[English] 日本語
Yorodumi
- PDB-5vin: Crystal Structure of the R515Q missense variant of human PGM1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vin
TitleCrystal Structure of the R515Q missense variant of human PGM1
ComponentsPhosphoglucomutase-1PGM1
KeywordsISOMERASE / phosphoglucomutase-1 / PGM1 / phosphoryl transfer
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 / MOLECULAR REPLACEMENT / Resolution: 2.60004291837 Å
AuthorsStiers, K.M. / Beamer, L.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1409898 United States
CitationJournal: Structure / Year: 2018
Title: A Hotspot for Disease-Associated Variants of Human PGM1 Is Associated with Impaired Ligand Binding and Loop Dynamics.
Authors: Stiers, K.M. / Beamer, L.J.
History
DepositionApr 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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: Phosphoglucomutase-1
B: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,24523
Polymers128,3252
Non-polymers1,91921
Water1,63991
1
A: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,45515
Polymers64,1631
Non-polymers1,29214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoglucomutase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7908
Polymers64,1631
Non-polymers6277
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)173.960, 173.960, 99.483
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

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


Mass: 64162.664 Da / Num. of mol.: 2 / Mutation: R515Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGM1 / Production host: Escherichia coli (E. coli)
References: UniProt: P36871, phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent)
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.06 Å3/Da / Density % sol: 59.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.01 M Cobalt (II) chloride hexahydrate, O.1 M MES monohydrate pH 6.5, Ammonium Sulfate 1.8-2.1M

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.6→61.51 Å / Num. obs: 47453 / % possible obs: 100 % / Redundancy: 13.9 % / Biso Wilson estimate: 50.495264229 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.052 / Net I/σ(I): 15.2
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.846 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4566 / CC1/2: 0.796 / Rpim(I) all: 0.518 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575phasing
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EPC

