[English] 日本語
Yorodumi
- PDB-5wig: Structure of New Delhi Metallo-Beta-lactamase 4 (NDM-4) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wig
TitleStructure of New Delhi Metallo-Beta-lactamase 4 (NDM-4)
ComponentsNDM-4
KeywordsHYDROLASE / 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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NDM-4 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsVanPelt, J. / Williams, C. / Page, R.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111926 United States
CitationJournal: Acs Infect Dis. / Year: 2017
Title: Clinical Variants of New Delhi Metallo-beta-Lactamase Are Evolving To Overcome Zinc Scarcity.
Authors: Stewart, A.C. / Bethel, C.R. / VanPelt, J. / Bergstrom, A. / Cheng, Z. / Miller, C.G. / Williams, C. / Poth, R. / Morris, M. / Lahey, O. / Nix, J.C. / Tierney, D.L. / Page, R.C. / Crowder, M. ...Authors: Stewart, A.C. / Bethel, C.R. / VanPelt, J. / Bergstrom, A. / Cheng, Z. / Miller, C.G. / Williams, C. / Poth, R. / Morris, M. / Lahey, O. / Nix, J.C. / Tierney, D.L. / Page, R.C. / Crowder, M.W. / Bonomo, R.A. / Fast, W.
History
DepositionJul 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / 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 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NDM-4
B: NDM-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8666
Polymers48,6052
Non-polymers2624
Water10,935607
1
A: NDM-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4333
Polymers24,3021
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NDM-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4333
Polymers24,3021
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.414, 59.154, 84.500
Angle α, β, γ (deg.)90.00, 98.70, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein NDM-4


Mass: 24302.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0G2ST15, UniProt: C7C422*PLUS
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 2.11 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M bis-tris, 20% polyethylene glycol monomethyl ether 550

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jun 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→39.18 Å / Num. obs: 79231 / % possible obs: 99.6 % / Redundancy: 3.5 % / CC1/2: 0.998 / Net I/σ(I): 9.68
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 7915 / CC1/2: 0.396 / % possible all: 99.89

