[English] 日本語
Yorodumi
- PDB-5epc: Crystal structure of wild-type human phosphoglucomutase 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5epc
TitleCrystal structure of wild-type human phosphoglucomutase 1
ComponentsPhosphoglucomutase-1PGM1
KeywordsISOMERASE / isomerase metabolism
Function / homology
Function and homology information


Defective PGM1 causes PGM1-CDG / Galactose catabolism / phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphoglucomutase activity / Glycogen breakdown (glycogenolysis) / Glycogen synthesis / gluconeogenesis / glycolytic process / glucose metabolic process / tertiary granule lumen ...Defective PGM1 causes PGM1-CDG / Galactose catabolism / phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) / phosphoglucomutase activity / Glycogen breakdown (glycogenolysis) / Glycogen synthesis / gluconeogenesis / glycolytic process / glucose metabolic process / tertiary granule lumen / ficolin-1-rich granule lumen / carbohydrate metabolic process / Neutrophil degranulation / magnesium ion binding / extracellular exosome / extracellular region / cytosol / cytoplasm
Similarity search - Function
Phosphoglucomutase / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, C-terminal domain / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III / Alpha-D-phosphohexomutase, conserved site ...Phosphoglucomutase / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, C-terminal domain / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III / Alpha-D-phosphohexomutase, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / Alpha-D-phosphohexomutase, alpha/beta/alpha domain I / Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III / Alpha-D-phosphohexomutase, C-terminal domain superfamily / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I / TATA-Binding Protein / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoglucomutase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsBeamer, L.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Patton Trust United States
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Induced Structural Disorder as a Molecular Mechanism for Enzyme Dysfunction in Phosphoglucomutase 1 Deficiency.
Authors: Stiers, K.M. / Kain, B.N. / Graham, A.C. / Beamer, L.J.
History
DepositionNov 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoglucomutase-1
B: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,02921
Polymers128,3832
Non-polymers1,64619
Water14,754819
1
A: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,15712
Polymers64,1921
Non-polymers96511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8739
Polymers64,1921
Non-polymers6818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.590, 172.590, 99.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1218-

HOH

-
Components

#1: Protein Phosphoglucomutase-1 / PGM1 / PGM 1 / Glucose phosphomutase 1


Mass: 64191.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P36871, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 819 / 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: 3.04 Å3/Da / Density % sol: 59.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Lithium or ammonium sulfate (1.35 - 1.85 M) with 0.1 M Tris, pH 8.0
PH range: 7.5-8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00001 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jun 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.75→61.051 Å / Num. obs: 150855 / % possible obs: 100 % / Redundancy: 32.5 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.163 / Net I/σ(I): 15.1
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 27.7 % / Rmerge(I) obs: 3.51 / Mean I/σ(I) obs: 1 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALAdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3PMG

3pmg


Resolution: 1.85→61.051 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 19.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 6404 5.01 %random
Rwork0.1696 ---
obs0.171 127879 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→61.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8438 0 96 819 9353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078754
X-RAY DIFFRACTIONf_angle_d0.99811884
X-RAY DIFFRACTIONf_dihedral_angle_d12.3813149
X-RAY DIFFRACTIONf_chiral_restr0.0431344
X-RAY DIFFRACTIONf_plane_restr0.0051543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8710.35121830.30874013X-RAY DIFFRACTION100
1.871-1.8930.3182070.28023994X-RAY DIFFRACTION100
1.893-1.91610.27632190.25144015X-RAY DIFFRACTION100
1.9161-1.94040.30172080.24364020X-RAY DIFFRACTION100
1.9404-1.96590.27671980.23463979X-RAY DIFFRACTION100
1.9659-1.99290.2372010.21894029X-RAY DIFFRACTION100
1.9929-2.02130.24241990.21114000X-RAY DIFFRACTION100
2.0213-2.05150.19621920.2094034X-RAY DIFFRACTION100
2.0515-2.08360.23752210.20293995X-RAY DIFFRACTION100
2.0836-2.11770.21132370.19873993X-RAY DIFFRACTION100
2.1177-2.15420.22122020.19384009X-RAY DIFFRACTION100
2.1542-2.19340.2152050.18164054X-RAY DIFFRACTION100
2.1934-2.23560.20632320.1813978X-RAY DIFFRACTION100
2.2356-2.28120.20872210.17814006X-RAY DIFFRACTION100
2.2812-2.33080.22332250.174032X-RAY DIFFRACTION100
2.3308-2.38510.19911950.17344024X-RAY DIFFRACTION100
2.3851-2.44470.2211970.17324063X-RAY DIFFRACTION100
2.4447-2.51080.20872440.16744009X-RAY DIFFRACTION100
2.5108-2.58470.20732010.17064054X-RAY DIFFRACTION100
2.5847-2.66810.20282370.16973993X-RAY DIFFRACTION100
2.6681-2.76350.19772310.16574023X-RAY DIFFRACTION100
2.7635-2.87410.20231980.16824078X-RAY DIFFRACTION100
2.8741-3.00490.20842150.17924053X-RAY DIFFRACTION100
3.0049-3.16330.20062170.1714071X-RAY DIFFRACTION100
3.1633-3.36150.20772090.16334074X-RAY DIFFRACTION100
3.3615-3.6210.1612200.15094091X-RAY DIFFRACTION100
3.621-3.98540.1622270.13464108X-RAY DIFFRACTION100
3.9854-4.56190.1492070.13294138X-RAY DIFFRACTION100
4.5619-5.74680.1752270.14514171X-RAY DIFFRACTION100
5.7468-61.0840.19582290.17624374X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8485-0.10590.06153.5741-0.16592.1581-0.0617-0.0994-0.2010.23430.1234-0.04580.56420.1731-0.06090.36680.03350.01540.17390.00440.195137.5064-73.50235.4307
20.7125-0.3764-0.1071.23540.65181.4819-0.04780.0097-0.0033-0.10470.0681-0.04880.0572-0.0328-0.01420.1658-0.06340.00490.17110.00810.183327.2354-53.5527-0.139
31.71320.58510.50921.20840.02092.7930.0118-0.38030.0580.0893-0.04390.0896-0.0223-0.38580.01290.14310.0236-0.01020.2523-0.03580.220220.7381-40.606923.9638
41.84721.2051-1.46031.8909-1.57163.0365-0.12140.52240.2241-0.14360.49840.25880.0623-0.6936-0.16080.20240.0685-0.06510.50080.09390.2295-19.9489-50.7931-11.2099
51.3254-0.04280.3062.89370.93924.90750.11330.58790.1909-0.44960.102-0.0416-0.451-0.2351-0.14080.35560.01860.02990.60060.1120.3207-7.1031-37.1641-33.9869
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 405 )
3X-RAY DIFFRACTION3chain 'A' and (resid 406 through 562 )
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 405 )
5X-RAY DIFFRACTION5chain 'B' and (resid 406 through 562 )

+
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