[English] 日本語
Yorodumi
- PDB-5zg6: Crystal structure of beta-lactamase PenP mutant-E166Y in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zg6
TitleCrystal structure of beta-lactamase PenP mutant-E166Y in complex with cephaloridine as "post-acylation" intermediate
ComponentsBeta-lactamase
KeywordsHYDROLASE / class A beta-lactamase / antibiotic resistance
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Beta-lactamase / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CED / Beta-lactamase
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPan, X. / Zhao, Y.
CitationJournal: Sci Rep / Year: 2020
Title: The hydrolytic water molecule of Class A beta-lactamase relies on the acyl-enzyme intermediate ES* for proper coordination and catalysis.
Authors: He, Y. / Lei, J. / Pan, X. / Huang, X. / Zhao, Y.
History
DepositionMar 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,4054
Polymers59,7242
Non-polymers6812
Water1,910106
1
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2022
Polymers29,8621
Non-polymers3401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2022
Polymers29,8621
Non-polymers3401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.292, 46.459, 65.981
Angle α, β, γ (deg.)77.43, 75.53, 69.34
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Beta-lactamase / Penicillinase


Mass: 29861.859 Da / Num. of mol.: 2 / Mutation: E166Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: penP, blaP
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P00808, beta-lactamase
#2: Chemical ChemComp-CED / 5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID / DEGRADED CEPHALORIDINE, open form


Mass: 340.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16N2O4S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 1.99 Å3/Da / Density % sol: 38.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris pH8.0, 25% PEG 3350, 0.4M ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Aug 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→63.2 Å / Num. obs: 29472 / % possible obs: 94 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.073 / Rrim(I) all: 0.135 / Χ2: 1.92 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.032.80.31313070.8640.2130.3811.49883.9
2.03-2.073.10.28914230.9110.1910.3481.4790.9
2.07-2.113.10.2614540.9070.170.3121.44992.2
2.11-2.153.20.24814260.9410.1610.2971.45291.9
2.15-2.23.20.21414690.9440.1370.2551.53392
2.2-2.253.30.21314410.9470.1370.2541.57192
2.25-2.313.30.19614510.9530.1240.2331.54192.4
2.31-2.373.40.18614440.9590.1160.221.58993.3
2.37-2.443.40.17514840.970.110.2071.66493.6
2.44-2.523.40.16314480.9690.1030.1941.69793.9
2.52-2.613.40.1515000.9740.0950.1781.71694.8
2.61-2.713.40.14515060.9780.0920.1731.72495.3
2.71-2.843.40.1414820.980.0880.1661.8195.2
2.84-2.993.40.12315100.9790.0770.1461.87696.2
2.99-3.173.50.11115010.9820.070.1312.06996.2
3.17-3.423.50.08915300.9860.0560.1062.29197
3.42-3.763.50.08115000.9860.0510.0962.76196.3
3.76-4.313.40.07615510.9890.0490.0912.75597.5
4.31-5.433.30.07415080.9890.0490.0892.91197.1
5.43-63.23.10.06715370.9920.0460.0822.6197.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BLM

4blm


Resolution: 2→43.06 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.89 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25845 1486 5.1 %RANDOM
Rwork0.20819 ---
obs0.21075 27895 94.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.879 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4012 0 44 106 4162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134114
X-RAY DIFFRACTIONr_bond_other_d0.0350.0173936
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.6575554
X-RAY DIFFRACTIONr_angle_other_deg2.3931.599130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5545502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.33422.5224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26815740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8821530
X-RAY DIFFRACTIONr_chiral_restr0.0760.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024560
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02810
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3461.6962038
X-RAY DIFFRACTIONr_mcbond_other1.3461.6952037
X-RAY DIFFRACTIONr_mcangle_it2.1632.532530
X-RAY DIFFRACTIONr_mcangle_other2.1632.5322531
X-RAY DIFFRACTIONr_scbond_it1.6741.9252076
X-RAY DIFFRACTIONr_scbond_other1.6741.9252077
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.752.8093025
X-RAY DIFFRACTIONr_long_range_B_refined4.38919.8514506
X-RAY DIFFRACTIONr_long_range_B_other4.38519.8494501
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 97 -
Rwork0.232 1999 -
obs--90.31 %

+
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