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- PDB-2gm7: TenA Homolog/Thi-4 Thiaminase from Pyrobaculum Aerophilum -

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Basic information

Entry
Database: PDB / ID: 2gm7
TitleTenA Homolog/Thi-4 Thiaminase from Pyrobaculum Aerophilum
ComponentstenA homolog/Thi-4 Thiaminase
KeywordsTRANSFERASE / THIAMINASE / TRANSCRIPTION
Function / homology
Function and homology information


thiaminase activity / thiamine metabolic 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
PHOSPHATE ION / Conserved protein (TenA homolog)
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSawaya, M.R. / Chan, S. / Han, G.W. / Perry, L.J.
CitationJournal: To be Published
Title: Crystal Structure of a Ten A Homolog/Thi-4 Thiaminase from Pyrobaculum Aerophilum
Authors: Sawaya, M.R. / Chan, S. / Han, G.W. / Perry, L.J. / Yeates, T.O.
History
DepositionApr 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: tenA homolog/Thi-4 Thiaminase
B: tenA homolog/Thi-4 Thiaminase
C: tenA homolog/Thi-4 Thiaminase
D: tenA homolog/Thi-4 Thiaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1909
Polymers100,9394
Non-polymers1,2505
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-29 kcal/mol
Surface area31710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.757, 134.926, 144.029
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11D-601-

PO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13A
23B
14C
24D
15A
25B
16C
26D
17A
27B
18C
28D

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALASPASPAA2 - 4311 - 52
21VALVALASPASPBB2 - 4311 - 52
12VALVALASPASPCC2 - 4311 - 52
22VALVALASPASPDD2 - 4311 - 52
13LEULEUMETMETAA47 - 6756 - 76
23LEULEUMETMETBB47 - 6756 - 76
14LEULEUMETMETCC47 - 6756 - 76
24LEULEUMETMETDD47 - 6756 - 76
15LYSLYSTYRTYRAA90 - 11199 - 120
25LYSLYSTYRTYRBB90 - 11199 - 120
16LYSLYSTYRTYRCC90 - 11199 - 120
26LYSLYSTYRTYRDD90 - 11199 - 120
17ALAALATYRTYRAA113 - 169122 - 178
27ALAALATYRTYRBB113 - 169122 - 178
18ALAALATYRTYRCC113 - 169122 - 178
28ALAALATYRTYRDD113 - 169122 - 178

NCS ensembles :
ID
1
2
3
4
5
6
7
8
DetailsThe asymmetric unit contains the biological assembly, a tetramer with D2 symmetry.

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Components

#1: Protein
tenA homolog/Thi-4 Thiaminase


Mass: 25234.812 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Strain: str. IM2 / Gene: tena/thi4 (pag5_170) / Plasmid: pTrcHis-2-TOPO / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZZM9, thiamine pyridinylase
#2: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 3 microliters of 10 mg/mL TenA in 20 mM Tris pH8, 20 mM NaCl, mixed with 3 microliters reservoir = 16% PEG 2000MME, and 0.1 M sodium phosphate, pH 6.6., VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 29, 2001 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→90 Å / Num. all: 27783 / Num. obs: 27783 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.4 % / Biso Wilson estimate: 76 Å2 / Rmerge(I) obs: 0.095 / Χ2: 1.02 / Net I/σ(I): 11.6
Reflection shellResolution: 2.8→2.9 Å / % possible obs: 100 % / Rmerge(I) obs: 0.586 / Num. unique obs: 2747 / Χ2: 0.921 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
CrystalClear(MSC/RIGAKU)data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UDD

