[English] 日本語
Yorodumi
- PDB-7nrj: Crystal Structure of a Class D carbapenemase complexed with iodide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nrj
TitleCrystal Structure of a Class D carbapenemase complexed with iodide
ComponentsBeta-lactamase
KeywordsHYDROLASE / OXA / apo / iodide
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/transpeptidase-like
Similarity search - Domain/homology
1-BUTANOL / IODIDE ION / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsZhou, Q. / He, Y. / Jin, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31400663 China
CitationJournal: Acs Cent.Sci. / Year: 2023
Title: An Ion-Pair Induced Intermediate Complex Captured in Class D Carbapenemase Reveals Chloride Ion as a Janus Effector Modulating Activity
Authors: Zhou, Q. / Catalan, P. / Bell, H. / Baumann, P. / Cooke, R. / Evans, R. / Yang, J. / Zhang, Z. / Zappala, D. / Zhang, Y. / Blackburn, G.M. / He, Y. / Jin, Y.
History
DepositionMar 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2Mar 6, 2024Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Beta-lactamase
BBB: Beta-lactamase
CCC: Beta-lactamase
DDD: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,93431
Polymers121,0174
Non-polymers2,91827
Water16,592921
1
AAA: Beta-lactamase
CCC: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,83814
Polymers60,5082
Non-polymers1,33012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Beta-lactamase
DDD: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,09617
Polymers60,5082
Non-polymers1,58815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.764, 126.860, 111.100
Angle α, β, γ (deg.)90.000, 98.354, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Beta-lactamase


Mass: 30254.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaOXA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A482LRD5, beta-lactamase
#2: Chemical
ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL


Mass: 74.122 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 921 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH 8.0, 10% PEG 8000, 10% 1-BUTANOL mixed with the 10 mg/mL protein stock in 0.1M HEPES pH 7.5 buffer at 1:1 ratio
PH range: 7.5-8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.67→19.78 Å / Num. obs: 147826 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.996 / Net I/σ(I): 11
Reflection shellResolution: 1.67→1.7 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 7222 / CC1/2: 0.646

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S2P

4s2p


Resolution: 1.67→19.741 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.419 / SU ML: 0.074 / Cross valid method: FREE R-VALUE / ESU R: 0.083 / ESU R Free: 0.085
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1966 7450 5.041 %
Rwork0.166 140341 -
all0.168 --
obs-147791 99.849 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.36 Å2
Baniso -1Baniso -2Baniso -3
1-3.098 Å20 Å20.985 Å2
2---2.398 Å20 Å2
3----0.948 Å2
Refinement stepCycle: LAST / Resolution: 1.67→19.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7923 0 75 921 8919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0138266
X-RAY DIFFRACTIONr_bond_other_d0.0010.0187753
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.63411173
X-RAY DIFFRACTIONr_angle_other_deg1.351.58517790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8695984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29622.875473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.465151432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0411548
X-RAY DIFFRACTIONr_chiral_restr0.0820.21034
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029470
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022058
X-RAY DIFFRACTIONr_nbd_refined0.2110.21324
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1620.26184
X-RAY DIFFRACTIONr_nbtor_refined0.1570.23784
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.23349
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2474
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1550.27
X-RAY DIFFRACTIONr_nbd_other0.1450.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1330.229
X-RAY DIFFRACTIONr_mcbond_it1.8112.2643918
X-RAY DIFFRACTIONr_mcbond_other1.8082.2633917
X-RAY DIFFRACTIONr_mcangle_it2.53.3814908
X-RAY DIFFRACTIONr_mcangle_other2.5013.3814909
X-RAY DIFFRACTIONr_scbond_it2.8752.6444348
X-RAY DIFFRACTIONr_scbond_other2.8742.6454349
X-RAY DIFFRACTIONr_scangle_it4.4543.8286265
X-RAY DIFFRACTIONr_scangle_other4.4543.8296266
X-RAY DIFFRACTIONr_lrange_it5.7326.8569139
X-RAY DIFFRACTIONr_lrange_other5.53126.1338931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.7130.4335240.42310343X-RAY DIFFRACTION99.9081
1.713-1.760.365690.35310046X-RAY DIFFRACTION99.9153
1.76-1.8110.3355070.3049877X-RAY DIFFRACTION99.9807
1.811-1.8670.2644900.2479599X-RAY DIFFRACTION100
1.867-1.9280.2275290.1999184X-RAY DIFFRACTION99.8869
1.928-1.9960.2254740.1948892X-RAY DIFFRACTION99.6489
1.996-2.0710.1845040.1538594X-RAY DIFFRACTION100
2.071-2.1560.2024600.1748305X-RAY DIFFRACTION99.6362
2.156-2.2520.1894410.1557989X-RAY DIFFRACTION99.9881
2.252-2.3620.1953700.177622X-RAY DIFFRACTION99.7753
2.362-2.4890.1794000.1387262X-RAY DIFFRACTION100
2.489-2.640.1683630.1326878X-RAY DIFFRACTION100
2.64-2.8220.1733370.156451X-RAY DIFFRACTION99.9853
2.822-3.0480.1882810.1376044X-RAY DIFFRACTION100
3.048-3.3390.1772830.1435596X-RAY DIFFRACTION100
3.339-3.7330.1672710.1394993X-RAY DIFFRACTION99.962
3.733-4.310.172530.1244412X-RAY DIFFRACTION99.9143
4.31-5.2770.1581880.1323769X-RAY DIFFRACTION100
5.277-7.4560.191230.1852958X-RAY DIFFRACTION100

+
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://pdbjlvh1.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