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- PDB-4h6d: Crystal structure of PLP-soaked HMP synthase Thi5 from S. cerevisiae -

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Basic information

Entry
Database: PDB / ID: 4h6d
TitleCrystal structure of PLP-soaked HMP synthase Thi5 from S. cerevisiae
ComponentsPyrimidine precursor biosynthesis enzyme THI5
KeywordsTRANSFERASE / Synthase
Function / homology
Function and homology information


4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase activity from histidine and PLP / Transferases / thiamine diphosphate biosynthetic process / thiamine 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
PYRIDOXAL-5'-PHOSPHATE / 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase THI5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 / Refinement description / Structure summary
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Sep 20, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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
F: Pyrimidine precursor biosynthesis enzyme THI5
A: Pyrimidine precursor biosynthesis enzyme THI5
B: Pyrimidine precursor biosynthesis enzyme THI5
C: Pyrimidine precursor biosynthesis enzyme THI5
D: Pyrimidine precursor biosynthesis enzyme THI5
E: Pyrimidine precursor biosynthesis enzyme THI5
G: Pyrimidine precursor biosynthesis enzyme THI5
H: Pyrimidine precursor biosynthesis enzyme THI5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,31312
Polymers315,3258
Non-polymers9894
Water00
1
F: Pyrimidine precursor biosynthesis enzyme THI5
A: Pyrimidine precursor biosynthesis enzyme THI5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0783
Polymers78,8312
Non-polymers2471
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-0 kcal/mol
Surface area26010 Å2
MethodPISA
2
B: Pyrimidine precursor biosynthesis enzyme THI5
H: Pyrimidine precursor biosynthesis enzyme THI5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3254
Polymers78,8312
Non-polymers4942
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-1 kcal/mol
Surface area25650 Å2
MethodPISA
3
C: Pyrimidine precursor biosynthesis enzyme THI5
G: Pyrimidine precursor biosynthesis enzyme THI5


Theoretical massNumber of molelcules
Total (without water)78,8312
Polymers78,8312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint1 kcal/mol
Surface area26160 Å2
MethodPISA
4
D: Pyrimidine precursor biosynthesis enzyme THI5
E: Pyrimidine precursor biosynthesis enzyme THI5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0783
Polymers78,8312
Non-polymers2471
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-1 kcal/mol
Surface area25180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.480, 191.840, 101.890
Angle α, β, γ (deg.)90.00, 112.72, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain F and (resseq 4:10 or resseq 13:44 or resseq...
211chain A and (resseq 4:10 or resseq 13:44 or resseq...
311chain B and (resseq 4:10 or resseq 13:44 or resseq...
411chain C and (resseq 4:10 or resseq 13:44 or resseq...
511chain D and (resseq 4:10 or resseq 13:44 or resseq...
611chain E and (resseq 4:10 or resseq 13:44 or resseq...
711chain G and (resseq 4:10 or resseq 13:44 or resseq...
811chain H and (resseq 4:10 or resseq 13:44 or resseq...

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Components

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


Mass: 39415.586 Da / Num. of mol.: 8 / Mutation: E101K, D102S, 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: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P

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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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 18% 2-propanol, 0.1 M sodium citrate, pH 5.5, 20% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9394 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2012
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9394 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 61802 / Num. obs: 61802 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 4.82 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 12.9
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 4.44 % / Rmerge(I) obs: 0.896 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4564 / % possible all: 98.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CCP4model building
PHENIX(phenix.refine: 1.6.1_353)refinement
XDSdata reduction
XDSdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4H65

4h65


Resolution: 2.9→19.922 Å / SU ML: 0.39 / σ(F): 1.99 / Phase error: 29.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2626 3081 5 %RANDOM
Rwork0.221 ---
obs0.2231 61605 99.27 %-
all-62058 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.81 Å2 / ksol: 0.277 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.6147 Å20 Å24.75 Å2
2--15.9269 Å2-0 Å2
3----14.3122 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20816 0 60 0 20876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121355
X-RAY DIFFRACTIONf_angle_d1.13728825
X-RAY DIFFRACTIONf_dihedral_angle_d15.0578071
X-RAY DIFFRACTIONf_chiral_restr0.0783104
X-RAY DIFFRACTIONf_plane_restr0.0043631
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11F2380X-RAY DIFFRACTIONPOSITIONAL
12A2380X-RAY DIFFRACTIONPOSITIONAL0.061
13B2509X-RAY DIFFRACTIONPOSITIONAL0.058
14C2527X-RAY DIFFRACTIONPOSITIONAL0.056
15D2527X-RAY DIFFRACTIONPOSITIONAL0.065
16E2274X-RAY DIFFRACTIONPOSITIONAL0.066
17G2527X-RAY DIFFRACTIONPOSITIONAL0.079
18H2497X-RAY DIFFRACTIONPOSITIONAL0.054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.94520.37631400.32372654X-RAY DIFFRACTION98
2.9452-2.99330.38931390.33092637X-RAY DIFFRACTION100
2.9933-3.04470.39291390.32872636X-RAY DIFFRACTION99
3.0447-3.09990.3741410.31432675X-RAY DIFFRACTION99
3.0999-3.15930.34471380.28492626X-RAY DIFFRACTION99
3.1593-3.22350.34091380.28052625X-RAY DIFFRACTION99
3.2235-3.29330.34981420.25332700X-RAY DIFFRACTION99
3.2933-3.36960.2771370.24852610X-RAY DIFFRACTION99
3.3696-3.45340.281400.22692653X-RAY DIFFRACTION99
3.4534-3.54630.26331400.2272661X-RAY DIFFRACTION100
3.5463-3.650.27031400.22432661X-RAY DIFFRACTION99
3.65-3.76710.24741400.21882663X-RAY DIFFRACTION100
3.7671-3.90070.2851400.20862646X-RAY DIFFRACTION99
3.9007-4.05570.24321380.19312641X-RAY DIFFRACTION99
4.0557-4.23860.25231420.18452689X-RAY DIFFRACTION99
4.2386-4.45970.23861410.18342675X-RAY DIFFRACTION99
4.4597-4.73560.21231390.1832647X-RAY DIFFRACTION100
4.7356-5.09550.20721420.17882687X-RAY DIFFRACTION100
5.0955-5.5980.26551400.19912667X-RAY DIFFRACTION100
5.598-6.38460.25841420.21122691X-RAY DIFFRACTION100
6.3846-7.95770.20771410.19392688X-RAY DIFFRACTION100
7.9577-19.9230.17651420.17682692X-RAY DIFFRACTION99

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