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- PDB-7n3r: The ternary complex of human Bisphosphoglycerate mutase with 3-ph... -

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Basic information

Entry
Database: PDB / ID: 7n3r
TitleThe ternary complex of human Bisphosphoglycerate mutase with 3-phosphoglycerate and 2-phosphoglycolate
ComponentsBisphosphoglycerate mutase
KeywordsISOMERASE / BPGM / Bisphosphoglycerate mutase / 2 / 3-bisphosphoglycerate phosphatase / 3-phosphoglycerate / 2-phosphoglycolate / erythrocyte
Function / homology
Function and homology information


carbohydrate derivative catabolic process / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / neuroinflammatory response / respiratory gaseous exchange by respiratory system / establishment of blood-brain barrier / Glycolysis / cellular response to stress ...carbohydrate derivative catabolic process / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / neuroinflammatory response / respiratory gaseous exchange by respiratory system / establishment of blood-brain barrier / Glycolysis / cellular response to stress / defense response to protozoan / erythrocyte development / oxygen transport / glycolytic process / carbohydrate metabolic process / hydrolase activity / extracellular exosome / cytosol
Similarity search - Function
Phosphoglycerate mutase 1 / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily
Similarity search - Domain/homology
3-PHOSPHOGLYCERIC ACID / 2-PHOSPHOGLYCOLIC ACID / Bisphosphoglycerate mutase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsAljahdali, A.S. / Musayev, F.N. / Safo, M.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)R01MD009124 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Molecular insight into 2-phosphoglycolate activation of the phosphatase activity of bisphosphoglycerate mutase.
Authors: Aljahdali, A.S. / Musayev, F.N. / Burgner 2nd, J.W. / Ghatge, M.S. / Shekar, V. / Zhang, Y. / Omar, A.M. / Safo, M.K.
History
DepositionJun 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bisphosphoglycerate mutase
B: Bisphosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7355
Polymers62,2372
Non-polymers4983
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-18 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.072, 70.865, 159.803
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bisphosphoglycerate mutase / BPGM / 2 / 3-bisphosphoglycerate mutase / erythrocyte / 3-bisphosphoglycerate synthase / 3- ...BPGM / 2 / 3-bisphosphoglycerate mutase / erythrocyte / 3-bisphosphoglycerate synthase / 3-diphosphoglycerate mutase / DPGM / BPG-dependent PGAM


Mass: 31118.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BPGM / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: P07738, bisphosphoglycerate mutase, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent)
#2: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M BIS TRIS propane, 18% polyethylene glycol 8000, 10% v/v polyethylene glycol 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54056 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.25→27.65 Å / Num. obs: 29181 / % possible obs: 99.2 % / Redundancy: 7.9 % / Biso Wilson estimate: 33.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.031 / Rrim(I) all: 0.09 / Net I/σ(I): 15
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 8 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 2677 / CC1/2: 0.916 / Rpim(I) all: 0.181 / Rrim(I) all: 0.524 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.61 Å27.65 Å
Translation4.61 Å27.65 Å

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHASER2.8.1phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
CrysalisPro41_64_69adata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H4Z

2h4z


Resolution: 2.25→27.648 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2736 1466 5.05 %
Rwork0.2025 27539 -
obs0.206 29005 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.32 Å2 / Biso mean: 41.7833 Å2 / Biso min: 13.23 Å2
Refinement stepCycle: final / Resolution: 2.25→27.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4028 0 29 249 4306
Biso mean--52.1 41.01 -
Num. residues----492
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.25-2.33040.37331450.3229274299
2.3304-2.42370.32981440.2625271599
2.4237-2.53390.35171540.2499275099
2.5339-2.66740.31111410.24022728100
2.6674-2.83440.29071490.2306274899
2.8344-3.0530.31811340.2342275599
3.053-3.35970.29261460.2236276599
3.3597-3.84480.24521330.1903278099
3.8448-4.83980.24381430.1524275697
4.8398-27.6480.22761770.1665280095

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