[English] 日本語
Yorodumi
- PDB-2fu6: Zinc-beta-lactamase l1 from stenotrophomonas maltophilia (apo form) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fu6
TitleZinc-beta-lactamase l1 from stenotrophomonas maltophilia (apo form)
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
Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsNauton, L. / Garau, G. / Kahn, R. / Dideberg, O.
Citation
Journal: To be Published
Title: Crystal structure of the zinc-beta-lactamase L1 from stenotrophomonas maltophilia (apo form)
Authors: Nauton, L. / Garau, G. / Kahn, R. / Dideberg, O.
#1: 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.
#2: Journal: J.Mol.Biol. / Year: 2005
Title: A metallo-beta-lactamase enzyme in action: crystal structures of the monozinc carbapenemase CphA and its complex with biapenem
Authors: Garau, G. / Bebrone, C. / Anne, C. / Galleni, M. / Frere, J.M. / Dideberg, O.
History
DepositionJan 26, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 30, 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 25, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,52613
Polymers57,4812
Non-polymers1,04511
Water9,476526
1
A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3097
Polymers28,7401
Non-polymers5686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2176
Polymers28,7401
Non-polymers4765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Metallo-beta-lactamase L1
B: Metallo-beta-lactamase L1
hetero molecules

A: Metallo-beta-lactamase L1
B: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,05126
Polymers114,9624
Non-polymers2,09022
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area13620 Å2
ΔGint-182 kcal/mol
Surface area39550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.050, 105.050, 196.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

-
Components

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


Mass: 28740.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Strain: IID 1275 / Cellular location: PERIPLASM / Gene: L1 / Plasmid details: PUB 5832 / Plasmid: PET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: P52700, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS COORDINATES ARE USED NON-SEQUENTIAL RESIDUE NUMBERING. MANY NUMBERS WERE SIMPLY SKIPPED IN THE ...THIS COORDINATES ARE USED NON-SEQUENTIAL RESIDUE NUMBERING. MANY NUMBERS WERE SIMPLY SKIPPED IN THE NUMBERING AND HAVE NOTHING TO DO WITH LACK OF ELECTRON DENSITY.

-
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: 280 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: AS, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 280K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54179 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.541791
21.54181
ReflectionResolution: 2.05→20 Å / Num. obs: 40479 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 7.4
Reflection shellResolution: 2.05→2.103 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.49 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CCP4model building
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SML

1sml


Resolution: 2.05→19.89 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.745 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20937 2023 5 %RANDOM
Rwork0.16038 ---
all0.1631 ---
obs0.16286 38425 98.9 %-
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: 18.596 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å20 Å2
2--0.05 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4002 0 58 526 4586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0214173
X-RAY DIFFRACTIONr_bond_other_d0.0040.023769
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.9665677
X-RAY DIFFRACTIONr_angle_other_deg0.86638719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4275522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82323.258178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77315616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5671532
X-RAY DIFFRACTIONr_chiral_restr0.0960.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024617
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02817
X-RAY DIFFRACTIONr_nbd_refined0.3410.2904
X-RAY DIFFRACTIONr_nbd_other0.2010.23716
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21965
X-RAY DIFFRACTIONr_nbtor_other0.0870.22281
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2397
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.2108
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.253
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2051.53359
X-RAY DIFFRACTIONr_mcbond_other0.2331.51085
X-RAY DIFFRACTIONr_mcangle_it1.40224203
X-RAY DIFFRACTIONr_scbond_it2.47331746
X-RAY DIFFRACTIONr_scangle_it3.4944.51471
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 147 -
Rwork0.196 2734 -
obs--97.63 %

+
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