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- PDB-7n3s: Human bisphosphoglycerate mutase complex with 2-phosphoglycolate -

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Basic information

Entry
Database: PDB / ID: 7n3s
TitleHuman bisphosphoglycerate mutase complex with 2-phosphoglycolate
ComponentsBisphosphoglycerate mutase
KeywordsISOMERASE / BPGM / Bisphosphoglycerate mutase / 2 / 3-bisphosphoglycerate phosphatase / 2-phosphoglycolate / activation / erythrocyte
Function / homology
Function and homology information


carbohydrate derivative catabolic process / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / neuroinflammatory response / establishment of blood-brain barrier / respiratory gaseous exchange by respiratory system / Glycolysis / defense response to protozoan ...carbohydrate derivative catabolic process / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / neuroinflammatory response / establishment of blood-brain barrier / respiratory gaseous exchange by respiratory system / Glycolysis / defense response to protozoan / oxygen transport / erythrocyte development / 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
2-PHOSPHOGLYCOLIC ACID / Bisphosphoglycerate mutase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.48 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)62,7055
Polymers62,2372
Non-polymers4683
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.643, 70.808, 158.933
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-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H5O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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 meas: 49.3 Mg/m3 / Density % sol: 48.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M BIS TRIS propane, 18% polyethylene glycol 8000, 10% 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 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.48→29 Å / Num. obs: 21810 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 45.78 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.047 / Rrim(I) all: 0.12 / Net I/σ(I): 9.7 / Num. measured all: 140609 / Scaling rejects: 69
Reflection shellResolution: 2.48→2.58 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.71 / Num. unique obs: 2412 / CC1/2: 0.881 / Rpim(I) all: 0.3 / Rrim(I) all: 0.772 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.27data extraction
CrysalisPro41_64_69adata reduction
PHENIX1.9-1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H4Z

2h4z


Resolution: 2.48→28.999 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2843 1093 5.03 %
Rwork0.2098 20627 -
obs0.2135 21720 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.97 Å2 / Biso mean: 53.1307 Å2 / Biso min: 23.15 Å2
Refinement stepCycle: final / Resolution: 2.48→28.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 27 118 4201
Biso mean--60.95 47.25 -
Num. residues----497
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4801-2.59290.36911350.25552527
2.5929-2.72950.32791520.25732514
2.7295-2.90040.38051270.26422531
2.9004-3.12410.32341440.25632551
3.1241-3.4380.34071310.23632560
3.438-3.93440.26861310.2072595
3.9344-4.9530.21511360.17062602
4.953-28.9990.26591370.18682747

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