[English] 日本語
Yorodumi
- PDB-3o0t: Crystal structure of human phosphoglycerate mutase family member ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3o0t
TitleCrystal structure of human phosphoglycerate mutase family member 5 (PGAM5) in complex with phosphate
ComponentsSerine/threonine-protein phosphatase PGAM5, mitochondrial
KeywordsHYDROLASE / Structural Genomics / Structural Genomics Consortium / SGC / Phosphoglycerate mutase family member 5 / PGAM5 / BXLBv68 / MGC5352 protein / Serine/Threonine phosphatase / mitochondrial protein
Function / homology
Function and homology information


negative regulation of cold-induced thermogenesis / myosin phosphatase activity / positive regulation of mitochondrial fission / Receptor Mediated Mitophagy / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / necroptotic process / GTPase activator activity / macroautophagy ...negative regulation of cold-induced thermogenesis / myosin phosphatase activity / positive regulation of mitochondrial fission / Receptor Mediated Mitophagy / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / necroptotic process / GTPase activator activity / macroautophagy / mitochondrial outer membrane / mitochondrial inner membrane / protein-containing complex binding / mitochondrion
Similarity search - Function
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
PHOSPHATE ION / Serine/threonine-protein phosphatase PGAM5, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChaikuad, A. / Alfano, I. / Picaud, S. / Filippakopoulos, P. / Barr, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. ...Chaikuad, A. / Alfano, I. / Picaud, S. / Filippakopoulos, P. / Barr, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Takeda, K. / Ichijo, H. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2017
Title: Structures of PGAM5 Provide Insight into Active Site Plasticity and Multimeric Assembly.
Authors: Chaikuad, A. / Filippakopoulos, P. / Marcsisin, S.R. / Picaud, S. / Schroder, M. / Sekine, S. / Ichijo, H. / Engen, J.R. / Takeda, K. / Knapp, S.
History
DepositionJul 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 12, 2017Group: Database references / Category: citation / citation_author
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 1.3Jul 26, 2023Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein phosphatase PGAM5, mitochondrial
B: Serine/threonine-protein phosphatase PGAM5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,06917
Polymers46,0072
Non-polymers1,06315
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein phosphatase PGAM5, mitochondrial
hetero molecules

A: Serine/threonine-protein phosphatase PGAM5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,06917
Polymers46,0072
Non-polymers1,06315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y+1/2,-z-1/21
Buried area4130 Å2
ΔGint-17 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.960, 73.090, 81.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Serine/threonine-protein phosphatase PGAM5, mitochondrial / Phosphoglycerate mutase family member 5 / Bcl-XL-binding protein v68


Mass: 23003.281 Da / Num. of mol.: 2 / Fragment: UNP residues 90-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGAM5 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3
References: UniProt: Q96HS1, protein-serine/threonine phosphatase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15% PEG-smear (PEG3350 & PEG MME5K), 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 13, 2009
RadiationMonochromator: Flat graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.9→36.54 Å / Num. all: 34056 / Num. obs: 33999 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 15.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4896 / % possible all: 100

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.6.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→36.54 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.974 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS BUT NOT OUTPUT TO COORDINATE FILE
RfactorNum. reflection% reflectionSelection details
Rfree0.22813 1697 5 %RANDOM
Rwork0.18299 ---
obs0.18524 32302 99.98 %-
all-33999 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.081 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20 Å2
2---0.12 Å20 Å2
3----0.94 Å2
Refine analyzeLuzzati coordinate error obs: 0.246 Å
Refinement stepCycle: LAST / Resolution: 1.9→36.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 64 178 3281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213207
X-RAY DIFFRACTIONr_bond_other_d0.0020.022273
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.9664324
X-RAY DIFFRACTIONr_angle_other_deg0.88635466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.835393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.50521.818154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3915545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6231540
X-RAY DIFFRACTIONr_chiral_restr0.0960.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213525
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02693
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 116 -
Rwork0.373 2368 -
obs--99.96 %
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)
11.03890.1441-0.6660.5370.02841.8417-0.173-0.1745-0.18180.03120.0534-0.01930.44020.270.11960.25480.11480.00940.15850.02520.035118.04-7.137-19.742
22.71311.16232.61622.15140.77034.815-0.25050.10180.1066-0.16150.05250.15180.07660.17330.19790.2381-0.0469-0.01310.11290.01750.06750.287-6.156-22.007
30.36720.4045-0.15370.4737-0.11470.9941-0.0188-0.03590.0380.00490.02590.05440.14120.161-0.00720.1920.049-0.00770.16850.00780.038612.5283.086-17.878
41.4025-1.3926-0.24582.86920.54772.68280.2545-0.0650.7607-0.29430.1641-0.7904-0.46990.4368-0.41860.1524-0.13330.17360.1479-0.06730.446324.36324.867-23.557
51.128-2.0014-0.03153.81190.8682.6260.09830.04070.4084-0.3497-0.1109-0.7028-0.4503-0.07950.01260.27720.031-0.0190.0495-0.00580.1699.56431.527-23.622
61.1784-0.9015-0.26741.7250.48251.08550.051-0.00550.2445-0.12060.0493-0.0685-0.1150.1618-0.10030.1422-0.0159-0.01630.1233-0.00660.075415.26516.971-23.569
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 177
2X-RAY DIFFRACTION2A178 - 214
3X-RAY DIFFRACTION3A215 - 289
4X-RAY DIFFRACTION4B-1 - 175
5X-RAY DIFFRACTION5B176 - 219
6X-RAY DIFFRACTION6B220 - 289

+
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