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- PDB-2qcx: Crystal structure of Bacillus subtilis TenA Y112F mutant complexe... -

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Basic information

Entry
Database: PDB / ID: 2qcx
TitleCrystal structure of Bacillus subtilis TenA Y112F mutant complexed with formyl aminomethyl pyrimidine
ComponentsTranscriptional activator tenA
KeywordsHYDROLASE / Up-down Bundle
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
Chem-PF1 / Aminopyrimidine aminohydrolase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhang, Y. / Jenkins, A.L. / Begley, T.P. / Ealick, S.E.
CitationJournal: Bioorg.Chem. / Year: 2008
Title: Mutagenesis studies on TenA: A thiamin salvage enzyme from Bacillus subtilis
Authors: Jenkins, A.L. / Zhang, Y. / Ealick, S.E. / Begley, T.P.
History
DepositionJun 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 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 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional activator tenA
B: Transcriptional activator tenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5284
Polymers61,1082
Non-polymers4202
Water1,910106
1
A: Transcriptional activator tenA
B: Transcriptional activator tenA
hetero molecules

A: Transcriptional activator tenA
B: Transcriptional activator tenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,0578
Polymers122,2164
Non-polymers8414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.625, 58.625, 296.469
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-328-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLYGLYAA1 - 7728 - 104
21METMETGLYGLYBB1 - 7728 - 104
32LYSLYSASPASPAA101 - 220128 - 247
42LYSLYSASPASPBB101 - 220128 - 247
DetailsThe biological unit is a tetramer. The second part of the biological assembly is generated by the two fold axis: y, x, -z

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Components

#1: Protein Transcriptional activator tenA / Thiaminase II / Thiaminase-2


Mass: 30553.998 Da / Num. of mol.: 2 / Mutation: Y112F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: tenA / Production host: Escherichia coli (E. coli) / References: UniProt: P25052, aminopyrimidine aminohydrolase
#2: Chemical ChemComp-PF1 / N-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-N-(2-HYDROXYETHYL)FORMAMIDE


Mass: 210.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.08 Å3/Da / Density % sol: 40.97 %
Crystal growpH: 4.1
Details: 100 mM acetate pH 4.1, 0.6 - 1.0 M 1,6-hexanediol, 0.01 M CoCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 26664 / Num. obs: 26664 / % possible obs: 96.3 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Χ2: 0.919 / Net I/σ(I): 10.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1972 / Rsym value: 0.315 / Χ2: 0.671 / % possible all: 73.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.3.0037refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1yaf

1yaf


Resolution: 2.2→41.7 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU B: 11.058 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.296 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2224 8.4 %RANDOM
Rwork0.197 ---
obs0.2 26547 96.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.894 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å20 Å2
2--1.34 Å20 Å2
3----2.68 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3703 0 30 106 3839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223867
X-RAY DIFFRACTIONr_angle_refined_deg0.9541.9295231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5225450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50523.512205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46415611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.581520
X-RAY DIFFRACTIONr_chiral_restr0.0710.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023070
X-RAY DIFFRACTIONr_nbd_refined0.180.21906
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22680
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2146
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.210
X-RAY DIFFRACTIONr_mcbond_it0.491.52298
X-RAY DIFFRACTIONr_mcangle_it0.83723562
X-RAY DIFFRACTIONr_scbond_it1.05331880
X-RAY DIFFRACTIONr_scangle_it1.6284.51669
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A780MEDIUM POSITIONAL0.130.5
2B832LOOSE POSITIONAL0.4210
3A780MEDIUM THERMAL0.442
4B832LOOSE THERMAL0.5420
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 134 -
Rwork0.224 1287 -
obs-1421 71.3 %
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)
11.11610.23560.26351.51350.69833.6090.00790.02930.06820.0436-0.0413-0.0086-0.2535-0.13170.0333-0.15140.05540.0151-0.13940.009-0.1618-14.4424-6.930222.4118
22.6594-0.31740.44882.6818-0.03714.1432-0.00110.1666-0.2793-0.08040.0299-0.43340.56880.966-0.0288-0.14150.16560.02250.2371-0.0601-0.00029.0491-20.65859.555
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 22028 - 247
2X-RAY DIFFRACTION2BB1 - 22628 - 253

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