[English] 日本語
Yorodumi
- PDB-5zjv: Crystal structure of the catalytic domain of MCR-1 (cMCR-1) in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zjv
TitleCrystal structure of the catalytic domain of MCR-1 (cMCR-1) in complex with xylose
ComponentsProbable phosphatidylethanolamine transferase Mcr-1
KeywordsTRANSFERASE / MCR-1 / xylose / complex / colistin resistance / STRUCTURAL PROTEIN
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / Transferases; Transferring phosphorus-containing groups / sulfuric ester hydrolase activity / response to antibiotic / plasma membrane
Similarity search - Function
Phosphoethanolamine transferase, N-terminal / Phosphoethanolamine transferase EptA/EptB / Phosphoethanolamine transferase / Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-L-xylopyranose / Probable phosphatidylethanolamine transferase Mcr-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsLiu, Z.X. / Han, Z. / Yu, X.L. / Wen, G. / Zeng, C.
CitationJournal: Crystals / Year: 2018
Title: Crystal Structure of the Catalytic Domain of MCR-1 (cMCR-1) in Complex with d-Xylose
Authors: Liu, Z.X. / Han, Z. / Yu, X.L. / Wen, G. / Zeng, C.
History
DepositionMar 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 22, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable phosphatidylethanolamine transferase Mcr-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3303
Polymers37,1141
Non-polymers2162
Water7,008389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint2 kcal/mol
Surface area13980 Å2
Unit cell
Length a, b, c (Å)51.580, 73.130, 82.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Probable phosphatidylethanolamine transferase Mcr-1 / cMCR-1 / Polymyxin resistance protein MCR-1


Mass: 37114.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mcr1, mcr-1, APZ14_31440 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0R6L508, Transferases; Transferring phosphorus-containing groups
#2: Sugar ChemComp-LXC / beta-L-xylopyranose / beta-L-xylose / L-xylose / xylose / L-XYLOSE (CYCLIC FORM) / Xylose


Type: L-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-xylopyranoseCOMMON NAMEGMML 1.0
b-L-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: PEG 1000, PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.82→43.71 Å / Num. obs: 28258 / % possible obs: 99 % / Redundancy: 2 % / Biso Wilson estimate: 13.74 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.03472 / Rrim(I) all: 0.0491 / Net I/σ(I): 10.61
Reflection shellResolution: 1.82→1.9 Å / Rmerge(I) obs: 0.1112 / Mean I/σ(I) obs: 4.94 / Num. unique obs: 2789 / CC1/2: 0.949 / Rrim(I) all: 0.1573

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GRR
Resolution: 1.82→43.71 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.63
RfactorNum. reflection% reflection
Rfree0.1862 1997 7.08 %
Rwork0.1476 --
obs0.1502 28224 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.82→43.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 11 389 3004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092892
X-RAY DIFFRACTIONf_angle_d0.8913960
X-RAY DIFFRACTIONf_dihedral_angle_d15.4851738
X-RAY DIFFRACTIONf_chiral_restr0.055433
X-RAY DIFFRACTIONf_plane_restr0.005530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.86550.22161410.17931863X-RAY DIFFRACTION99
1.8655-1.9160.23291400.16671840X-RAY DIFFRACTION99
1.916-1.97240.19761410.1541841X-RAY DIFFRACTION99
1.9724-2.0360.19361410.1521848X-RAY DIFFRACTION99
2.036-2.10880.16971380.15521821X-RAY DIFFRACTION98
2.1088-2.19320.19541410.14561845X-RAY DIFFRACTION98
2.1932-2.2930.1741400.14261852X-RAY DIFFRACTION98
2.293-2.41390.21721400.15041827X-RAY DIFFRACTION98
2.4139-2.56520.20421410.1521855X-RAY DIFFRACTION97
2.5652-2.76320.20971430.15041877X-RAY DIFFRACTION99
2.7632-3.04130.17631450.14291905X-RAY DIFFRACTION100
3.0413-3.48130.15761440.13731895X-RAY DIFFRACTION99
3.4813-4.38580.15331480.12781934X-RAY DIFFRACTION100
4.3858-54.6910.19891540.15972024X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 18.984 Å / Origin y: 0.9163 Å / Origin z: 2.7269 Å
111213212223313233
T0.0729 Å20.0087 Å20.001 Å2-0.0529 Å2-0.0111 Å2--0.0613 Å2
L1.0198 °20.3207 °2-0.1062 °2-0.7969 °2-0.1584 °2--0.8868 °2
S-0.0081 Å °-0.0266 Å °0.0144 Å °0.0446 Å °0.0006 Å °-0.0128 Å °0.0201 Å °0.0212 Å °0.0094 Å °
Refinement TLS groupSelection details: all

+
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