[English] 日本語
Yorodumi
- PDB-5zgq: Crystal structure of NDM-1 at pH7.5 (Tris-HCl, (NH4)2SO4) in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zgq
TitleCrystal structure of NDM-1 at pH7.5 (Tris-HCl, (NH4)2SO4) in complex with hydrolyzed ampicillin
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE/ANTIBIOTIC / NDM-1 / metallo-beta-lactamase / antibiotic resistent / conformational change / HYDROLASE-ANTIBIOTIC complex
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; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HYDROXIDE ION / Chem-ZZ7 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsZhang, H. / Hao, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31670753 China
CitationJournal: Antimicrob. Agents Chemother. / Year: 2018
Title: Active-Site Conformational Fluctuations Promote the Enzymatic Activity of NDM-1.
Authors: Zhang, H. / Ma, G. / Zhu, Y. / Zeng, L. / Ahmad, A. / Wang, C. / Pang, B. / Fang, H. / Zhao, L. / Hao, Q.
History
DepositionMar 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 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 / struct_conn
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,29410
Polymers51,2642
Non-polymers1,0308
Water10,539585
1
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1475
Polymers25,6321
Non-polymers5154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1475
Polymers25,6321
Non-polymers5154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.200, 79.068, 134.162
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#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: 25631.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Plasmid: pRHisMBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C7C422, beta-lactamase
#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-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 2.03 Å3/Da / Density % sol: 39.35 % / Mosaicity: 0.352 ° / Mosaicity esd: 0.004 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris-HCl pH7.5, 25% PEG 4000, 0.7M (NH4)2SO4, 20mg/ml ampicillin

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 66725 / % possible obs: 98.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.081 / Χ2: 1.014 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.5-1.556.30.45763180.677195
1.55-1.626.20.38364000.71196.3
1.62-1.696.20.30365620.76197.9
1.69-1.786.20.2365850.82198.7
1.78-1.896.30.17366540.893199.1
1.89-2.046.40.12966781.092199.6
2.04-2.246.60.1167291.371199.8
2.24-2.566.80.0967821.444199.8
2.56-3.236.90.05368551.147199.9
3.23-507.10.03271621.0691100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q6X

3q6x
PDB Unreleased entry


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.305 / SU ML: 0.038 / SU R Cruickshank DPI: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.061
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1536 3374 5.1 %RANDOM
Rwork0.118 ---
obs0.1198 63271 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 69.53 Å2 / Biso mean: 18.135 Å2 / Biso min: 10.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.17 Å2
Refinement stepCycle: final / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 56 585 4235
Biso mean--14.58 32.62 -
Num. residues----482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193783
X-RAY DIFFRACTIONr_bond_other_d0.0020.023417
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.9475154
X-RAY DIFFRACTIONr_angle_other_deg0.9623.0037875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2145492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.83524.534161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.23115565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1111518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214298
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02742
X-RAY DIFFRACTIONr_rigid_bond_restr0.92837192
X-RAY DIFFRACTIONr_sphericity_free26.075330
X-RAY DIFFRACTIONr_sphericity_bonded4.73157343
LS refinement shellResolution: 1.501→1.54 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.178 219 -
Rwork0.156 4401 -
all-4620 -
obs--94.13 %
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)
16.87540.8827-3.73781.85323.241910.0177-0.06120.1175-0.27540.39310.016-0.07880.9250.04620.04520.22740.1412-0.00750.21210.01210.01647.50193.623336.9301
29.2837-1.3811-4.7371.09790.718411.65050.35210.1179-0.3757-0.0977-0.1251-0.08630.65860.5645-0.22710.15070.0536-0.04270.0607-0.02260.100649.8998-1.557145.9058
36.33860.64332.55941.2460.36213.69520.00930.0744-0.1312-0.081-0.0053-0.12920.19480.0077-0.00390.13030.0190.0040.03380.0130.064249.9415.660748.3896
41.05530.15190.5491.1604-0.33152.57350.0745-0.0719-0.08590.0661-0.0235-0.04340.2474-0.002-0.0510.12090.0016-0.01410.05340.0090.053646.02336.461954.2574
50.6290.0774-0.010.8224-0.15070.4926-0.0177-0.11570.02130.05060-0.00560.0409-0.00340.01770.0780.0042-0.00460.0801-0.00120.051945.07422.184156.4704
61.175-0.19690.29181.4759-0.1870.8522-0.00160.051-0.0345-0.1271-0.0104-0.09770.06510.08390.0120.07830.00790.01610.08050.00130.052954.673821.531243.7273
72.6668-3.03651.34755.4644-1.82422.38040.13430.26620.1341-0.4635-0.2314-0.1906-0.04780.21440.09710.1123-0.00030.04460.0790.01150.047157.565625.304736.6921
810.5276-2.68743.21572.276-2.90843.7262-0.05030.20990.37360.373-0.091-0.1138-0.50780.09130.14130.22660.0854-0.05390.1045-0.02430.029533.414462.829839.9594
917.4131-0.40583.91862.37960.39497.4593-0.18940.08790.1291-0.18780.02410.255-0.9698-0.67980.16530.1530.1041-0.01090.08560.0120.068235.525768.021848.837
103.09520.2273-2.10630.732-0.01275.1224-0.04220.1490.1216-0.11470.03380.0397-0.0228-0.02640.00840.0877-0.0015-0.01490.0515-0.00120.07736.965460.66250.2246
110.4695-0.0457-0.03110.83330.51511.5451-0.0033-0.01330.0662-0.03060.0272-0.0008-0.0920.0325-0.02380.073-0.0039-0.00530.0691-0.00270.06643.467957.253154.2739
120.56680.19930.01880.70810.16620.36-0.002-0.0563-0.00770.01830.0011-0.0178-0.00640.03380.00080.07190.0029-0.00570.0749-0.00070.059343.712543.360457.4527
130.69440.0354-0.14891.20780.27531.0524-0.00230.03820.0295-0.1018-0.02410.1042-0.0197-0.06190.02640.06480.0012-0.01850.0896-0.01010.085130.145444.575148.2866
142.2696-2.0251-1.36944.9462.88555.80550.02290.2038-0.111-0.2839-0.16290.17420.243-0.22150.14010.0697-0.0089-0.01870.0711-0.02520.081724.588240.475244.0623
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 39
2X-RAY DIFFRACTION2A40 - 48
3X-RAY DIFFRACTION3A49 - 67
4X-RAY DIFFRACTION4A68 - 112
5X-RAY DIFFRACTION5A113 - 197
6X-RAY DIFFRACTION6A198 - 253
7X-RAY DIFFRACTION7A254 - 270
8X-RAY DIFFRACTION8B30 - 39
9X-RAY DIFFRACTION9B40 - 48
10X-RAY DIFFRACTION10B49 - 68
11X-RAY DIFFRACTION11B69 - 129
12X-RAY DIFFRACTION12B130 - 201
13X-RAY DIFFRACTION13B202 - 254
14X-RAY DIFFRACTION14B255 - 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