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- PDB-4h67: Crystal structure of HMP synthase Thi5 from S. cerevisiae -

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Basic information

Entry
Database: PDB / ID: 4h67
TitleCrystal structure 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 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: 2.7 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

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Assembly

Deposited unit
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
F: 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)316,51526
Polymers314,6358
Non-polymers1,88018
Water2,684149
1
A: Pyrimidine precursor biosynthesis enzyme THI5
B: Pyrimidine precursor biosynthesis enzyme THI5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1946
Polymers78,6592
Non-polymers5354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-39 kcal/mol
Surface area26120 Å2
MethodPISA
2
C: Pyrimidine precursor biosynthesis enzyme THI5
E: Pyrimidine precursor biosynthesis enzyme THI5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3319
Polymers78,6592
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-82 kcal/mol
Surface area26340 Å2
MethodPISA
3
D: Pyrimidine precursor biosynthesis enzyme THI5
H: Pyrimidine precursor biosynthesis enzyme THI5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0436
Polymers78,6592
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-59 kcal/mol
Surface area25600 Å2
MethodPISA
4
F: Pyrimidine precursor biosynthesis enzyme THI5
G: Pyrimidine precursor biosynthesis enzyme THI5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9475
Polymers78,6592
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-58 kcal/mol
Surface area26370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.790, 188.460, 101.670
Angle α, β, γ (deg.)90.00, 112.51, 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 'A' and (resseq 4:187 or resseq 197:285 or resseq 289:310 or resseq 312:336 )
211chain 'B' and (resseq 4:187 or resseq 197:285 or resseq 289:309 or resseq 331:336 )
311chain 'C' and (resseq 4:128 or resseq 132:187 or resseq...
411chain 'D' and (resseq 4:187 or resseq 197:285 or resseq 289:310 or resseq 312:336 )
511chain 'E' and (resseq 4:187 or resseq 197:285 or resseq 289:308 or resseq 332:336 )
611chain 'F' and (resseq 4:187 or resseq 197:285 or resseq 289:310 or resseq 312:336 )
711chain 'G' and (resseq 4:187 or resseq 197:285 or resseq 289:310 or resseq 312:336 )
811chain 'H' and (resseq 4:187 or resseq 197:285 or resseq 289:309 or resseq 331:336 )

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Components

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


Mass: 39329.367 Da / Num. of mol.: 8 / 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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M lithium sulfate monohydrate, 0.1 M Bis-Tris, pH 5.5, 25% PEG3350, 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: 0.98011 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2011
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.7→49.142 Å / Num. obs: 71456 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 1.92 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 13.68
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 1.92 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 1.77 / Num. unique all: 5348 / % possible all: 96.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CCP4model building
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4H65

4h65


Resolution: 2.7→49.142 Å / SU ML: 0.43 / σ(F): 1.99 / Phase error: 28.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2469 2009 2.81 %
Rwork0.2075 --
obs0.2087 71456 95.27 %
all-75142 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.393 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.447 Å20 Å25.097 Å2
2--13.3813 Å2-0 Å2
3----11.9343 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20679 0 100 149 20928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01221254
X-RAY DIFFRACTIONf_angle_d1.43528713
X-RAY DIFFRACTIONf_dihedral_angle_d16.3687969
X-RAY DIFFRACTIONf_chiral_restr0.13081
X-RAY DIFFRACTIONf_plane_restr0.0063623
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2396X-RAY DIFFRACTIONPOSITIONAL
12B2396X-RAY DIFFRACTIONPOSITIONAL0.171
13C2544X-RAY DIFFRACTIONPOSITIONAL0.224
14D2568X-RAY DIFFRACTIONPOSITIONAL0.258
15E2392X-RAY DIFFRACTIONPOSITIONAL0.162
16F2568X-RAY DIFFRACTIONPOSITIONAL0.238
17G2568X-RAY DIFFRACTIONPOSITIONAL0.261
18H2405X-RAY DIFFRACTIONPOSITIONAL0.177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.76750.38571470.32785009X-RAY DIFFRACTION97
2.7675-2.84240.39221510.31125035X-RAY DIFFRACTION97
2.8424-2.9260.32031450.28875001X-RAY DIFFRACTION96
2.926-3.02040.36871480.27025044X-RAY DIFFRACTION97
3.0204-3.12830.32571480.2654989X-RAY DIFFRACTION97
3.1283-3.25360.28351430.25065018X-RAY DIFFRACTION97
3.2536-3.40160.30151450.23425035X-RAY DIFFRACTION96
3.4016-3.58090.27871420.22144912X-RAY DIFFRACTION95
3.5809-3.80520.26331400.21514944X-RAY DIFFRACTION95
3.8052-4.09890.23551400.19424954X-RAY DIFFRACTION95
4.0989-4.51110.21461380.16924867X-RAY DIFFRACTION94
4.5111-5.16320.19291430.16814902X-RAY DIFFRACTION94
5.1632-6.50280.21951420.20494848X-RAY DIFFRACTION93
6.5028-49.15030.18391370.17044889X-RAY DIFFRACTION92

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