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- PDB-2a6p: Structure Solution to 2.2 Angstrom and Functional Characterisatio... -

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Basic information

Entry
Database: PDB / ID: 2a6p
TitleStructure Solution to 2.2 Angstrom and Functional Characterisation of the Open Reading Frame Rv3214 from Mycobacterium tuberculosis
ComponentsPOSSIBLE PHOSPHOGLYCERATE MUTASE GPM2
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / predicted phosphoglycerate mutase / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / gluconeogenesis / protein homodimerization activity
Similarity search - Function
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
Acid phosphatase / Phosphoglycerate mutase family protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsWatkins, H.A. / Yu, M. / Baker, E.N. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Bacteriol. / Year: 2006
Title: Structural and Functional Analysis of Rv3214 from Mycobacterium tuberculosis, a Protein with Conflicting Functional Annotations, Leads to Its Characterization as a Phosphatase.
Authors: Watkins, H.A. / Baker, E.N.
History
DepositionJul 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POSSIBLE PHOSPHOGLYCERATE MUTASE GPM2
B: POSSIBLE PHOSPHOGLYCERATE MUTASE GPM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2416
Polymers44,8652
Non-polymers3764
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.343, 79.844, 52.839
Angle α, β, γ (deg.)90.00, 109.11, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological Unit is the dimer found in the assymetric unit

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Components

#1: Protein POSSIBLE PHOSPHOGLYCERATE MUTASE GPM2 / PHOSPHOGLYCEROMUTASE / PGAM / BPG-DEPENDENT PGAM


Mass: 22432.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv3214 (EntD) / Plasmid: pPROEX HTa / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q6MWZ7, UniProt: Q7D5X2*PLUS, EC: 5.4.2.1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: MPD, Lithium sulphate, Imidazole-HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.91840, 0.97972
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.979721
ReflectionResolution: 2.15→50 Å / Num. obs: 22262 / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 57.3
Reflection shellResolution: 2.15→2.25 Å / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 10.1 / Num. unique all: 10306 / % possible all: 96.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→28.9 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1373222.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.226 793 4.9 %RANDOM
Rwork0.209 ---
obs0.209 16299 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.5739 Å2 / ksol: 0.352897 e/Å3
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å2-5.05 Å2
2--5 Å20 Å2
3----5.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.2→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 0 22 106 3088
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.712.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.251 117 5.1 %
Rwork0.229 2157 -
obs--76.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3gol.pargol.top

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