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- PDB-3ano: Crystal Structure of a Novel Diadenosine 5',5'''-P1,P4-Tetraphosp... -

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Basic information

Entry
Database: PDB / ID: 3ano
TitleCrystal Structure of a Novel Diadenosine 5',5'''-P1,P4-Tetraphosphate Phosphorylase from Mycobacterium tuberculosis H37Rv
ComponentsAP-4-A phosphorylase
KeywordsTRANSFERASE / Mycobacterium / diadenosine polyphosphate / phosphorylase / HIT motif
Function / homology
Function and homology information


diadenosine tetraphosphate catabolic process / ATP adenylyltransferase / bis(5'-nucleosyl)-tetraphosphatase activity / ATP:ADP adenylyltransferase 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 / SAD / Resolution: 1.894 Å
AuthorsMori, S. / Shibayama, K. / Wachino, J. / Arakawa, Y.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural insights into the novel diadenosine 5',5-P1,P4-tetraphosphate phosphorylase from Mycobacterium tuberculosis H37Rv
Authors: Mori, S. / Shibayama, K. / Wachino, J. / Arakawa, Y.
History
DepositionSep 6, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Mar 13, 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: AP-4-A phosphorylase
B: AP-4-A phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1597
Polymers49,4862
Non-polymers6735
Water4,197233
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)100,31914
Polymers98,9724
Non-polymers1,34710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area15510 Å2
ΔGint-81 kcal/mol
Surface area27490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.454, 63.554, 79.123
Angle α, β, γ (deg.)90.000, 110.920, 90.000
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: 24742.986 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT2688, Rv2613c / Plasmid: pCold I / 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 / Phosphate


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


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.41 Å3/Da / Density % sol: 48.91 % / Mosaicity: 0.389 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Sodium Cacodylate, 30% PEG 400, 0.2M LiSO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 28, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.894→50 Å / Num. obs: 37314 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.061 / Χ2: 1.585 / Net I/σ(I): 17
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.936.40.3818260.994198.3
1.93-1.976.70.35118370.992199.4
1.97-2.0170.28418690.994199.8
2.01-2.057.20.24818561.053199.9
2.05-2.097.40.2318511.066199.9
2.09-2.147.50.17918811.041199.9
2.14-2.197.60.15518291.114199.9
2.19-2.257.60.14218691.203199.9
2.25-2.327.60.12618651.25199.9
2.32-2.397.60.11118691.278199.8
2.39-2.487.60.118411.351199.9
2.48-2.587.60.09418491.4191100
2.58-2.77.60.07818911.52199.9
2.7-2.847.60.07118701.7199.9
2.84-3.027.60.06118601.933199.9
3.02-3.257.50.05318632.268199.8
3.25-3.587.50.04618852.5381100
3.58-4.097.40.03918832.5791100
4.09-5.167.30.03518952.571199.9
5.16-5070.03519252.656198.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.894→39.406 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8747 / SU ML: 0.23 / σ(F): 0.07 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2011 1807 5.01 %RANDOM
Rwork0.1761 ---
obs0.1774 36096 96.09 %-
all-36102 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.617 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 73.74 Å2 / Biso mean: 30.1482 Å2 / Biso min: 11.11 Å2
Baniso -1Baniso -2Baniso -3
1--6.0192 Å2-0 Å25.6811 Å2
2---2.316 Å2-0 Å2
3---8.3352 Å2
Refinement stepCycle: LAST / Resolution: 1.894→39.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 41 233 2921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052745
X-RAY DIFFRACTIONf_angle_d1.0253726
X-RAY DIFFRACTIONf_chiral_restr0.073413
X-RAY DIFFRACTIONf_plane_restr0.005479
X-RAY DIFFRACTIONf_dihedral_angle_d18.5331018
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.8936-1.94480.26621150.194922122327221281
1.9448-2.00210.26311360.186424872623248791
2.0021-2.06670.18041380.177425742712257495
2.0667-2.14050.2031520.166926182770261896
2.1405-2.22620.18521330.161926322765263297
2.2262-2.32750.19061120.168926962808269697
2.3275-2.45020.21011480.17726522800265297
2.4502-2.60370.21241320.173327012833270198
2.6037-2.80470.22251480.181426642812266499
2.8047-3.08690.20061510.188727352886273599
3.0869-3.53330.20861450.177275829032758100
3.5333-4.45060.17241570.1592273628932736100
4.4506-39.41480.19561400.177828242964282499

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