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- PDB-3idd: Cofactor-Independent Phosphoglycerate Mutase from Thermoplasma ac... -

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Basic information

Entry
Database: PDB / ID: 3idd
TitleCofactor-Independent Phosphoglycerate Mutase from Thermoplasma acidophilum DSM 1728
Components2,3-bisphosphoglycerate-independent phosphoglycerate mutase
KeywordsISOMERASE / phosphoglycerate mutase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Glycolysis
Function / homology
Function and homology information


phosphoglycerate mutase (2,3-diphosphoglycerate-independent) / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity / glycolytic process / metal ion binding
2,3-bisphosphoglycerate-independent phosphoglycerate mutase / Metalloenzyme / Alkaline-phosphatase-like, core domain superfamily / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, prokaryotes / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase superfamily / Metalloenzyme superfamily / 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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)89,8432
Polymers89,8432
Non-polymers00
Water1,51384
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)88.605, 136.744, 63.289
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsdimer present in asymmetric unit of cell

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Components

#1: Protein/peptide 2,3-bisphosphoglycerate-independent phosphoglycerate mutase / Phosphoglyceromutase / BPG-independent PGAM / aPGAM / Cofactor-Independent Phosphoglycerate Mutase


Mass: 44921.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: apgM, Ta0413 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q9HL27, phosphoglycerate mutase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.20 M NaCl, 0.10 M phosphate citrate, pH 4.2, 10% PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924, 0.97948
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2009
RadiationMonochromator: double-crystal Si(111) monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979241
20.979481
ReflectionResolution: 2.6→74.36 Å / Num. all: 24446 / Num. obs: 22991 / % possible obs: 99.04 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 74.33 / Redundancy: 3.7 % / Rmerge(I) obs: 0.098
Reflection shellResolution: 2.6→2.62 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 1.5 / % possible all: 99

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MLPHAREphasing
REFMAC5.5.0072refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→74.36 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.833 / SU B: 19.386 / SU ML: 0.379 / Cross valid method: THROUGHOUT / ESU R Free: 0.492
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31106 995 5.1 %RANDOM
Rwork0.23022 ---
Obs0.23439 18474 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.466 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å20 Å20 Å2
2---2.08 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.8→74.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5585 0 0 84 5669
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0140.0225689
r_bond_other_d
r_angle_refined_deg1.611.9817688
r_angle_other_deg
r_dihedral_angle_1_deg6.7745715
r_dihedral_angle_2_deg34.56923.268257
r_dihedral_angle_3_deg23.70415977
r_dihedral_angle_4_deg20.8551556
r_chiral_restr0.1190.2848
r_gen_planes_refined0.0070.0214334
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it0.731.53597
r_mcbond_other
r_mcangle_it1.4325786
r_scbond_it2.07132092
r_scangle_it3.614.51902
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.469 64 -
Rwork0.308 1378 -
Obs--99.79 %

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