[English] 日本語
Yorodumi
- PDB-8gpc: Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with h... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gpc
TitleCrystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed ampicillin
ComponentsMetallo beta lactamase NDM-1
KeywordsHYDROLASE
Function / homology: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / beta-lactamase activity / metal ion binding / Chem-ZZ7 / NDM-1
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsShi, X. / Dai, Y. / Zhang, Q. / Liu, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Interplay between the beta-lactam side chain and an active-site mobile loop of NDM-1 in penicillin hydrolysis as a potential target for mechanism-based inhibitor design.
Authors: Shi, X. / Dai, Y. / Lan, Z. / Wang, S. / Cui, L. / Xiao, C. / Zhao, K. / Li, X. / Liu, W. / Zhang, Q.
History
DepositionAug 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metallo beta lactamase NDM-1
B: Metallo beta lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0749
Polymers57,0552
Non-polymers1,0197
Water10,791599
1
A: Metallo beta lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0495
Polymers28,5271
Non-polymers5214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area10020 Å2
MethodPISA
2
B: Metallo beta lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0264
Polymers28,5271
Non-polymers4983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.260, 79.110, 134.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Metallo beta lactamase NDM-1 / New Delhi Metallo carbapenemase-1 / New Delhi metallo-beta-lactamase NDM-1 / New Delhi metallo-beta-lactamse 1


Mass: 28527.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1, bla NDM-1, blaNDM1, NDM-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: E9NWK5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZZ7 / (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form)


Mass: 367.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21N3O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / 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: 1.83 Å3/Da / Density % sol: 32.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Succinate pH5.5, 28%PEG3350 / PH range: 5.4-5.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.4→33.59 Å / Num. obs: 81150 / % possible obs: 97.4 % / Redundancy: 7.9 % / Biso Wilson estimate: 13.79 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.51
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 16271 / CC1/2: 0.858

-
Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
Cootmodel building
PHENIX1.19.1_4122phasing
PHENIX1.19.1_4122refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RL2

4rl2


Resolution: 1.4→33.59 Å / SU ML: 0.1086 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 14.0768
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1603 4139 5.1 %
Rwork0.13 77011 -
obs0.1315 81150 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.26 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3576 0 55 599 4230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093748
X-RAY DIFFRACTIONf_angle_d1.1765120
X-RAY DIFFRACTIONf_chiral_restr0.0958574
X-RAY DIFFRACTIONf_plane_restr0.011689
X-RAY DIFFRACTIONf_dihedral_angle_d6.3274554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.23711180.18391918X-RAY DIFFRACTION75.16
1.42-1.430.23791120.14732089X-RAY DIFFRACTION80.77
1.43-1.450.14911260.12632263X-RAY DIFFRACTION86.12
1.45-1.470.17521270.12012382X-RAY DIFFRACTION91.54
1.47-1.490.17121210.12122472X-RAY DIFFRACTION95.12
1.49-1.510.17011380.12212468X-RAY DIFFRACTION94.63
1.51-1.530.20081420.11422569X-RAY DIFFRACTION98.91
1.53-1.550.16741440.11422596X-RAY DIFFRACTION99.6
1.55-1.580.17061380.11342635X-RAY DIFFRACTION99.82
1.58-1.60.16851310.11252575X-RAY DIFFRACTION99.96
1.6-1.630.17691410.11042623X-RAY DIFFRACTION99.93
1.63-1.660.16531560.10842586X-RAY DIFFRACTION99.93
1.66-1.690.17591560.10652610X-RAY DIFFRACTION99.93
1.69-1.730.14861370.10692608X-RAY DIFFRACTION99.96
1.73-1.760.15221360.10812624X-RAY DIFFRACTION99.93
1.76-1.80.17221540.11632601X-RAY DIFFRACTION99.93
1.8-1.850.16291300.11942618X-RAY DIFFRACTION99.82
1.85-1.90.16861450.12352613X-RAY DIFFRACTION99.89
1.9-1.960.14671470.11352654X-RAY DIFFRACTION99.93
1.96-2.020.13721450.1192591X-RAY DIFFRACTION99.93
2.02-2.090.15831410.12322645X-RAY DIFFRACTION99.93
2.09-2.170.17491180.12612669X-RAY DIFFRACTION99.82
2.17-2.270.15871400.12542636X-RAY DIFFRACTION100
2.27-2.390.18721370.13342649X-RAY DIFFRACTION99.96
2.39-2.540.15541420.13662655X-RAY DIFFRACTION99.82
2.54-2.740.15451520.14262665X-RAY DIFFRACTION99.93
2.74-3.020.1641200.14232715X-RAY DIFFRACTION99.89
3.02-3.450.15271480.14082682X-RAY DIFFRACTION99.96
3.45-4.350.13451410.13352747X-RAY DIFFRACTION99.79
4.35-33.590.16671560.14442853X-RAY DIFFRACTION99.64

+
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