[English] 日本語
Yorodumi
- PDB-6cfu: Structure of Human alpha-Phosphomannomutase 1 containing mutation... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cfu
TitleStructure of Human alpha-Phosphomannomutase 1 containing mutations R180K and R183K
ComponentsPhosphomannomutase 1
KeywordsISOMERASE / phosphatase / haloalkanoate dehalogenase superfamily / mutase
Function / homology
Function and homology information


Synthesis of GDP-mannose / phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / mannose metabolic process / protein N-linked glycosylation / cellular response to leukemia inhibitory factor / neuronal cell body / metal ion binding / cytosol
Similarity search - Function
Eukaryotic phosphomannomutase, cap domain / Phosphomannomutase / Phosphomannomutase, cap domain / Eukaryotic phosphomannomutase / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold ...Eukaryotic phosphomannomutase, cap domain / Phosphomannomutase / Phosphomannomutase, cap domain / Eukaryotic phosphomannomutase / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphomannomutase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.244 Å
AuthorsJi, T. / Dunaway-Mariano, D. / Allen, K.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
CitationJournal: Biochemistry / Year: 2018
Title: Structural Basis of the Molecular Switch between Phosphatase and Mutase Functions of Human Phosphomannomutase 1 under Ischemic Conditions.
Authors: Ji, T. / Zhang, C. / Zheng, L. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionFeb 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Jun 27, 2018Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.3Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.5Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphomannomutase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7793
Polymers29,7311
Non-polymers492
Water2,216123
1
A: Phosphomannomutase 1
hetero molecules

A: Phosphomannomutase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5596
Polymers59,4622
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area2650 Å2
ΔGint-37 kcal/mol
Surface area21920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.650, 50.650, 213.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Phosphomannomutase 1 / PMM 1 / PMMH-22


Mass: 29730.783 Da / Num. of mol.: 1 / Mutation: R180K, R183K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PMM1, PMMH22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92871, phosphomannomutase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 20% polyethylene glycol 3350, 0.15 M DL-malate, pH 7.0, 50 mM MgCl2, and 8 mM beta-mercaptoethanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.24→49.28 Å / Num. obs: 13960 / % possible obs: 98.41 % / Redundancy: 2 % / Net I/σ(I): 9.62
Reflection shellResolution: 2.24→2.32 Å

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FUC

2fuc


Resolution: 2.244→49.28 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.72
RfactorNum. reflection% reflection
Rfree0.2739 1403 10.06 %
Rwork0.2166 --
obs0.2223 13952 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.244→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 2 123 2087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082001
X-RAY DIFFRACTIONf_angle_d1.1342690
X-RAY DIFFRACTIONf_dihedral_angle_d14.699756
X-RAY DIFFRACTIONf_chiral_restr0.079288
X-RAY DIFFRACTIONf_plane_restr0.006355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2442-2.32440.31561340.26021189X-RAY DIFFRACTION96
2.3244-2.41750.32771340.2661206X-RAY DIFFRACTION97
2.4175-2.52750.34151370.25711205X-RAY DIFFRACTION98
2.5275-2.66080.30971370.24631234X-RAY DIFFRACTION98
2.6608-2.82740.36161380.26271226X-RAY DIFFRACTION98
2.8274-3.04570.31681390.25231239X-RAY DIFFRACTION99
3.0457-3.35220.3361380.22431260X-RAY DIFFRACTION99
3.3522-3.83710.2611410.20541266X-RAY DIFFRACTION99
3.8371-4.83360.23131460.17961299X-RAY DIFFRACTION99
4.8336-49.29290.21031590.19441425X-RAY DIFFRACTION100

+
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