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- PDB-8x2s: The Crystal Structure of BPGM from Biortus -

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Basic information

Entry
Database: PDB / ID: 8x2s
TitleThe Crystal Structure of BPGM from Biortus
ComponentsBisphosphoglycerate mutase
KeywordsISOMERASE / Hydrolase / Glycolysis
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
Bisphosphoglycerate mutase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Li, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of BPGM from Biortus
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Li, J.
History
DepositionNov 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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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)60,6439
Polymers60,2092
Non-polymers4347
Water9,422523
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint8 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.661, 61.524, 122.802
Angle α, β, γ (deg.)90.000, 95.320, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 1 - 249 / Label seq-ID: 2 - 250

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Bisphosphoglycerate mutase


Mass: 30104.281 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 (E. coli) / References: UniProt: P07738
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: HM(P07738) 0.1M Hepes-NaOH pH 7.2, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.953743 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953743 Å / Relative weight: 1
ReflectionResolution: 1.9→43.37 Å / Num. obs: 44995 / % possible obs: 99.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 7.2
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2 / Num. unique obs: 3090 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→43.37 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.573 / SU ML: 0.125 / Cross valid method: FREE R-VALUE / ESU R: 0.161 / ESU R Free: 0.147
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2293 2189 4.865 %
Rwork0.1872 42806 -
all0.189 --
obs-44995 98.975 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.064 Å2
Baniso -1Baniso -2Baniso -3
1--1.353 Å2-0 Å20.47 Å2
2--3.573 Å20 Å2
3----2.268 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4103 0 28 525 4656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134275
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174069
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.6395795
X-RAY DIFFRACTIONr_angle_other_deg1.2381.5779379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2855522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39622.278259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70415770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3591536
X-RAY DIFFRACTIONr_chiral_restr0.0660.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024843
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021001
X-RAY DIFFRACTIONr_nbd_refined0.1990.2862
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.24001
X-RAY DIFFRACTIONr_nbtor_refined0.1550.22039
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.22070
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2417
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0990.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1490.217
X-RAY DIFFRACTIONr_nbd_other0.1870.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.231
X-RAY DIFFRACTIONr_mcbond_it1.5762.4382028
X-RAY DIFFRACTIONr_mcbond_other1.5752.4362027
X-RAY DIFFRACTIONr_mcangle_it2.5263.6442537
X-RAY DIFFRACTIONr_mcangle_other2.5253.6462538
X-RAY DIFFRACTIONr_scbond_it1.9212.7162247
X-RAY DIFFRACTIONr_scbond_other1.922.7162248
X-RAY DIFFRACTIONr_scangle_it3.1983.9553247
X-RAY DIFFRACTIONr_scangle_other3.1983.9553248
X-RAY DIFFRACTIONr_lrange_it5.3129.0845034
X-RAY DIFFRACTIONr_lrange_other5.11228.5364893
X-RAY DIFFRACTIONr_ncsr_local_group_10.0840.058461
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.084050.05008
12BX-RAY DIFFRACTIONLocal ncs0.084050.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.3071850.3023090X-RAY DIFFRACTION97.5283
1.949-2.0030.3281400.2823095X-RAY DIFFRACTION99.6918
2.003-2.0610.2831370.2632978X-RAY DIFFRACTION97.8329
2.061-2.1240.2611360.2352932X-RAY DIFFRACTION99.6104
2.124-2.1940.2641380.2212802X-RAY DIFFRACTION98.5255
2.194-2.2710.2611320.2122748X-RAY DIFFRACTION98.9351
2.271-2.3570.2921300.22624X-RAY DIFFRACTION99.6382
2.357-2.4530.2541120.2082532X-RAY DIFFRACTION98.8042
2.453-2.5620.2411420.192448X-RAY DIFFRACTION99.8843
2.562-2.6870.2451200.1782308X-RAY DIFFRACTION99.0212
2.687-2.8320.2141290.1762182X-RAY DIFFRACTION99.4406
2.832-3.0040.2241060.182126X-RAY DIFFRACTION99.554
3.004-3.2110.2411090.1711968X-RAY DIFFRACTION99.3305
3.211-3.4680.1871070.1691832X-RAY DIFFRACTION99.1309
3.468-3.7990.199980.1581672X-RAY DIFFRACTION98.8827
3.799-4.2460.18650.1441525X-RAY DIFFRACTION97.7259
4.246-4.9020.141710.131372X-RAY DIFFRACTION99.3802
4.902-6.0020.234600.161151X-RAY DIFFRACTION99.5888
6.002-8.4780.215490.16901X-RAY DIFFRACTION98.8554

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