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- PDB-5muf: Crystal structure of human phosphoglycerate mutase family member ... -

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Basic information

Entry
Database: PDB / ID: 5muf
TitleCrystal structure of human phosphoglycerate mutase family member 5 (PGAM5) in its enzymatically active dodecameric form induced by the presence of the N-terminal WDPNWD motif
ComponentsSerine/threonine-protein phosphatase PGAM5, mitochondrial
KeywordsHYDROLASE / PHOSPHOGLYCERATE MUTASE FAMILY MEMBER 5 / PGAM5 / SERINE/THREONINE PHOSPHATASE / MITOCHONDRIAL PROTEIN / WDPNWD motif / WDXNWD motif / dimer / dodecamer / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


negative regulation of cold-induced thermogenesis / protein serine/threonine phosphatase activity / Receptor Mediated Mitophagy / positive regulation of mitochondrial fission / histone H2AXS139 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity ...negative regulation of cold-induced thermogenesis / protein serine/threonine phosphatase activity / Receptor Mediated Mitophagy / positive regulation of mitochondrial fission / histone H2AXS139 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / necroptotic process / phosphoprotein phosphatase activity / Regulation of pyruvate metabolism / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsChaikuad, A. / Alfano, I. / Picaud, S. / Filippakopoulos, P. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / 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
DepositionJan 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,7026
Polymers81,4173
Non-polymers2853
Water91951
1
A: Serine/threonine-protein phosphatase PGAM5, mitochondrial
B: Serine/threonine-protein phosphatase PGAM5, mitochondrial
C: Serine/threonine-protein phosphatase PGAM5, mitochondrial
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)326,80624
Polymers325,66712
Non-polymers1,14012
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
MethodPISA
Unit cell
Length a, b, c (Å)82.215, 141.403, 183.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 56 - 289 / Label seq-ID: 5 - 238

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 27138.895 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGAM5 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-pRARE2
References: UniProt: Q96HS1, protein-serine/threonine phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7 / Details: 18% PEG 3350 and 0.1 M MES, pH 5.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.1→41.03 Å / Num. obs: 18243 / % possible obs: 94.3 % / Redundancy: 7 % / Biso Wilson estimate: 55.3 Å2 / Rmerge(I) obs: 0.271 / Rpim(I) all: 0.101 / Net I/σ(I): 6.8
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.993 / Mean I/σ(I) obs: 2 / Num. unique obs: 2709 / Rpim(I) all: 0.373 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MXO

3mxo


Resolution: 3.1→41.03 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.868 / SU B: 46.834 / SU ML: 0.369 / Cross valid method: THROUGHOUT / ESU R Free: 0.451 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25553 933 5.1 %RANDOM
Rwork0.22648 ---
obs0.22793 17300 92.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.597 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å2-0 Å2
2--1.02 Å20 Å2
3----1.51 Å2
Refinement stepCycle: 1 / Resolution: 3.1→41.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5062 0 15 51 5128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195197
X-RAY DIFFRACTIONr_bond_other_d0.0020.024833
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.9557052
X-RAY DIFFRACTIONr_angle_other_deg0.779311142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3085623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.08321.905252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34715870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0271563
X-RAY DIFFRACTIONr_chiral_restr0.0660.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215747
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021136
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6232.0462509
X-RAY DIFFRACTIONr_mcbond_other0.6232.0462508
X-RAY DIFFRACTIONr_mcangle_it1.1563.0663127
X-RAY DIFFRACTIONr_mcangle_other1.1563.0673128
X-RAY DIFFRACTIONr_scbond_it0.4662.0962687
X-RAY DIFFRACTIONr_scbond_other0.4622.0882674
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8813.1123907
X-RAY DIFFRACTIONr_long_range_B_refined2.38523.1455641
X-RAY DIFFRACTIONr_long_range_B_other2.38523.1525641
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A138760.05
12B138760.05
21A139040.04
22C139040.04
31B138420.05
32C138420.05
LS refinement shellResolution: 3.105→3.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 78 -
Rwork0.347 1300 -
obs--94.45 %
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)
10.32030.1906-0.00660.797-0.27550.55380.00580.03410.1621-0.05470.04870.00070.00460.0093-0.05450.324-0.0153-0.00830.58840.02240.115-0.210555.5579-52.5378
20.84390.09740.03330.1638-0.22440.61070.0535-0.0521-0.01140.01730.02460.02610.04780.0064-0.07810.3417-0.00270.01070.6076-0.01360.03590.440134.421-38.5234
30.9538-0.32330.28441.5381-0.31141.04350.20460.07680.0265-0.0733-0.0778-0.07310.2138-0.0099-0.12680.39290.0331-0.01390.5957-0.00660.0262-0.357721.2479-12.6646
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A56 - 289
2X-RAY DIFFRACTION2B56 - 289
3X-RAY DIFFRACTION3C56 - 289

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