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4tyf

4tyf


Resolution: 1.4→39.177 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.33
RfactorNum. reflection% reflection
Rfree0.2252 3826 2.51 %
Rwork0.2003 --
obs0.2009 79231 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→39.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 0 4 608 4005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113542
X-RAY DIFFRACTIONf_angle_d1.4734842
X-RAY DIFFRACTIONf_dihedral_angle_d13.2751244
X-RAY DIFFRACTIONf_chiral_restr0.099539
X-RAY DIFFRACTIONf_plane_restr0.008647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41770.40881400.38235475X-RAY DIFFRACTION96
1.4177-1.43640.38531420.37935454X-RAY DIFFRACTION96
1.4364-1.45610.41791420.36295478X-RAY DIFFRACTION98
1.4561-1.47690.39241420.35545616X-RAY DIFFRACTION98
1.4769-1.49890.27321430.33625432X-RAY DIFFRACTION98
1.4989-1.52230.36221420.32845556X-RAY DIFFRACTION99
1.5223-1.54730.30981410.31595566X-RAY DIFFRACTION98
1.5473-1.5740.30781420.29395516X-RAY DIFFRACTION99
1.574-1.60260.2961480.28965606X-RAY DIFFRACTION99
1.6026-1.63340.29541440.27035564X-RAY DIFFRACTION99
1.6334-1.66680.30021400.26115532X-RAY DIFFRACTION99
1.6668-1.7030.26851400.25165516X-RAY DIFFRACTION98
1.703-1.74260.26021470.23185623X-RAY DIFFRACTION99
1.7426-1.78620.23331410.22035626X-RAY DIFFRACTION99
1.7862-1.83450.24391460.2085578X-RAY DIFFRACTION99
1.8345-1.88850.22821430.20325591X-RAY DIFFRACTION99
1.8885-1.94940.21951400.20185550X-RAY DIFFRACTION99
1.9494-2.01910.20621460.18515558X-RAY DIFFRACTION98
2.0191-2.09990.22871410.17875484X-RAY DIFFRACTION98
2.0999-2.19550.25231420.17695569X-RAY DIFFRACTION98
2.1955-2.31120.21081440.18625468X-RAY DIFFRACTION97
2.3112-2.4560.20421410.16735453X-RAY DIFFRACTION97
2.456-2.64560.19211380.16985424X-RAY DIFFRACTION97
2.6456-2.91180.18951420.16225437X-RAY DIFFRACTION96
2.9118-3.33290.19761430.15655362X-RAY DIFFRACTION95
3.3329-4.19840.14591380.14865319X-RAY DIFFRACTION94
4.1984-39.19210.17611280.14525079X-RAY DIFFRACTION90
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)
12.91761.72241.44375.62335.36647.26110.0045-0.09180.11370.1428-0.02240.48620.1116-0.19540.05640.1437-0.01710.03720.12730.01090.1879-15.908236.580886.1304
22.508-0.25210.39355.05630.44923.9083-0.0364-0.2317-0.43610.2554-0.0281-0.06150.38910.1445-0.01860.1223-0.01910.01880.11780.02640.1661-6.621628.652787.2206
31.7841-1.21590.34525.2547-0.51931.49910.04750.07990.0345-0.1355-0.06160.1254-0.0303-0.12460.00390.08110.00050.00980.0840.00540.0853-7.582340.545681.2176
41.19290.0412-0.07752.12430.33751.27250.0664-0.06330.00780.1689-0.0292-0.47220.02830.0565-0.03910.12-0.008-0.02530.09440.01930.18816.977842.546586.7576
52.345-1.23770.23594.328-1.72441.46860.0998-0.3185-0.07840.5279-0.0019-0.24180.2019-0.0524-0.09290.3887-0.0398-0.08030.180.00340.14260.987535.548798.7436
60.52050.63280.27790.76850.33760.14820.15-0.3432-0.15520.6745-0.0788-0.19920.26410.0023-0.04170.5443-0.059-0.07210.24630.01720.1609-0.316136.668104.1028
70.50561.41650.92574.74212.26362.2427-0.0043-0.09610.09770.0737-0.05150.54460.0542-0.26690.06420.0872-0.01680.01670.1855-0.01620.2604-22.229735.8685128.0265
85.2665-3.8085-1.82362.80941.32941.6331-0.2064-0.2134-0.54670.24870.01810.31230.28660.05630.16050.1215-0.01820.0250.1570.00880.2473-12.142526.6739129.1249
91.3495-0.15550.16521.4036-0.04870.677-0.01710.0364-0.0558-0.0002-0.01440.26890.0251-0.11630.01880.0591-0.00380.00620.1044-0.01510.1306-13.999839.9601123.0735
100.63050.08870.26062.32080.45271.9027-0-0.0202-0.03630.0178-0.0113-0.12050.08870.01550.01040.0387-0.00970.01110.10090.00570.08680.50841.7144128.3605
112.3423-0.83950.68293.5417-1.46732.3289-0.0497-0.1585-0.14720.20080.10.1880.234-0.1296-0.03060.1598-0.02990.02520.1618-0.00850.082-5.144835.0288140.2033
123.25040.88950.44391.7384-0.04694.00270.0492-0.1739-0.09280.3066-0.00520.17910.0982-0.1383-0.04160.1533-0.00790.05170.1380.01110.088-6.387135.713145.5169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 42 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 70 )
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 118 )
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 194 )
5X-RAY DIFFRACTION5chain 'A' and (resid 195 through 228 )
6X-RAY DIFFRACTION6chain 'A' and (resid 229 through 270 )
7X-RAY DIFFRACTION7chain 'B' and (resid 42 through 57 )
8X-RAY DIFFRACTION8chain 'B' and (resid 58 through 70 )
9X-RAY DIFFRACTION9chain 'B' and (resid 71 through 118 )
10X-RAY DIFFRACTION10chain 'B' and (resid 119 through 194 )
11X-RAY DIFFRACTION11chain 'B' and (resid 195 through 228 )
12X-RAY DIFFRACTION12chain 'B' and (resid 229 through 270 )

+
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