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- PDB-6h26: Rabbit muscle phosphoglycerate mutase -

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Basic information

Entry
Database: PDB / ID: 6h26
TitleRabbit muscle phosphoglycerate mutase
ComponentsPhosphoglycerate mutase
KeywordsISOMERASE / phosphoglycerate / mutase / glycolysis / gluconeogenesis / rabbit / pgam / pgam2
Function / homology
Function and homology information


: / bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / canonical glycolysis / striated muscle contraction / Notch signaling pathway / identical protein binding / cytosol
Similarity search - Function
Phosphoglycerate mutase 1 / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / 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
Phosphoglycerate mutase
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.288 Å
AuthorsWisniewski, J. / Barciszewski, J. / Jaskolski, M. / Rakus, D.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2015/19/B/NZ1/00332 Poland
CitationJournal: To Be Published
Title: Rabbit muscle phosphoglycerate mutase
Authors: Wisniewski, J. / Barciszewski, J. / Jaskolski, M. / Rakus, D.
History
DepositionJul 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8724
Polymers28,7121
Non-polymers1603
Water2,810156
1
A: Phosphoglycerate mutase
hetero molecules

A: Phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7438
Polymers57,4242
Non-polymers3196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2420 Å2
ΔGint-18 kcal/mol
Surface area22430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.308, 71.308, 112.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-303-

CL

21A-464-

HOH

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Components

#1: Protein Phosphoglycerate mutase


Mass: 28712.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Gaps in the sequence indicate residues that were not modeled because of poor electron density
Source: (natural) Oryctolagus cuniculus (rabbit)
References: UniProt: G1U7S4, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent), bisphosphoglycerate mutase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.6 % / Description: tetragonal prism
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M NaCl, 20%PEG6000, 100 mM HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 3, 2013
RadiationMonochromator: Double Crystal Monochromator, Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.288→33.99 Å / Num. obs: 73677 / % possible obs: 99.7 % / Redundancy: 18.82 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 31.05
Reflection shellResolution: 1.288→1.37 Å / Redundancy: 16.7 % / Rmerge(I) obs: 1.155 / Mean I/σ(I) obs: 2.88 / Num. unique obs: 11616 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YFK

1yfk


Resolution: 1.288→33.987 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / Phase error: 16.97
Details: Anisotropic refinement. H atoms were added at riding positions.
RfactorNum. reflection% reflectionSelection details
Rfree0.1868 1011 1.37 %Random selection
Rwork0.152 ---
obs0.1525 73675 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.288→33.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 9 156 2113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012109
X-RAY DIFFRACTIONf_angle_d1.0732863
X-RAY DIFFRACTIONf_dihedral_angle_d21.974825
X-RAY DIFFRACTIONf_chiral_restr0.09303
X-RAY DIFFRACTIONf_plane_restr0.008375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.288-1.35590.22681410.181710106X-RAY DIFFRACTION98
1.3559-1.44080.19131430.146710260X-RAY DIFFRACTION100
1.4408-1.55210.15941430.122210287X-RAY DIFFRACTION100
1.5521-1.70820.13771430.113310323X-RAY DIFFRACTION100
1.7082-1.95540.15261440.122510369X-RAY DIFFRACTION100
1.9554-2.46350.16481460.148910488X-RAY DIFFRACTION100
2.4635-33.99920.21871510.170310831X-RAY DIFFRACTION100

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