[English] 日本語
Yorodumi
- PDB-2hp5: Crystal Structure of the OXA-10 W154G mutant at pH 7.0 -

+
Open data


ID or keywords:

Loading...

-
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 / response to antibiotic
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more