[English] 日本語
Yorodumi
- PDB-6nvt: Crystal structure of TLA-1 extended spectrum Beta-lactamase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nvt
TitleCrystal structure of TLA-1 extended spectrum Beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / Lactamase / Antibiotic / Resistance
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRudino-Pinera, E. / Cifuentes-Castro, V.H. / Rodriguez-Almazan, C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: The crystal structure of ESBL TLA-1 in complex with clavulanic acid reveals a second acylation site.
Authors: Cifuentes-Castro, V. / Rodriguez-Almazan, C. / Silva-Sanchez, J. / Rudino-Pinera, E.
History
DepositionFeb 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)129,14079
Polymers123,7904
Non-polymers5,35075
Water18,6641036
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,36421
Polymers30,9471
Non-polymers1,41620
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,01015
Polymers30,9471
Non-polymers1,06214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,46322
Polymers30,9471
Non-polymers1,51621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,30321
Polymers30,9471
Non-polymers1,35620
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.060, 99.010, 99.700
Angle α, β, γ (deg.)90.000, 90.040, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Beta-lactamase


Mass: 30947.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21(DE3) / Gene: tla-1 / Plasmid: pJ411 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X6W1, beta-lactamase
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical...
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1036 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.71 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 2.4 M Ammonium sulfate, 100 mMSodium Phosphate dibasic/Citric acid

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979131 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 30, 2017 / Details: Sagitally focusing second crystal
RadiationMonochromator: Si (111) Rosenbaum-Rock double-crystal monochromator: water cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979131 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 97662 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.01 % / Biso Wilson estimate: 39.639 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.077 / Rsym value: 0.069 / Net I/σ(I): 4.08
Reflection shellResolution: 2.2→2.3 Å / Mean I/σ(I) obs: 4.08 / Num. unique obs: 12124 / CC1/2: 0.839 / Rrim(I) all: 0.647 / Rsym value: 0.579 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+25 / Resolution: 2.2→35.148 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 4857 4.98 %Random 5 percent
Rwork0.1813 92757 --
obs0.1826 97614 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.12 Å2 / Biso mean: 39.7915 Å2 / Biso min: 18.22 Å2
Refinement stepCycle: final / Resolution: 2.2→35.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8712 0 306 1039 10057
Biso mean--63.29 46.48 -
Num. residues----1104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0279237
X-RAY DIFFRACTIONf_angle_d1.81112485
X-RAY DIFFRACTIONf_chiral_restr0.21405
X-RAY DIFFRACTIONf_plane_restr0.0131567
X-RAY DIFFRACTIONf_dihedral_angle_d4.8177617
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2250.30541770.276430673244100
2.225-2.25120.28711620.271730783240100
2.2512-2.27860.31881680.260129973165100
2.2786-2.30750.27411540.251631703324100
2.3075-2.33780.26381600.246330453205100
2.3378-2.36980.26371460.238530833229100
2.3698-2.40370.24321510.235531193270100
2.4037-2.43960.29511680.232130493217100
2.4396-2.47770.29331910.235430743265100
2.4777-2.51830.24661890.226630243213100
2.5183-2.56170.29831520.220431303282100
2.5617-2.60830.31720.215531283300100
2.6083-2.65840.281570.215530013158100
2.6584-2.71260.22311610.220530833244100
2.7126-2.77160.25321680.218230943262100
2.7716-2.83610.22271590.22230943253100
2.8361-2.90690.24491610.217730673228100
2.9069-2.98550.25521460.210731353281100
2.9855-3.07330.24151550.211330973252100
3.0733-3.17240.21821580.198930733231100
3.1724-3.28570.19321310.186831343265100
3.2857-3.41720.18781350.17531583293100
3.4172-3.57260.20751820.159530683250100
3.5726-3.76070.16351580.143230613219100
3.7607-3.9960.17161780.135530973275100
3.996-4.30410.12411540.123931333287100
4.3041-4.73630.17741030.118931563259100
4.7363-5.41950.17031910.145731143305100
5.4195-6.81980.20071510.189431173268100
6.8198-35.1520.16352190.1663111333098

+
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