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- PDB-3mxo: Crystal structure oh human phosphoglycerate mutase family member ... -

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Basic information

Entry
Database: PDB / ID: 3mxo
TitleCrystal structure oh human phosphoglycerate mutase family member 5 (PGAM5)
ComponentsSerine/threonine-protein phosphatase PGAM5, mitochondrial
KeywordsHYDROLASE / PGAM5 / phosphoglycerate mutase family member 5 / BXLBv68 / MGC5352 protein / Structural Genomics Consortium / SGC
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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Serine/threonine-protein phosphatase PGAM5, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.7 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
DepositionMay 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,45922
Polymers46,0072
Non-polymers1,45220
Water5,531307
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)47,45922
Polymers46,0072
Non-polymers1,45220
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
Buried area4160 Å2
ΔGint-7 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.602, 70.946, 81.476
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 6 types, 327 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG-smear (PEG3350 & PEG MME5K), 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: Sep 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.7→29.48 Å / Num. all: 45741 / Num. obs: 45512 / % possible obs: 99.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 16.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 2.2 / Num. unique all: 6408 / Rsym value: 0.724 / % possible all: 97.6

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Phasing

PhasingMethod: SIRAS
Phasing MADD res high: 1.95 Å / D res low: 29.87 Å / FOM acentric: 0.187 / FOM centric: 0.173 / Reflection acentric: 27745 / Reflection centric: 3391
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_11.9529.8700277453391
ISO_21.9529.870.7230.692178231287
ANO_11.9529.870000
ANO_21.9529.870.5540178230
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_18.39-29.8700283161
ISO_16.05-8.3900533164
ISO_14.98-6.0500705176
ISO_14.32-4.9800841168
ISO_13.88-4.3200972164
ISO_13.54-3.88001084171
ISO_13.28-3.54001168163
ISO_13.07-3.28001271176
ISO_12.9-3.07001350169
ISO_12.75-2.9001439170
ISO_12.62-2.75001523172
ISO_12.51-2.62001590173
ISO_12.42-2.51001663164
ISO_12.33-2.42001723170
ISO_12.25-2.33001742171
ISO_12.18-2.25001846171
ISO_12.11-2.18001900172
ISO_12.06-2.11001992170
ISO_12-2.06002024175
ISO_11.95-2002096171
ANO_18.39-29.870000
ANO_16.05-8.390000
ANO_14.98-6.050000
ANO_14.32-4.980000
ANO_13.88-4.320000
ANO_13.54-3.880000
ANO_13.28-3.540000
ANO_13.07-3.280000
ANO_12.9-3.070000
ANO_12.75-2.90000
ANO_12.62-2.750000
ANO_12.51-2.620000
ANO_12.42-2.510000
ANO_12.33-2.420000
ANO_12.25-2.330000
ANO_12.18-2.250000
ANO_12.11-2.180000
ANO_12.06-2.110000
ANO_12-2.060000
ANO_11.95-20000
ISO_28.39-29.872.2081.52728386
ISO_26.05-8.392.0431.36953381
ISO_24.98-6.051.4350.86870590
ISO_24.32-4.980.8720.61984190
ISO_23.88-4.320.6470.47497278
ISO_23.54-3.880.5890.531108491
ISO_23.28-3.540.5740.417116884
ISO_23.07-3.280.5790.429127188
ISO_22.9-3.070.5820.531135084
ISO_22.75-2.90.5470.445143987
ISO_22.62-2.750.5020.415152386
ISO_22.51-2.620.4860.413159087
ISO_22.42-2.510.4690.367166284
ISO_22.33-2.420.4480.288172286
ISO_22.25-2.330.3730.281167384
ISO_22.18-2.250.4920.66271
ISO_22.11-2.180000
ISO_22.06-2.110000
ISO_22-2.060000
ISO_21.95-20000
ANO_28.39-29.871.99302830
ANO_26.05-8.392.28505330
ANO_24.98-6.051.95407050
ANO_24.32-4.981.65708410
ANO_23.88-4.321.36209720
ANO_23.54-3.881.183010840
ANO_23.28-3.540.867011680
ANO_23.07-3.280.662012710
ANO_22.9-3.070.514013500
ANO_22.75-2.90.417014390
ANO_22.62-2.750.339015230
ANO_22.51-2.620.274015900
ANO_22.42-2.510.233016620
ANO_22.33-2.420.209017220
ANO_22.25-2.330.169016730
ANO_22.18-2.250.19070
ANO_22.11-2.180000
ANO_22.06-2.110000
ANO_22-2.060000
ANO_21.95-20000
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-57.854-26.746-15.674I33.760.85
2-90.765-29.676-17.703I42.620.86
3-86.447-11.499-7.06I54.720.49
4-79.855-8.9381.688I57.60.45
5-58.614-44.878-5.839I81.620.46
6-55.111-67.932-6.881I57.050.34
7-11.931-60.882-8.958I39.990.31
8-71.049-3.51-11.083I27.640.23
9-28.926-59.027-1.881I53.770.27
10-66.154-29.535-13.965I17.10.16
11-22.344-7.073-7.853I55.240.21
12-40.545-38.515-1.675I39.160.18
Phasing MAD shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
8.39-29.870.80.571283161
6.05-8.390.7350.462533164
4.98-6.050.6660.377705176
4.32-4.980.5650.271841168
3.88-4.320.4820.234972164
3.54-3.880.4130.2081084171
3.28-3.540.3490.1871168163
3.07-3.280.3170.1871271176
2.9-3.070.270.1831350169
2.75-2.90.2290.1861439170
2.62-2.750.2070.1591523172
2.51-2.620.1740.1421590173
2.42-2.510.1420.1091663164
2.33-2.420.1210.1151723170
2.25-2.330.0950.1031742171
2.18-2.250.0010.0011846171
2.11-2.18001900172
2.06-2.11001992170
2-2.06002024175
1.95-2002096171
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 31135
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.96-10054.30.835518
6.29-7.9650.40.864506
5.41-6.2949.30.854556
4.81-5.4155.30.89637
4.38-4.8154.90.928703
4.05-4.3855.80.926751
3.78-4.0558.40.923810
3.56-3.7862.10.924864
3.37-3.5665.20.909910
3.21-3.3764.70.904951
3.07-3.2167.10.895990
2.95-3.0766.90.8831032
2.84-2.9573.90.8671081
2.75-2.8473.20.8851110
2.66-2.7575.20.8721130
2.58-2.6676.60.8771184
2.5-2.5880.70.8731227
2.44-2.579.20.8531262
2.37-2.4481.30.8671267
2.32-2.3779.60.8741291
2.26-2.32830.8461307
2.21-2.2689.80.8611357
2.17-2.2192.20.861380
2.12-2.1789.20.8631448
2.08-2.1291.70.8451454
2.04-2.0889.20.8561468
2-2.0488.20.8251523
1.95-2900.7642418

