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- PDB-3wo5: Crystal structure of S147Q of Rv2613c from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 3wo5
TitleCrystal structure of S147Q of Rv2613c from Mycobacterium tuberculosis
ComponentsAP-4-A phosphorylase
KeywordsTRANSFERASE / Mycobacterium / diadenosine polyphosphate / phosphorylase / HIT motif
Function / homology
Function and homology information


diadenosine tetraphosphate catabolic process / ATP adenylyltransferase / ATP:ADP adenylyltransferase activity / bis(5'-nucleosyl)-tetraphosphatase activity / ATP binding / plasma membrane
Similarity search - Function
: / FHIT family / HIT domain / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / AP-4-A phosphorylase / AP-4-A phosphorylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsMori, S. / Wachino, J. / Arakawa, Y. / Shibayama, K.
CitationJournal: To be Published
Title: Role of Ser-147 and Ala-149 in catalytic activity of diadenosine tetraphosphate phosphorylase from Mycobacterium tuberculosis H37Rv
Authors: Mori, S. / Wachino, J. / Kim, H. / Rimbara, E. / Arakawa, Y. / Shibayama, K.
History
DepositionDec 20, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: AP-4-A phosphorylase
B: AP-4-A phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3348
Polymers49,5682
Non-polymers7656
Water1,27971
1
A: AP-4-A phosphorylase
B: AP-4-A phosphorylase
hetero molecules

A: AP-4-A phosphorylase
B: AP-4-A phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,66716
Polymers99,1364
Non-polymers1,53112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area19570 Å2
ΔGint-109 kcal/mol
Surface area26900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.015, 63.550, 79.025
Angle α, β, γ (deg.)90.00, 111.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein AP-4-A phosphorylase / ATP adenylyltransferase / Diadenosine 5' / 5'''-P1 / P4-tetraphosphate phosphorylase / AP / A phosphorylase


Mass: 24784.037 Da / Num. of mol.: 2 / Mutation: S147Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT2688, Rv2613c / Plasmid: pColdI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: O06201, UniProt: P9WMK9*PLUS, ATP adenylyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.1M sodium cacodylate, 0.2M lithium sulfate, 28.5% polyethylene glycol 400, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 7, 2010
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. all: 11717 / Num. obs: 11269 / % possible obs: 96.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 23.58 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 21.3
Reflection shellResolution: 2.79→2.85 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.19 / Num. unique all: 518 / % possible all: 87.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ANO

3ano


Resolution: 2.79→31.775 Å / FOM work R set: 0.8834 / SU ML: 0.38 / σ(F): 0.8 / Phase error: 19.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 531 4.71 %RANDOM
Rwork0.1754 ---
obs0.1782 11269 95.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.533 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso max: 62.16 Å2 / Biso mean: 20.95 Å2 / Biso min: 7.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.3633 Å2-0 Å25.8852 Å2
2---2.1539 Å2-0 Å2
3---7.5173 Å2
Refinement stepCycle: LAST / Resolution: 2.79→31.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 0 47 71 2771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052764
X-RAY DIFFRACTIONf_angle_d0.8853755
X-RAY DIFFRACTIONf_dihedral_angle_d17.7131026
X-RAY DIFFRACTIONf_chiral_restr0.059413
X-RAY DIFFRACTIONf_plane_restr0.004481
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7891-3.06960.27281240.2136243387
3.0696-3.51330.25021370.1825274198
3.5133-4.42450.211350.1486274398
4.4245-31.7770.21671350.1711282198

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