[English] 日本語
Yorodumi
- PDB-2hb9: Crystal Structure of the Zinc-Beta-Lactamase L1 from Stenotrophom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hb9
TitleCrystal Structure of the Zinc-Beta-Lactamase L1 from Stenotrophomonas Maltophilia (Inhibitor 3)
ComponentsMetallo-beta-lactamase L1
KeywordsHYDROLASE / METALLO / ZN / LACTAMASE
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 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-L13 / Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsNauton, L. / Garau, G. / Kahn, R. / Dideberg, O.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Structural insights into the design of inhibitors for the L1 metallo-beta-lactamase from Stenotrophomonas maltophilia.
Authors: Nauton, L. / Kahn, R. / Garau, G. / Hernandez, J.F. / Dideberg, O.
#1: Journal: Antimicrob.Agents Chemother. / Year: 2004
Title: Update of the Standard Numbering Scheme for Class B Beta-Lactamases
Authors: Garau, G. / Garcia-Saez, I. / Bebrone, C. / Anne, C. / Mercuri, P. / Galleni, M. / Frere, J.-M. / Dideberg, O.
#2: Journal: Embo J. / Year: 1995
Title: The 3-D Structure of a Zinc Metallo-Beta-Lactamase from Bacillus Cereus Reveals a New Type of Protein Fold
Authors: Carfi, A. / Pares, S. / Duee, E. / Galleni, M. / Duez, C. / Frere, J.-M. / Dideberg, O.
History
DepositionJun 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 30, 2023Group: 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 / pdbx_struct_special_symmetry / struct_conn / struct_site
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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999 SEQUENCE THE RESIDUE NUMBERING OF THE COORDINATES IS NON-SEQUENTIAL. MANY NUMBERS WERE SIMPLY ... SEQUENCE THE RESIDUE NUMBERING OF THE COORDINATES IS NON-SEQUENTIAL. MANY NUMBERS WERE SIMPLY SKIPPED IN THE NUMBERING AND HAVE NOTHING TO DO WITH LACK OF ELECTRON DENSITY.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4767
Polymers28,7401
Non-polymers7356
Water3,927218
1
A: Metallo-beta-lactamase L1
hetero molecules

A: Metallo-beta-lactamase L1
hetero molecules

A: Metallo-beta-lactamase L1
hetero molecules

A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,90428
Polymers114,9624
Non-polymers2,94224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area16190 Å2
ΔGint-451 kcal/mol
Surface area37820 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.090, 104.090, 98.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-589-

HOH

-
Components

#1: Protein Metallo-beta-lactamase L1 / Beta-lactamase type II / Penicillinase


Mass: 28740.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Strain: IID 1275 / Cellular location: PERIPLASM / Gene: L1 / Plasmid: PET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: P52700, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-L13 / 4-AMINO-5-(2-METHYLPHENYL)-2,4-DIHYDRO-3H-1,2,4-TRIAZOLE-3-THIONE


Mass: 206.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10N4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 1.8M AMMONIUM SULFATE, 0.1M HEPES PH 7.75, 1.5% V/V PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 281K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→19.51 Å / Num. all: 31993 / Num. obs: 31993 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.059 / Rsym value: 0.054 / Net I/σ(I): 11.2
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2 / Rsym value: 0.287 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
XDSdata scaling
SCALAdata scaling
CCP4model building
REFMAC5.2.0019refinement
XDSdata reduction
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SML

1sml


Resolution: 1.75→19.67 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.747 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1912 1623 5.1 %RANDOM
Rwork0.1697 ---
obs0.17081 30361 99.43 %-
all-31993 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.876 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 40 218 2259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212098
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.972853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2815260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23223.29588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10715304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.451515
X-RAY DIFFRACTIONr_chiral_restr0.0890.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021606
X-RAY DIFFRACTIONr_nbd_refined0.2790.21101
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21399
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2239
X-RAY DIFFRACTIONr_metal_ion_refined0.1340.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.227
X-RAY DIFFRACTIONr_mcbond_it0.7051.51347
X-RAY DIFFRACTIONr_mcangle_it1.15822098
X-RAY DIFFRACTIONr_scbond_it1.8543847
X-RAY DIFFRACTIONr_scangle_it2.9944.5755
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 111 -
Rwork0.211 2186 -
obs--99.14 %

+
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