[English] 日本語
Yorodumi
- PDB-5zs8: Acetylation of lysine 100 of Phosphoglycerate mutase 1 complexed ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zs8
TitleAcetylation of lysine 100 of Phosphoglycerate mutase 1 complexed with KH_ol
Components(Phosphoglycerate mutase ...) x 2
KeywordsISOMERASE / Phosphoglycerate mutase 1
Function / homology
Function and homology information


bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / secretory granule lumen / ficolin-1-rich granule lumen ...bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / secretory granule lumen / ficolin-1-rich granule lumen / hydrolase activity / Neutrophil degranulation / protein kinase binding / extracellular exosome / extracellular region / membrane / cytoplasm / cytosol
Similarity search - Function
Phosphoglycerate mutase 1 / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9JF / Phosphoglycerate mutase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsJiang, L.L. / Zhou, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21472026 China
CitationJournal: To Be Published
Title: Acetylation of lysine 100 of Phosphoglycerate mutase 1 complexed with KH_ol
Authors: Jiang, L.L. / Zhou, L.
History
DepositionApr 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Phosphoglycerate mutase 1
C: Phosphoglycerate mutase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8725
Polymers54,2302
Non-polymers6423
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-8 kcal/mol
Surface area21300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.743, 83.101, 100.368
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Phosphoglycerate mutase ... , 2 types, 2 molecules BC

#1: Protein Phosphoglycerate mutase 1 / BPG-dependent PGAM 1 / Phosphoglycerate mutase isozyme B / PGAM-B


Mass: 26682.377 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGAM1, PGAMA, CDABP0006 / Production host: Escherichia coli (E. coli)
References: UniProt: P18669, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent), bisphosphoglycerate mutase
#2: Protein Phosphoglycerate mutase 1 / BPG-dependent PGAM 1 / Phosphoglycerate mutase isozyme B / PGAM-B


Mass: 27547.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGAM1, PGAMA, CDABP0006 / Production host: Escherichia coli (E. coli)
References: UniProt: P18669, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent), bisphosphoglycerate mutase

-
Non-polymers , 4 types, 240 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-9JF / N-(3,4-dihydroxy-9,10-dioxo-9,10-dihydroanthracen-2-yl)-2-hydroxybenzene-1-sulfonamide


Mass: 411.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H13NO7S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: MES, pH 6.0, PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 34396 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 41.38 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.035 / Rrim(I) all: 0.089 / Χ2: 0.899 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.286.40.80433840.7490.3440.8760.625100
2.28-2.376.30.54333750.8770.2350.5930.478100
2.37-2.485.90.38633930.9270.1720.4240.523100
2.48-2.616.20.30233970.9510.1310.330.53799.9
2.61-2.776.60.21534060.9740.090.2330.643100
2.77-2.996.50.15234190.9860.0640.1650.762100
2.99-3.296.10.10534370.9920.0460.1151.00599.9
3.29-3.766.60.07634440.9960.0320.0831.40599.9
3.76-4.746.20.05434860.9970.0240.0591.65999.8
4.74-506.10.04336550.9970.0190.0481.28999.8

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.24data extraction
HKL-2000data collection
PHASERphasing
RefinementResolution: 2.2→49.669 Å / FOM work R set: 0.8588 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 1720 5.05 %
Rwork0.1787 32333 -
obs0.1808 34053 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.57 Å2 / Biso mean: 40.53 Å2 / Biso min: 20.55 Å2
Refinement stepCycle: final / Resolution: 2.2→49.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3816 0 55 237 4108
Biso mean--73.44 42.23 -
Num. residues----473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083965
X-RAY DIFFRACTIONf_angle_d1.0455388
X-RAY DIFFRACTIONf_chiral_restr0.073562
X-RAY DIFFRACTIONf_plane_restr0.005695
X-RAY DIFFRACTIONf_dihedral_angle_d14.8881496
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.26480.26721280.22426222750
2.2648-2.33790.24581490.20326722821
2.3379-2.42140.24721440.190426332777
2.4214-2.51840.23041520.192526572809
2.5184-2.6330.25941310.185126792810
2.633-2.77180.23921480.179226812829
2.7718-2.94540.24281350.184826782813
2.9454-3.17280.21541570.184926912848
3.1728-3.4920.26141400.185126832823
3.492-3.99710.20541340.161127382872
3.9971-5.03520.17591560.152227262882
5.0352-49.68140.22091460.192728733019

+
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