[English] 日本語
Yorodumi
- PDB-2q4r: Ensemble refinement of the protein crystal structure of human pho... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q4r
TitleEnsemble refinement of the protein crystal structure of human phosphomannomutase 2 (PMM2)
ComponentsPhosphomannomutase 2
KeywordsISOMERASE / Ensemble Refinement / Refinement Methodology Development / HS.459855 / HS.313504 / BC008310 / PHOSPHATASE / PFAM PF03332 / HAD SUPERFAMILY / JAECKEN DISEASE / CARBOHYDRATE-DEFICIENT GLYCOPROTEIN SYNDROME / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


GDP-mannose biosynthetic process from mannose / GDP-mannose biosynthetic process from fructose-6-phosphate / Defective PMM2 causes PMM2-CDG / mannose catabolic process / Synthesis of GDP-mannose / phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / mannose metabolic process / protein N-linked glycosylation ...GDP-mannose biosynthetic process from mannose / GDP-mannose biosynthetic process from fructose-6-phosphate / Defective PMM2 causes PMM2-CDG / mannose catabolic process / Synthesis of GDP-mannose / phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / mannose metabolic process / protein N-linked glycosylation / protein glycosylation / neuronal cell body / nucleoplasm / 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
GLYCINE / Phosphomannomutase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Re-refinement using ensemble model / Resolution: 2.09 Å
AuthorsLevin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Structure / Year: 2007
Title: Ensemble refinement of protein crystal structures: validation and application.
Authors: Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips, G.N.
History
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 10, 2011Group: Other
Revision 1.4Aug 30, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphomannomutase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5515
Polymers28,2641
Non-polymers2874
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.622, 70.622, 100.150
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Number of models16
Components on special symmetry positions
IDModelComponents
11A-449-

HOH

22A-449-

HOH

33A-449-

HOH

44A-449-

HOH

55A-449-

HOH

66A-449-

HOH

77A-449-

HOH

88A-449-

HOH

99A-449-

HOH

1010A-449-

HOH

1111A-449-

HOH

1212A-449-

HOH

1313A-449-

HOH

1414A-449-

HOH

1515A-449-

HOH

1616A-449-

HOH

-
Components

#1: Protein Phosphomannomutase 2 / PMM 2


Mass: 28263.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PMM2, HS.459855 / Plasmid: PVP16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: O15305, phosphomannomutase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 51.9 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2AMY.

-
Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
CNS1.1phasing
RefinementMethod to determine structure: Re-refinement using ensemble model
Starting model: PDB entry 2AMY

2amy


Resolution: 2.09→30.58 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1443312.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: maximum likelihood using amplitudes
Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2amy and the first data set in the deposited structure factor file for 2amy ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2amy and the first data set in the deposited structure factor file for 2amy along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 16 identical copies of the protein and non-water hetero-atoms assigned fractional occupancies adding up to one, and a single copy of the solvent molecules. Refinement was carried out with all the conformers present simultaneously and with the potential energy terms corresponding to interactions between the different conformers excluded. The helix and sheet records were calculated using coordinates from the first conformer only. The structure visualization program PYMOL is well-suited for directly viewing the ensemble model presented in this PDB file.
RfactorNum. reflection% reflectionSelection details
Rfree0.298 924 5.3 %RANDOM
Rwork0.207 ---
obs0.207 17513 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.447 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso mean: 41.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2.09→30.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 16 142 2101
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.511.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it2.652.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.09-2.220.2971756.20.22426470.0222886282297.8
2.22-2.390.3761545.40.2227230.032887287799.7
2.39-2.630.341515.20.23527480.0282909289999.7
2.63-3.020.3521655.70.25827390.02729042904100
3.02-3.80.3261424.80.2328100.02729522952100
3.8-30.580.2441374.50.17329220.0213080305999.3
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3gly_xplor_par.txt
X-RAY DIFFRACTION4edo.param

+
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