862-0.75890.15554.50510.67041.7893-0.1456-0.01690.1955-0.17860.0361-0.7309-0.10850.19650.1095-0.35250.0197-0.0659-0.24470.0529-0.22059.042913.5437-5.2059
23.0492-0.92980.11043.7953-1.54612.4724-0.026-0.1512-0.02920.30810.13640.3046-0.0626-0.1147-0.1104-0.2934-0.04730.0106-0.3227-0.0121-0.2862-5.2745-13.43365.5465
32.7722-0.6394-0.48713.2316-0.72172.2192-0.00010.03870.0660.13110.09110.1528-0.0544-0.1036-0.091-0.1693-0.02970.0949-0.2956-0.0311-0.28-19.342132.3188-36.1245
42.42890.8532-0.7936.034-0.28944.4015-0.17990.1119-0.09070.02210.0532-0.40580.04750.32320.1267-0.29650.0307-0.0312-0.16460.0607-0.2794-10.620958.1548-51.7276
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA19 - 2641 - 246
2X-RAY DIFFRACTION2BB19 - 2641 - 246
3X-RAY DIFFRACTION3CC20 - 2642 - 246
4X-RAY DIFFRACTION4DD21 - 2643 - 246

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