5epc


Resolution: 2.60004291837→61.5041478276 Å / SU ML: 0.453748262717 / Cross valid method: FREE R-VALUE / σ(F): 1.34691743164 / Phase error: 34.5518017215
RfactorNum. reflection% reflection
Rfree0.295418439253 2385 5.08952006999 %
Rwork0.238582434806 --
obs0.241435170817 46861 98.850356495 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 71.2698705059 Å2
Refinement stepCycle: LAST / Resolution: 2.60004291837→61.5041478276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8044 0 103 91 8238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009816689642048340
X-RAY DIFFRACTIONf_angle_d1.3835314434111362
X-RAY DIFFRACTIONf_chiral_restr0.08201619230741274
X-RAY DIFFRACTIONf_plane_restr0.01053871753941505
X-RAY DIFFRACTIONf_dihedral_angle_d5.206343968846454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.65310.4049171033231370.3308736012352577X-RAY DIFFRACTION99.7427416391
2.6531-2.71080.3804550940991700.3205103675782574X-RAY DIFFRACTION99.7455470738
2.7108-2.77390.3687984068561520.3066137894622571X-RAY DIFFRACTION99.7435897436
2.7739-2.84320.4328167196331140.3059344921012632X-RAY DIFFRACTION99.4207096307
2.8432-2.92010.355744950111340.3022282944962616X-RAY DIFFRACTION99.8185117967
2.9201-3.0060.4048642941381420.2893370048752612X-RAY DIFFRACTION99.8549673677
3.006-3.10310.33187499021460.2703922385272601X-RAY DIFFRACTION99.8183139535
3.1031-3.2140.3294202720371240.266345740652630X-RAY DIFFRACTION99.7103548154
3.214-3.34260.3311904133241500.2818420764882615X-RAY DIFFRACTION99.7834716709
3.3426-3.49470.2577801951511330.2435939352552622X-RAY DIFFRACTION100
3.4947-3.6790.3927400620971300.3076176693092430X-RAY DIFFRACTION91.6249105225
3.679-3.90940.2946920881621530.2326189936892384X-RAY DIFFRACTION91.7872648336
3.9094-4.21120.2190913122931200.2025308352782676X-RAY DIFFRACTION99.679144385
4.2112-4.63490.2329664912041420.1772670519452660X-RAY DIFFRACTION99.857448325
4.6349-5.30520.272583065361500.1859618615652684X-RAY DIFFRACTION100
5.3052-6.68270.2845092831121330.2378218060992736X-RAY DIFFRACTION100
6.6827-61.52130.2374039007871550.2092734525162856X-RAY DIFFRACTION99.8342175066
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)
10.143307716913-0.00278899760946-0.08144678121920.264681546107-0.1017450277250.0870406736160.102948057603-0.353039050124-0.03796416038990.185884365392-0.04179145193750.079628952944-0.06927587925610.5784490783670.02999382198150.165071773999-0.0314458076184-0.003362601269750.522813353156-0.04505711430760.24573322544571.14961188435.13997859-20.9499367958
20.0396877615168-0.0188531542208-0.04656284116840.02439501258620.0766364824460.181532619262-0.186505847450.1776681512720.1166204239920.008771568786360.01539919766720.017373991150.1161928560010.328664539129-0.2892473870280.1447896186870.2714357745580.0319135108218-0.255335832550.01388296354880.33053459973447.046369719925.219277367-24.2413622954
30.1183346335920.00864347531653-0.01213369457760.08618744256030.0612766782250.0486837837295-0.112947259194-0.27763320218-0.04013053960810.3122700231610.02513305713530.1211623234550.2428200948780.1012264254380.0008011349506450.4698058866220.09137925861530.003438921247550.2640927111870.00288281494920.32758439300142.485740234520.99045341092.29668815091
40.03527749642480.0257019140761-0.01446290222240.033242544686-0.02018538454130.01781758378330.105222161605-0.0533231390570.04536399111320.1672923264770.03684354317280.1302763068810.156871245728-0.160026309675-0.0008208304136261.22536217373-0.401942696986-0.1279120144541.093601512880.1833907017890.48899050609520.584999715655.5953547363-31.8418990381
50.38388645227-0.140443424889-0.2477785081520.2187328495820.05081992390490.2087822426550.325663192898-0.032510776558-0.01194108952880.25932270277-0.102032494717-0.2148909100770.121201805695-0.342021819670.1177365997330.667121937489-0.100561705872-0.06758331321840.334853433690.03568473031830.24602948972426.137871759260.0707662406-41.200318731
60.01172421181-0.03346564851340.02283242189650.145130997777-0.1281368039910.3673222130650.3221868776340.0435709663248-0.07205141826160.1125855697930.203218756191-0.08140759106480.05409895466250.1220824292040.2316644539140.5651249412210.19721213189-0.1322429395810.222578672306-0.1283297229790.54388499012550.580084496465.6272109988-43.986674037
70.0597302425165-0.0490443828165-0.04983942206110.1667973215950.01052072242340.1564579344070.111941100349-0.1241134989280.1456467094130.4271996846010.06009972320920.054878099037-0.1255989183950.03990299083870.2457762622990.9389926692540.02187701807270.03373020644570.254051951062-0.01510726855110.34061381672444.391921137981.2884191476-27.4742158451
80.0386171270776-0.03827556978160.04464433268510.0452913029963-0.04773561597870.05503638279910.067258922284-0.0413466382202-0.09488727760610.03017347792230.2249670862290.0984762646473-0.049302122290.1146962414890.002768302953761.05892053772-0.0571752645051-0.08861603526730.385410685225-0.02996692454350.41030493041352.013154678375.76831646-14.833118761
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 170 )
2X-RAY DIFFRACTION2chain 'A' and (resid 171 through 434 )
3X-RAY DIFFRACTION3chain 'A' and (resid 435 through 562 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 56 )
5X-RAY DIFFRACTION5chain 'B' and (resid 57 through 202 )
6X-RAY DIFFRACTION6chain 'B' and (resid 203 through 293 )
7X-RAY DIFFRACTION7chain 'B' and (resid 294 through 494 )
8X-RAY DIFFRACTION8chain 'B' and (resid 495 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