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- PDB-7thi: Human Bisphosphoglycerate Mutase complexed with 2-phosphoglycolate -

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Basic information

Entry
Database: PDB / ID: 7thi
TitleHuman Bisphosphoglycerate Mutase complexed with 2-phosphoglycolate
ComponentsBisphosphoglycerate mutase
KeywordsISOMERASE / ligand / activator
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsClark, K.L. / Kulathila, R. / Wright, K. / Isome, Y. / Sage, D. / Yang, Y. / Christodoulou, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Human Bisphosphoglycerate Mutase complexed with 2-phosphoglycolate
Authors: Clark, K.L. / Kulathila, R. / Wright, K. / Isome, Y. / Sage, D. / Yang, Y. / Christodoulou, C.
History
DepositionJan 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,5494
Polymers62,2372
Non-polymers3122
Water10,737596
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.607, 71.758, 159.294
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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 / Production host: Escherichia coli BL21(DE3) (bacteria)
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.: 2 / Source method: obtained synthetically / Formula: C2H5O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / 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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 27% to 30% PEG 6000, bisTris propane, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 R 300K / Detector: PIXEL / Date: May 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.33→65.43 Å / Num. obs: 129374 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.016 / Rrim(I) all: 0.058 / Net I/σ(I): 20.2 / Num. measured all: 1638029 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.33-1.412.91.009241143186820.8960.2911.052.5100
4.2-65.4311.50.0425107144470.9990.0130.04354.299.9

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
PHENIX1.19.2-4158refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H4X

2h4x


Resolution: 1.33→46.49 Å / SU ML: 0.1385 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.1971
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1602 6378 4.93 %
Rwork0.1343 122872 -
obs0.1356 129250 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.67 Å2
Refinement stepCycle: LAST / Resolution: 1.33→46.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4159 0 18 596 4773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00684385
X-RAY DIFFRACTIONf_angle_d0.90935954
X-RAY DIFFRACTIONf_chiral_restr0.075634
X-RAY DIFFRACTIONf_plane_restr0.0115782
X-RAY DIFFRACTIONf_dihedral_angle_d14.66441692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.340.25882140.24744060X-RAY DIFFRACTION99.91
1.34-1.360.24351840.22374051X-RAY DIFFRACTION99.93
1.36-1.380.24892060.20944077X-RAY DIFFRACTION99.98
1.38-1.390.23552160.19734034X-RAY DIFFRACTION99.93
1.39-1.410.22752080.17994021X-RAY DIFFRACTION99.91
1.41-1.430.20972050.16394090X-RAY DIFFRACTION100
1.43-1.450.2082010.14874028X-RAY DIFFRACTION100
1.45-1.470.17762090.13374100X-RAY DIFFRACTION100
1.47-1.50.18252110.12374034X-RAY DIFFRACTION99.93
1.5-1.520.15222090.11594085X-RAY DIFFRACTION100
1.52-1.550.14912040.10994040X-RAY DIFFRACTION99.98
1.55-1.570.14022020.11334087X-RAY DIFFRACTION100
1.57-1.60.1412090.11784048X-RAY DIFFRACTION100
1.6-1.640.16382200.1234057X-RAY DIFFRACTION100
1.64-1.670.15732150.11924062X-RAY DIFFRACTION100
1.67-1.710.15462090.12434086X-RAY DIFFRACTION99.98
1.71-1.750.14592100.12014056X-RAY DIFFRACTION99.98
1.75-1.80.17932280.11424103X-RAY DIFFRACTION100
1.8-1.860.14052230.10834034X-RAY DIFFRACTION100
1.86-1.910.14831800.11194111X-RAY DIFFRACTION100
1.91-1.980.13432080.11424101X-RAY DIFFRACTION100
1.98-2.060.16241960.12164133X-RAY DIFFRACTION99.98
2.06-2.160.1491850.12234121X-RAY DIFFRACTION100
2.16-2.270.15392200.11424109X-RAY DIFFRACTION100
2.27-2.410.12422220.1174143X-RAY DIFFRACTION100
2.41-2.60.15942460.1244065X-RAY DIFFRACTION100
2.6-2.860.1732460.13764154X-RAY DIFFRACTION100
2.86-3.270.15031990.14644196X-RAY DIFFRACTION100
3.27-4.120.15442330.13544202X-RAY DIFFRACTION99.93
4.13-46.490.16992600.15494384X-RAY DIFFRACTION99.94

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