[English] 日本語
Yorodumi
- PDB-5nw7: Crystal structure of candida albicans phosphomannose isomerase in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nw7
TitleCrystal structure of candida albicans phosphomannose isomerase in complex with inhibitor
ComponentsMannose-6-phosphate isomerase
KeywordsISOMERASE / ALDOSE-KETOSE ISOMERASE / COMPLEX INHIBITOR
Function / homology
Function and homology information


mannose-6-phosphate isomerase / mannose-6-phosphate isomerase activity / cell wall mannoprotein biosynthetic process / GDP-mannose biosynthetic process / fungal-type cell wall organization / protein glycosylation / carbohydrate metabolic process / zinc ion binding / cytosol
Similarity search - Function
Phosphomannose isomerase type I, C-terminal domain / Phosphomannose Isomerase; domain 2 / Phosphomannose Isomerase, domain 2 / Mannose-6-phosphate isomerase / Phosphomannose isomerase, type I, conserved site / Phosphomannose isomerase type I, helical insertion domain / Phosphomannose isomerase type I, helical insertion domain / Phosphomannose isomerase type I signature 1. / Phosphomannose isomerase type I signature 2. / Mannose-6-phosphate isomerase, type I ...Phosphomannose isomerase type I, C-terminal domain / Phosphomannose Isomerase; domain 2 / Phosphomannose Isomerase, domain 2 / Mannose-6-phosphate isomerase / Phosphomannose isomerase, type I, conserved site / Phosphomannose isomerase type I, helical insertion domain / Phosphomannose isomerase type I, helical insertion domain / Phosphomannose isomerase type I signature 1. / Phosphomannose isomerase type I signature 2. / Mannose-6-phosphate isomerase, type I / Phosphomannose isomerase type I, catalytic domain / Phosphomannose isomerase type I C-terminal / Phosphomannose isomerase type I, catalytic domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-9C2 / Mannose-6-phosphate isomerase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsLi de la Sierra-Gallay, I. / Ahmad, L. / Plancqueel, S. / van Tilbeurgh, H. / Salmon, L.
CitationJournal: FEBS Lett. / Year: 2018
Title: Crystal structure of phosphomannose isomerase from Candida albicans complexed with 5-phospho-d-arabinonhydrazide.
Authors: Ahmad, L. / Plancqueel, S. / Dubosclard, V. / Lazar, N. / Ghattas, W. / Li de la Sierra-Gallay, I. / van Tilbeurgh, H. / Salmon, L.
History
DepositionMay 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mannose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8553
Polymers50,5291
Non-polymers3262
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.970, 107.860, 44.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Mannose-6-phosphate isomerase / Phosphohexomutase / Phosphomannose isomerase / PMI


Mass: 50529.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: PMI1, MANA, CAALFM_C209640WA, CaO19.1390 / Production host: Escherichia coli (E. coli) / References: UniProt: P34948, mannose-6-phosphate isomerase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-9C2 / [(2~{R},3~{R},4~{S})-5-diazanyl-2,3,4-tris(oxidanyl)-5-oxidanylidene-pentyl] dihydrogen phosphate


Mass: 260.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H13N2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.13 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, magnesium chloride, Bis Tris buffer

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.85→45.98 Å / Num. obs: 36611 / % possible obs: 99.5 % / Redundancy: 5.3 % / Biso Wilson estimate: 40.43 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.12 / Net I/σ(I): 8.92
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.16 / Num. unique obs: 5752 / CC1/2: 0.61 / Rrim(I) all: 1.11 / % possible all: 98.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PMI

1pmi


Resolution: 1.85→45.98 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.058 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.127
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 1831 5 %RANDOM
Rwork0.1714 ---
obs0.1732 34779 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.97 Å2 / Biso mean: 33.241 Å2 / Biso min: 17.53 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å2-0 Å20 Å2
2--1.09 Å20 Å2
3---0.71 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.85→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3431 0 17 247 3695
Biso mean--25.08 39.54 -
Num. residues----440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193520
X-RAY DIFFRACTIONr_bond_other_d0.0020.023267
X-RAY DIFFRACTIONr_angle_refined_deg1.8731.9774758
X-RAY DIFFRACTIONr_angle_other_deg1.02237649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1485439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.0726.013158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.615627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6611510
X-RAY DIFFRACTIONr_chiral_restr0.1160.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213881
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02642
LS refinement shellResolution: 1.847→1.895 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 129 -
Rwork0.389 2447 -
all-2576 -
obs--96.7 %

+
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