[English] 日本語
Yorodumi
- PDB-5nbk: NDM-1 metallo-beta-lactamase: a parsimonious interpretation of th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nbk
TitleNDM-1 metallo-beta-lactamase: a parsimonious interpretation of the diffraction data
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / NDM-1 / metallo-beta-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
: / 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 type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsRaczynska, J.E. / Shabalin, I.G. / Jaskolski, M. / Minor, W. / Wlodawer, A.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Center for Research and DevelopmentAMR/1/2015 Poland
Citation
Journal: Drug Resist. Updat. / Year: 2018
Title: A close look onto structural models and primary ligands of metallo-beta-lactamases.
Authors: Raczynska, J.E. / Shabalin, I.G. / Minor, W. / Wlodawer, A. / Jaskolski, M.
#1: Journal: J. Med. Chem. / Year: 2015
Title: Approved Drugs Containing Thiols as Inhibitors of Metallo-beta-lactamases: Strategy To Combat Multidrug-Resistant Bacteria.
Authors: Klingler, F.M. / Wichelhaus, T.A. / Frank, D. / Cuesta-Bernal, J. / El-Delik, J. / Muller, H.F. / Sjuts, H. / Gottig, S. / Koenigs, A. / Pos, K.M. / Pogoryelov, D. / Proschak, E.
History
DepositionMar 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 13, 2019Group: Data collection / Experimental preparation / Category: diffrn_radiation_wavelength / exptl_crystal_grow
Item: _diffrn_radiation_wavelength.wt / _exptl_crystal_grow.temp
Revision 1.3Oct 16, 2019Group: Data collection / Category: diffrn_radiation_wavelength / reflns_shell / Item: _diffrn_radiation_wavelength.wt
Revision 1.4May 8, 2024Group: 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metallo-beta-lactamase type 2
C: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,86612
Polymers53,6682
Non-polymers1,19810
Water1,964109
1
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4776
Polymers26,8341
Non-polymers6435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3896
Polymers26,8341
Non-polymers5555
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.047, 108.047, 92.571
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 43 - 271 / Label seq-ID: 16 - 244

Dom-IDAuth asym-IDLabel asym-ID
1AA
2CB

-
Components

-
Protein , 1 types, 2 molecules AC

#1: Protein Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta- ...B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase type II / New Delhi metallo-beta-lactamase-1 / NDM-1


Mass: 26834.170 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: C7C422, beta-lactamase

-
Non-polymers , 5 types, 119 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C12H26O7 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.75 Å3/Da / Density % sol: 55.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 24 % PEG 1500 AND 0.05 M TBG (SODIUM TARTRATE/BIS - TRIS/GLYCYLGLYCINE) PH 4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→46.66 Å / Num. obs: 17411 / % possible obs: 100 % / Redundancy: 9.2 % / Net I/σ(I): 999

-
Processing

SoftwareName: REFMAC / Version: 5.8.0135 / Classification: refinement
RefinementResolution: 2.6→46.66 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.908 / SU B: 20.819 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / ESU R: 0.627 / ESU R Free: 0.283 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22928 871 5 %copied from 5a5z
Rwork0.18055 ---
obs0.18298 16540 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.719 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0 Å2
2--0.09 Å2-0 Å2
3----0.19 Å2
Refinement stepCycle: 1 / Resolution: 2.6→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3441 0 61 109 3611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193567
X-RAY DIFFRACTIONr_bond_other_d0.0050.023374
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9394833
X-RAY DIFFRACTIONr_angle_other_deg1.16537735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6265459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37124.474152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05215523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3291517
X-RAY DIFFRACTIONr_chiral_restr0.0840.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214107
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02822
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_it0.9882.5071848
X-RAY DIFFRACTIONr_mcbond_other0.9882.5061847
X-RAY DIFFRACTIONr_mcangle_it1.683.7532303
X-RAY DIFFRACTIONr_mcangle_other1.683.7542304
X-RAY DIFFRACTIONr_scbond_it1.3532.7561719
X-RAY DIFFRACTIONr_scbond_other1.342.7561719
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1442531
X-RAY DIFFRACTIONr_long_range_B_refined3.98920.0783787
X-RAY DIFFRACTIONr_long_range_B_other3.98720.083787
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 26464 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2C
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 64 -
Rwork0.299 1207 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
113.0399-1.91516.59243.2426-5.351513.29670.0714-0.41320.1311-0.01650.17760.53550.4487-0.4732-0.2490.25630.03350.06260.3373-0.0290.1904-9.313826.558370.427
23.62280.36250.44862.8919-0.70452.6418-0.0066-0.49180.06370.05030.06180.0738-0.0899-0.3375-0.05530.1295-0.01380.00360.270.01690.0056-1.715425.36660.9118
31.41010.4194-0.29990.9026-0.23581.68020.0184-0.0223-0.0410.00260.01960.03390.1031-0.0289-0.0380.1820.0013-0.01660.19210.00710.0268.149426.737550.2345
42.0462-0.2643-0.38872.9701-1.52244.71-0.0874-0.00340.30230.11690.15610.0094-0.1916-0.2939-0.06880.1106-0.0293-0.03470.24170.02860.0524-7.115333.074842.4653
55.8844-2.5544-0.35764.56110.56745.01340.44220.50070.5177-0.4337-0.38280.1602-0.55310.0732-0.05940.29690.04340.07350.15520.05830.11525.950945.912216.0493
64.2869-2.8654-3.40573.72211.32813.20410.02940.05240.1936-0.20050.029-0.30710.0896-0.0702-0.05840.25340.0285-0.01330.2020.05730.052823.810636.784817.8489
71.4996-0.0442-0.60640.3136-0.20221.93160.02180.05630.0382-0.102-0.0544-0.03160.0888-0.01490.03260.20060.01810.02120.16270.02510.007420.170833.80126.917
83.0926-1.1131-2.04963.7370.19582.75250.0546-0.17860.1582-0.2507-0.06340.1636-0.4557-0.07260.00880.2487-0.0166-0.06480.1791-0.04180.039720.198250.027336.678
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 49
2X-RAY DIFFRACTION2A50 - 106
3X-RAY DIFFRACTION3A107 - 195
4X-RAY DIFFRACTION4A196 - 272
5X-RAY DIFFRACTION5C43 - 75
6X-RAY DIFFRACTION6C76 - 101
7X-RAY DIFFRACTION7C102 - 210
8X-RAY DIFFRACTION8C211 - 272

+
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