[English] 日本語
Yorodumi
- PDB-2fuc: Human alpha-Phosphomannomutase 1 with Mg2+ cofactor bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fuc
TitleHuman alpha-Phosphomannomutase 1 with Mg2+ cofactor bound
ComponentsPhosphomannomutase 1
KeywordsISOMERASE / Phosphomannomutase / protein glycosylation / carbohydrate-deficient glycoprotein syndrome / Haloalkanoic Acid Dehalogenase Superfamily
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 / MAD / Resolution: 2.1 Å
AuthorsSilvaggi, N.R. / Zhang, C. / Lu, Z. / Dunaway-Mariano, D. / Allen, K.N.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The X-ray crystal structures of human alpha-phosphomannomutase 1 reveal the structural basis of congenital disorder of glycosylation type 1a.
Authors: Silvaggi, N.R. / Zhang, C. / Lu, Z. / Dai, J. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionJan 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphomannomutase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0233
Polymers29,9741
Non-polymers492
Water3,081171
1
A: Phosphomannomutase 1
hetero molecules

A: Phosphomannomutase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0466
Polymers59,9492
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)51.690, 51.690, 215.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe asymmetric unit contains one monomer of the biologically active dimer. The dimer can be generated by applying the following matrix to the deposited coordinates: | 3.123e-17, 1, 5.881e-16| | 1,-1.745e-16, 1.109e-15| | 1.049e-15, 5.487e-16, -1| (-7.416e-14,-1.349e-13, 216)

-
Components

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


Mass: 29974.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / 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.: 171 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growDetails: Crystals grown by hanging drop vapor diffusion over mother liquor containing 15-18% polyethylene glycol 3350, 0.15M D,L-malic acid, pH 7.0, 50mM MgCL2, and 8mM 2-mercaptoethanol. Drops were ...Details: Crystals grown by hanging drop vapor diffusion over mother liquor containing 15-18% polyethylene glycol 3350, 0.15M D,L-malic acid, pH 7.0, 50mM MgCL2, and 8mM 2-mercaptoethanol. Drops were formed by mixing 2ul of protein solution (10mM HEPES, pH 7.5, 100mM NaCl, 5mM MgCl2) at 15-25mg/ml with 2ul of mother liquor. Crystals grew after one to three days at 296 K.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9797, 0.9794, 0.9500
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 9, 2005
RadiationMonochromator: Si111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97941
30.951
ReflectionResolution: 2.1→50 Å / Num. all: 17978 / Num. obs: 17978 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.9 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 45.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 16 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 8.8 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→24.33 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.975 / SU ML: 0.112 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20597 868 5.2 %RANDOM
Rwork0.18629 ---
obs0.18733 15848 100 %-
all-15848 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.054 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2--0.79 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1969 0 2 171 2142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221993
X-RAY DIFFRACTIONr_bond_other_d0.0050.021801
X-RAY DIFFRACTIONr_angle_refined_deg1.1361.9652684
X-RAY DIFFRACTIONr_angle_other_deg0.66934193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1445246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48924.059101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25315354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4351515
X-RAY DIFFRACTIONr_chiral_restr0.0680.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022237
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02429
X-RAY DIFFRACTIONr_nbd_refined0.2310.3406
X-RAY DIFFRACTIONr_nbd_other0.2130.31762
X-RAY DIFFRACTIONr_nbtor_refined0.1860.5999
X-RAY DIFFRACTIONr_nbtor_other0.0880.51029
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.5209
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0920.51
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3470.334
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.520
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.39521476
X-RAY DIFFRACTIONr_mcbond_other0.1712505
X-RAY DIFFRACTIONr_mcangle_it1.52331957
X-RAY DIFFRACTIONr_scbond_it1.1872853
X-RAY DIFFRACTIONr_scangle_it1.6083726
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 69 -
Rwork0.202 1016 -
obs--100 %

+
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://pdbjlvh1.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