1udd


Resolution: 2.8→19.7 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.803 / SU B: 31.576 / SU ML: 0.301 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.492 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Data were omitted from refinement which fell outside the bounds of an ellipsoid with vertices of 1/3.4, 1/2.8, and 1/2.8 reciprocal ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Data were omitted from refinement which fell outside the bounds of an ellipsoid with vertices of 1/3.4, 1/2.8, and 1/2.8 reciprocal Angstroms along a, b, and c, respectively.
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1152 5.1 %RANDOM
Rwork0.231 ---
all0.234 22752 --
obs0.234 22752 82.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.666 Å2
Baniso -1Baniso -2Baniso -3
1-2.42 Å20 Å20 Å2
2---1.53 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6822 0 67 15 6904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227101
X-RAY DIFFRACTIONr_bond_other_d0.0040.024852
X-RAY DIFFRACTIONr_angle_refined_deg1.1231.9719622
X-RAY DIFFRACTIONr_angle_other_deg0.8783.00111710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.265858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99222.954325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.425151142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4661548
X-RAY DIFFRACTIONr_chiral_restr0.0610.21006
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027905
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021563
X-RAY DIFFRACTIONr_nbd_refined0.2180.21884
X-RAY DIFFRACTIONr_nbd_other0.1810.24987
X-RAY DIFFRACTIONr_nbtor_refined0.1910.23444
X-RAY DIFFRACTIONr_nbtor_other0.0850.23450
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2167
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0050.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2080.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.22
X-RAY DIFFRACTIONr_mcbond_it3.70224416
X-RAY DIFFRACTIONr_mcbond_other0.6821729
X-RAY DIFFRACTIONr_mcangle_it5.07336769
X-RAY DIFFRACTIONr_scbond_it4.5623231
X-RAY DIFFRACTIONr_scangle_it6.12132852
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A247TIGHT POSITIONAL0.030.05
1A361LOOSE POSITIONAL0.275
1A247TIGHT THERMAL0.050.5
1A361LOOSE THERMAL2.3410
2C247TIGHT POSITIONAL0.030.05
2C361LOOSE POSITIONAL0.425
2C247TIGHT THERMAL0.060.5
2C361LOOSE THERMAL2.810
3A125TIGHT POSITIONAL0.040.05
3A127LOOSE POSITIONAL0.435
3A125TIGHT THERMAL0.060.5
3A127LOOSE THERMAL2.9510
4C125TIGHT POSITIONAL0.030.05
4C127LOOSE POSITIONAL0.165
4C125TIGHT THERMAL0.060.5
4C127LOOSE THERMAL2.7910
5A130TIGHT POSITIONAL0.030.05
5A156LOOSE POSITIONAL0.35
5A130TIGHT THERMAL0.060.5
5A156LOOSE THERMAL3.210
6C130TIGHT POSITIONAL0.020.05
6C156LOOSE POSITIONAL0.325
6C130TIGHT THERMAL0.080.5
6C156LOOSE THERMAL2.7810
7A340TIGHT POSITIONAL0.030.05
7A459LOOSE POSITIONAL0.215
7A340TIGHT THERMAL0.060.5
7A459LOOSE THERMAL2.2310
8C342TIGHT POSITIONAL0.030.05
8C463LOOSE POSITIONAL0.335
8C342TIGHT THERMAL0.070.5
8C463LOOSE THERMAL2.610
LS refinement shellResolution: 2.801→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 19 -
Rwork0.312 435 -
obs-454 22.78 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.32310.17160.38312.7473-0.07241.3426-0.25670.42850.0624-0.0330.2507-0.5748-0.25410.50680.00610.2027-0.2553-0.11280.288-0.0610.179246.455245.268325.2516
21.6519-0.34321.18493.1212-0.69815.37340.0585-0.1266-0.03090.18230.1444-0.158-0.28420.0656-0.2029-0.0242-0.0753-0.0792-0.0904-0.1146-0.057735.227515.624142.9073
31.8758-0.10480.36212.7685-1.65183.2494-0.0693-0.0220.10560.41070.11650.2067-0.5905-0.1588-0.04720.0737-0.08970.1004-0.1233-0.0122-0.141218.533643.45559.2868
41.89080.6379-0.00812.02740.01461.43770.08960.0934-0.02810.12010.0754-0.2344-0.00110.1769-0.165-0.0988-0.0543-0.0107-0.2171-0.0486-0.234821.32017.313715.2641
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 212 / Label seq-ID: 10 - 221

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB
33CC
44DD

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