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- PDB-3kd8: Cofactor-Independent Phosphoglycerate mutase from Thermoplasma Ac... -

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Basic information

Entry
Database: PDB / ID: 3kd8
TitleCofactor-Independent Phosphoglycerate mutase from Thermoplasma Acidophilum DSM 1728
Components2,3-bisphosphoglycerate-independent phosphoglycerate mutase
KeywordsISOMERASE / phosphoglycerate mutase / structural genomics / PSI-2 / protein genomics / MCSG / glycolysis isomerase / Protein Structure Initiative / Midwest Center for Structural Genomics / Glycolysis
Function / homology
Function and homology information


phosphoglycerate mutase (2,3-diphosphoglycerate-independent) / phosphoglycerate mutase activity / glycolytic process / metal ion binding
Similarity search - Function
2,3-bisphosphoglycerate-independent phosphoglycerate mutase / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, prokaryotes / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase superfamily / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase / Metalloenzyme / Metalloenzyme superfamily / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsJoachimiak, A. / Duke, N.E.C. / Marshall, N. / Buck, K. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Cofactor-Independent Phosphoglycerate mutase from Thermoplasma Acidophilum DSM 1728
Authors: Joachimiak, A. / Duke, N.E.C. / Marshall, N. / Buck, K.
History
DepositionOct 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
B: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase


Theoretical massNumber of molelcules
Total (without water)87,9272
Polymers87,9272
Non-polymers00
Water2,612145
1
A: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase


Theoretical massNumber of molelcules
Total (without water)43,9641
Polymers43,9641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase


Theoretical massNumber of molelcules
Total (without water)43,9641
Polymers43,9641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.911, 137.081, 67.088
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 2,3-bisphosphoglycerate-independent phosphoglycerate mutase / Phosphoglyceromutase / BPG-independent PGAM / aPGAM


Mass: 43963.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Strain: DSM 1728 / Gene: apgM, Ta0413 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 Magic / References: UniProt: Q9HL27, EC: 5.4.2.1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.16M magnesium chloride 0.08M tris HCl, pH 8.5 24% PEG 4000 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97880, 0.97904
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 18, 2009 / Details: double-crystal monochromator Si(111)
RadiationMonochromator: Silicon (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.979041
ReflectionResolution: 2.6→73.92 Å / Num. obs: 25760 / % possible obs: 99.84 % / Observed criterion σ(F): 3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 30.75
Reflection shellResolution: 2.6→2.62 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.923 / % possible all: 99.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MLPHAREphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→73.92 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.885 / SU B: 12.677 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 1.18 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Authors state that residue B58 and B270 do not have well-defined side chain because of weak electron density at the region.
RfactorNum. reflection% reflectionSelection details
Rfree0.28782 1305 5.1 %RANDOM
Rwork0.20737 ---
obs0.21145 24352 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.771 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---2.3 Å20 Å2
3---2.14 Å2
Refinement stepCycle: LAST / Resolution: 2.6→73.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5616 0 0 145 5761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225731
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.9827743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2765723
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93923.256258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.48815982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3571557
X-RAY DIFFRACTIONr_chiral_restr0.1140.2853
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214369
X-RAY DIFFRACTIONr_mcbond_it0.7861.53633
X-RAY DIFFRACTIONr_mcangle_it1.52425836
X-RAY DIFFRACTIONr_scbond_it2.44732098
X-RAY DIFFRACTIONr_scangle_it4.0044.51907
LS refinement shellResolution: 2.598→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 111 -
Rwork0.257 1758 -
obs--99.84 %

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