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- PDB-2rd3: Crystal structure of TenA homologue (HP1287) from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 2rd3
TitleCrystal structure of TenA homologue (HP1287) from Helicobacter pylori
ComponentsTranscriptional regulatorTranscriptional regulation
KeywordsHYDROLASE / TenA / HP1287 / Helicobacter pylori / Thiamin / Vitamin B1 / thiaminase II / TRANSCRIPTION
Function / homology
Function and homology information


aminopyrimidine aminohydrolase / thiaminase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / cytosol
Similarity search - Function
Thiaminase II / Thiaminase-2/PQQC / TENA/THI-4/PQQC family / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Aminopyrimidine aminohydrolase / Aminopyrimidine aminohydrolase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBarison, N. / Cendron, L. / Trento, A. / Angelini, A. / Zanotti, G.
Citation
Journal: To be Published
Title: The structural and functional characterization of HP1287 from Helicobacter pylori demonstrates it is a TenA homologue
Authors: Barison, N. / Cendron, L. / Trento, A. / Angelini, A. / Zanotti, G.
#1: Journal: Biochemistry / Year: 2005
Title: Structural characterization of the regulatory proteins TenA and TenI from Bacillus subtilis and identification of TenA as a thiaminase II
Authors: Toms, A.V. / Haas, A.L. / Park, J.H. / Begley, T.P. / Ealick, S.E.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: The 2.35 A structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolism
Authors: Benach, J. / Edstrom, W.C. / Lee, I. / Das, K. / Cooper, B. / Xiao, R. / Liu, J. / Rost, B. / Acton, T.B. / Montelione, G.T. / Hunt, J.F.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure analysis of PH1161 protein, a transcriptional activator TenA homologue from the hyperthermophilic archaeon Pyrococcus horikoshii
Authors: Itou, H. / Yao, M. / Watanabe, N. / Tanaka, I.
#4: Journal: NAT.CHEM.BIOL. / Year: 2007
Title: A new thiamin salvage pathway
Authors: Jenkins, A.H. / Schyns, G. / Potot, S. / Sun, G. / Begley, T.P.
History
DepositionSep 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
Remark 999Sequence The gene author has cloned comes from a different strain.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator
D: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)51,3302
Polymers51,3302
Non-polymers00
Water93752
1
A: Transcriptional regulator
D: Transcriptional regulator

A: Transcriptional regulator
D: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)102,6614
Polymers102,6614
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y+1/2,-z+1/41
Buried area7700 Å2
MethodPISA
2
A: Transcriptional regulator

A: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)51,3302
Polymers51,3302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y+1/2,-z+1/41
Buried area1630 Å2
MethodPISA
3
D: Transcriptional regulator

D: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)51,3302
Polymers51,3302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y+1/2,-z+1/41
Buried area1630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.420, 148.420, 233.525
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11D-227-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 3 / Auth seq-ID: 2 - 217 / Label seq-ID: 8 - 223

Dom-IDAuth asym-IDLabel asym-ID
1AA
2DB
DetailsThe biological assembly is a tetramer. The dimer in the asymmetric unit generates the tetramer through one of the two crystallographic two-fold axes.

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Components

#1: Protein Transcriptional regulator / Transcriptional regulation / TenA


Mass: 25665.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: CCUG17874 / Gene: HP1287 / Plasmid: pET151 directional TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3
References: UniProt: O25874, UniProt: A8KRL3*PLUS, aminopyrimidine aminohydrolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 1.1 M Lithium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.7→125 Å / Num. all: 36057 / Num. obs: 36057 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.4
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.8 / Num. unique all: 5136 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TO9

1to9


Resolution: 2.7→125 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.508 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.277 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25761 1799 5 %RANDOM
Rwork0.23527 ---
obs0.23638 34257 99.8 %-
all-34257 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.183 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å20 Å2
2--0.93 Å20 Å2
3----1.86 Å2
Refinement stepCycle: LAST / Resolution: 2.7→125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 0 52 3620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223654
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.9334949
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0195437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.27125182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.72715628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1781510
X-RAY DIFFRACTIONr_chiral_restr0.1180.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022783
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2790.31891
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3440.52667
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.5264
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3520.341
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3510.511
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.64622219
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7933507
X-RAY DIFFRACTIONr_scbond_it1.48421652
X-RAY DIFFRACTIONr_scangle_it2.16431442
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
864tight positional0.050.05
892loose positional0.175
864tight thermal0.810.5
892loose thermal3.3310
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 119 -
Rwork0.36 2463 -
obs--97.95 %

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