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
SHARPphasing
DM6.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→29.48 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.187 / WRfactor Rwork: 0.155 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9 / SU B: 3.978 / SU ML: 0.065 / SU R Cruickshank DPI: 0.102 / SU Rfree: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2283 5 %RANDOM
Rwork0.168 ---
obs0.17 45419 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.3 Å2 / Biso mean: 27.699 Å2 / Biso min: 11.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2---0.38 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 92 307 3413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213300
X-RAY DIFFRACTIONr_bond_other_d0.0010.022410
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9714440
X-RAY DIFFRACTIONr_angle_other_deg0.91535803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8665413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.91121.783157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68615568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4481541
X-RAY DIFFRACTIONr_chiral_restr0.0950.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213613
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02709
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 160 -
Rwork0.375 3048 -
all-3208 -
obs--96.77 %
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)
11.3137-0.10620.29141.12250.54621.5978-0.0510.08670.09270.01120.0310.2825-0.0888-0.24250.020.02360.01780.01170.0710.05030.1008-7.89185.9902-4.4171
22.4131.0857-0.53261.2635-2.25076.4974-0.01490.06960.11390.1652-0.03240.0742-0.3-0.34360.04730.1073-0.05530.00710.2039-0.04630.1321-13.0789-10.0189-2.9984
31.3717-0.0478-0.03751.33520.08060.8907-0.00140.0849-0.0785-0.03770.03020.1252-0.0098-0.0663-0.02880.0175-0.0003-0.00060.0110.00130.03670.1274-2.8447-4.4771
40.48150.1207-0.06221.0303-0.62931.61470.0098-0.01170.00840.055-0.0708-0.1399-0.02210.24060.0610.0176-0.0146-0.00920.04760.00690.02124.45460.88091.1235
51.8881-0.31550.182.05591.96692.3384-0.00440.15110.0154-0.16210.0015-0.1189-0.17120.27060.00290.08540.0159-0.010.18340.0640.080123.8994-15.78411.7077
60.5577-0.005-0.05060.386-0.03110.99140.0237-0.0238-0.03930.0402-0.02590.00780.00130.06470.00220.0359-0.0068-0.00740.01040.00390.020813.7493-4.62661.6136
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A88 - 178
2X-RAY DIFFRACTION2A179 - 216
3X-RAY DIFFRACTION3A217 - 289
4X-RAY DIFFRACTION4B88 - 176
5X-RAY DIFFRACTION5B177 - 218
6X-RAY DIFFRACTION6B219 - 289

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