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- PDB-2dfj: Crystal Structure of the Diadenosine Tetraphosphate Hydrolase fro... -

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Basic information

Entry
Database: PDB / ID: 2dfj
TitleCrystal Structure of the Diadenosine Tetraphosphate Hydrolase from Shigella flexneri 2a
Componentsdiadenosinetetraphosphatase
KeywordsHYDROLASE / helices and strands mixture
Function / homology
Function and homology information


bis(5'-nucleosyl)-tetraphosphatase (symmetrical) / bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity
Similarity search - Function
Bis(5'-nucleosyl)-tetraphosphatase, symmetrical / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / : / Bis(5'-nucleosyl)-tetraphosphatase, symmetrical
Similarity search - Component
Biological speciesShigella flexneri 2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.72 Å
AuthorsWang, Q.H. / Hu, W.X. / Bi, R.C.
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of the diadenosine tetraphosphate hydrolase from Shigella flexneri 2a
Authors: Wang, Q.H. / Hu, W.X. / Gao, W. / Bi, R.C.
History
DepositionMar 2, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: diadenosinetetraphosphatase
B: diadenosinetetraphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8556
Polymers62,6352
Non-polymers2204
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.498, 54.965, 119.203
Angle α, β, γ (deg.)90.00, 129.14, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe two molecules in the asymmetric unit are related by a non-crystallographic two fold axis

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Components

#1: Protein diadenosinetetraphosphatase / Diadenosine Tetraphosphate Hydrolase


Mass: 31317.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a (bacteria) / Species: Shigella flexneri / Strain: strain 301 / Plasmid: pet22b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: GenBank: 24111495, UniProt: Q83SQ2*PLUS, bis(5'-nucleosyl)-tetraphosphatase (symmetrical)
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 3.4 Å3/Da / Density % sol: 63.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1M Bis-Tris, 0.2M Magnesium chloride and 25% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9793 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.72→50 Å / Num. obs: 22410 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rsym value: 0.123 / Net I/σ(I): 17
Reflection shellResolution: 2.72→2.82 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 6 / Num. unique all: 2233 / Rsym value: 0.469 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.72→38.95 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.881 / SU B: 12.945 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.641 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26775 1164 5.1 %RANDOM
Rwork0.22924 ---
all0.23128 ---
obs0.23128 21519 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.282 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.07 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.72→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4147 0 4 162 4313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224266
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9665821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6255532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31623.743187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.04915652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4231525
X-RAY DIFFRACTIONr_chiral_restr0.1050.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023307
X-RAY DIFFRACTIONr_nbd_refined0.2560.22193
X-RAY DIFFRACTIONr_nbtor_refined0.320.22836
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2205
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3220.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.26
X-RAY DIFFRACTIONr_mcbond_it0.7811.52705
X-RAY DIFFRACTIONr_mcangle_it0.89124259
X-RAY DIFFRACTIONr_scbond_it1.46731793
X-RAY DIFFRACTIONr_scangle_it2.1214.51562
LS refinement shellResolution: 2.716→2.787 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 60 -
Rwork0.385 1304 -
obs--81.09 %

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