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- PDB-2gm8: TenA Homolog/Thi-4 Thiaminase complexed with product 4-amino-5-hy... -

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Basic information

Entry
Database: PDB / ID: 2gm8
TitleTenA Homolog/Thi-4 Thiaminase complexed with product 4-amino-5-hydroxymethyl-2-methylpyrimidine
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
4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE / Conserved protein (TenA homolog)
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSawaya, M.R. / Chan, S. / Han, G.W. / Perry, L.J. / Pashkov, I.
CitationJournal: To be Published
Title: Crystal Structure of a TenA Homolog/Thi-4 Thiaminase from Pyrobaculum Aerophilum
Authors: Sawaya, M.R. / Chan, S. / Han, G.W. / Pashkov, I. / 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)101,62010
Polymers100,9394
Non-polymers6816
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-30 kcal/mol
Surface area31030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.647, 94.287, 73.198
Angle α, β, γ (deg.)90.00, 113.65, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D
131A
141B
151C
161D
171A
181B
191C
201D
211A
221B
231C
241D
251A
261B
271C
281D
291A
301B
311C
321D

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALARGARGAA2 - 1611 - 25
21VALVALARGARGBB2 - 1611 - 25
31VALVALARGARGCC2 - 1611 - 25
41VALVALARGARGDD2 - 1611 - 25
52LEULEUSERSERAA47 - 5956 - 68
62LEULEUSERSERBB47 - 5956 - 68
72LEULEUSERSERCC47 - 5956 - 68
82LEULEUSERSERDD47 - 5956 - 68
93LYSLYSTYRTYRAA90 - 11199 - 120
103LYSLYSTYRTYRBB90 - 11199 - 120
113LYSLYSTYRTYRCC90 - 11199 - 120
123LYSLYSTYRTYRDD90 - 11199 - 120
134ALAALALEULEUAA113 - 149122 - 158
144ALAALALEULEUBB113 - 149122 - 158
154ALAALALEULEUCC113 - 149122 - 158
164ALAALALEULEUDD113 - 149122 - 158
175GLUGLUGLYGLYAA189 - 211198 - 220
185GLUGLUGLYGLYBB189 - 211198 - 220
195GLUGLUGLYGLYCC189 - 211198 - 220
205GLUGLUGLYGLYDD189 - 211198 - 220
216ASNASNTYRTYRAA152 - 169161 - 178
226ASNASNTYRTYRBB152 - 169161 - 178
236ASNASNTYRTYRCC152 - 169161 - 178
246ASNASNTYRTYRDD152 - 169161 - 178
257ILEILEASPASPAA17 - 4326 - 52
267ILEILEASPASPBB17 - 4326 - 52
277ILEILEASPASPCC17 - 4326 - 52
287ILEILEASPASPDD17 - 4326 - 52
298ALAALAMETMETAA61 - 6770 - 76
308ALAALAMETMETBB61 - 6770 - 76
318ALAALAMETMETCC61 - 6770 - 76
328ALAALAMETMETDD61 - 6770 - 76
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-HMH / 4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE


Mass: 139.155 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H9N3O
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 18 mg/mL protein was complexed with thiamine diphosphate and enzyme mediated catalysis produced 4-amino-5-hydroxymethyl-2-methylpyrimidine. Reservoir contains 20% PEG 8000, 0.1M Tris pH 8.5, ...Details: 18 mg/mL protein was complexed with thiamine diphosphate and enzyme mediated catalysis produced 4-amino-5-hydroxymethyl-2-methylpyrimidine. Reservoir contains 20% PEG 8000, 0.1M Tris pH 8.5, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2005
RadiationMonochromator: LN2 cooled double-crystal silicon (111) monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→80 Å / Num. all: 32375 / Num. obs: 32375 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.11 / Χ2: 1.058 / Net I/σ(I): 13
Reflection shellResolution: 2.5→2.59 Å / % possible obs: 98.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.299 / Num. unique obs: 3175 / Χ2: 1.016 / % possible all: 98.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2GM7

2gm7


Resolution: 2.5→67.12 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 19.408 / SU ML: 0.207 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.792 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1533 5.1 %RANDOM
Rwork0.187 ---
all0.189 30264 --
obs0.189 30264 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.708 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å20 Å21.05 Å2
2---2.57 Å20 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.5→67.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6920 0 48 74 7042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0227174
X-RAY DIFFRACTIONr_bond_other_d0.0010.024854
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.9649732
X-RAY DIFFRACTIONr_angle_other_deg0.895311688
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4535862
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00722.798336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.166151152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.951550
X-RAY DIFFRACTIONr_chiral_restr0.1040.21016
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028026
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021592
X-RAY DIFFRACTIONr_nbd_refined0.2460.32036
X-RAY DIFFRACTIONr_nbd_other0.2060.35301
X-RAY DIFFRACTIONr_nbtor_refined0.210.53610
X-RAY DIFFRACTIONr_nbtor_other0.0960.53604
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.5458
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2540.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1220.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2180.353
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.54
X-RAY DIFFRACTIONr_mcbond_it7.3525545
X-RAY DIFFRACTIONr_mcbond_other1.96221742
X-RAY DIFFRACTIONr_mcangle_it8.08536816
X-RAY DIFFRACTIONr_scbond_it9.30123564
X-RAY DIFFRACTIONr_scangle_it10.86232914
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A956TIGHT POSITIONAL0.040.05
2B956TIGHT POSITIONAL0.050.05
3C956TIGHT POSITIONAL0.040.05
4D956TIGHT POSITIONAL0.040.05
1A1268MEDIUM POSITIONAL0.470.5
2B1268MEDIUM POSITIONAL0.330.5
3C1268MEDIUM POSITIONAL0.330.5
4D1268MEDIUM POSITIONAL0.420.5
1A956TIGHT THERMAL0.10.5
2B956TIGHT THERMAL0.110.5
3C956TIGHT THERMAL0.10.5
4D956TIGHT THERMAL0.10.5
1A1268MEDIUM THERMAL0.992
2B1268MEDIUM THERMAL12
3C1268MEDIUM THERMAL0.892
4D1268MEDIUM THERMAL0.932
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 105 -
Rwork0.243 2120 -
obs-2225 98.63 %
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)
10.9211-0.110.10371.9141.24931.377-0.04590.3405-0.04020.15380.03450.03050.1533-0.04530.0114-0.0552-0.09590.0016-0.0866-0.0252-0.066318.296-21.032-5.4789
21.534-0.477-0.33731.761-0.19810.3739-0.0031-0.16940.05920.00020.17240.07130.1462-0.171-0.1693-0.09540.0470.0012-0.10610.0814-0.06065.1764-8.506724.7992
32.2998-1.899-0.55382.25190.48932.4355-0.1952-0.24080.28420.20380.3689-0.3695-0.23120.3824-0.17370.05520.0628-0.02270.0254-0.14670.017944.6026-27.90710.3109
41.87911.12720.18921.46540.5873.2084-0.0278-0.1478-0.20650.03860.2405-0.26920.17480.5256-0.2127-0.08170.09870.00330.0455-0.129-0.000534.661-1.71533.339
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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