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- PDB-4h65: Crystal structure of SeMet derivative of HMP synthase Thi5 from S... -

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Basic information

Entry
Database: PDB / ID: 4h65
TitleCrystal structure of SeMet derivative of HMP synthase Thi5 from S. cerevisiae
ComponentsPyrimidine precursor biosynthesis enzyme THI5
KeywordsTRANSFERASE / HMP-P synthase / THI5-PLP complex / PLP binding
Function / homology
Function and homology information


4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase activity from histidine and PLP / Transferases / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / iron ion binding
Similarity search - Function
NMT1/THI5 family / SsuA/THI5-like / NMT1/THI5 like / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase THI5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsCoquille, S.C. / Roux, C. / Fitzpatrick, T. / Thore, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The Last Piece in the Vitamin B1 Biosynthesis Puzzle: STRUCTURAL AND FUNCTIONAL INSIGHT INTO YEAST 4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE PHOSPHATE (HMP-P) SYNTHASE.
Authors: Coquille, S. / Roux, C. / Fitzpatrick, T.B. / Thore, S.
History
DepositionSep 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyrimidine precursor biosynthesis enzyme THI5
B: Pyrimidine precursor biosynthesis enzyme THI5


Theoretical massNumber of molelcules
Total (without water)79,5032
Polymers79,5032
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-2 kcal/mol
Surface area26440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.440, 109.210, 122.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pyrimidine precursor biosynthesis enzyme THI5 / HMP synthase Thi5


Mass: 39751.418 Da / Num. of mol.: 2 / Mutation: K240S, E241G, Q317T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: THI5, YFL058W / Production host: Escherichia coli (E. coli) / References: UniProt: P43534
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 0.2 M potassium thiocyanate, 0.1 M Bis-Tris, pH 5.7, 27% PEG3350, 10% dodecyl-beta-D-maltoside, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97795 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 26, 2012
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals (DCCM)
Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97795 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 24546 / Num. obs: 24539 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 19.37 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 25.14
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 19.39 % / Rmerge(I) obs: 1.293 / Mean I/σ(I) obs: 2.85 / Num. unique all: 3224 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
CCP4model building
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→19.998 Å / SU ML: 0.41 / σ(F): 1.44 / Phase error: 27.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 2011 8.2 %RANDOM
Rwork0.2106 ---
obs0.2141 24535 99.98 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 12.056 Å2 / ksol: 0.263 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-17.7609 Å20 Å20 Å2
2--38.9729 Å20 Å2
3---9.7506 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4608 0 0 109 4717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014714
X-RAY DIFFRACTIONf_angle_d1.3126371
X-RAY DIFFRACTIONf_dihedral_angle_d15.1191756
X-RAY DIFFRACTIONf_chiral_restr0.086693
X-RAY DIFFRACTIONf_plane_restr0.007806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.63560.38441340.31521539X-RAY DIFFRACTION100
2.6356-2.67310.37061430.29881591X-RAY DIFFRACTION100
2.6731-2.71290.37551430.29951616X-RAY DIFFRACTION100
2.7129-2.75520.31181410.29981558X-RAY DIFFRACTION100
2.7552-2.80030.3181380.27951565X-RAY DIFFRACTION100
2.8003-2.84840.33141480.28921606X-RAY DIFFRACTION100
2.8484-2.90010.32331420.26871579X-RAY DIFFRACTION100
2.9001-2.95570.33131400.26141567X-RAY DIFFRACTION100
2.9557-3.01580.33421440.27091601X-RAY DIFFRACTION100
3.0158-3.08120.28991420.25881599X-RAY DIFFRACTION100
3.0812-3.15260.34441420.26041558X-RAY DIFFRACTION100
3.1526-3.23110.31171370.25121597X-RAY DIFFRACTION100
3.2311-3.31810.26581420.23311581X-RAY DIFFRACTION100
3.3181-3.41520.25261460.21141617X-RAY DIFFRACTION100
3.4152-3.52490.26571400.21711570X-RAY DIFFRACTION100
3.5249-3.65020.25151420.2161586X-RAY DIFFRACTION100
3.6502-3.79540.31251400.19361565X-RAY DIFFRACTION100
3.7954-3.96680.19881450.1891580X-RAY DIFFRACTION100
3.9668-4.17420.17741410.16891605X-RAY DIFFRACTION100
4.1742-4.4330.2161350.16021586X-RAY DIFFRACTION100
4.433-4.7710.17751420.16471571X-RAY DIFFRACTION100
4.771-5.24330.23371390.16561593X-RAY DIFFRACTION100
5.2433-5.98410.29011380.21891596X-RAY DIFFRACTION100
5.9841-7.47340.26681460.21361577X-RAY DIFFRACTION100
7.4734-19.99820.22231460.20411580X-RAY DIFFRACTION100

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