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- PDB-4y4m: Thiazole synthase Thi4 from Methanocaldococcus jannaschii -

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Basic information

Entry
Database: PDB / ID: 4y4m
TitleThiazole synthase Thi4 from Methanocaldococcus jannaschii
ComponentsPutative ribose 1,5-bisphosphate isomerase
KeywordsBIOSYNTHETIC PROTEIN / Thiazole synthase / ISOMERASE
Function / homology
Function and homology information


sulfide-dependent adenosine diphosphate thiazole synthase / thiazole biosynthetic process / pentosyltransferase activity / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / iron ion binding
Similarity search - Function
Thiazole biosynthetic enzyme, prokaryotic / Thiazole biosynthetic enzyme Thi4 family / Thi4 family / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
Chem-48F / Thiamine thiazole synthase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsZhang, X. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2016
Title: Structural Basis for Iron-Mediated Sulfur Transfer in Archael and Yeast Thiazole Synthases.
Authors: Zhang, X. / Eser, B.E. / Chanani, P.K. / Begley, T.P. / Ealick, S.E.
History
DepositionFeb 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative ribose 1,5-bisphosphate isomerase
B: Putative ribose 1,5-bisphosphate isomerase
C: Putative ribose 1,5-bisphosphate isomerase
D: Putative ribose 1,5-bisphosphate isomerase
E: Putative ribose 1,5-bisphosphate isomerase
F: Putative ribose 1,5-bisphosphate isomerase
G: Putative ribose 1,5-bisphosphate isomerase
H: Putative ribose 1,5-bisphosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,48121
Polymers250,9708
Non-polymers5,51113
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)180.760, 180.760, 73.328
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A3 - 300
2111B3 - 300
3111C3 - 300
4111D3 - 300
5111E3 - 300
6111F3 - 300
7111G3 - 300
8111H3 - 300

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.453442, -0.839324, 0.299876), (-0.838538, -0.515764, -0.17562), (0.302067, -0.171824, -0.937674)10.01166, 2.73902, -40.718
3given(0.834989, 0.494301, 0.241784), (0.493803, -0.86698, 0.06712), (0.2428, 0.063349, -0.968006)21.73484, -64.55105, -33.15097
4given(0.011075, 0.970249, -0.241856), (-0.997698, -0.005461, -0.067594), (-0.066903, 0.242048, 0.967955)65.6912, 23.73042, 8.29738
5given(-0.953241, -0.025878, -0.3011), (-0.028675, -0.984087, 0.17536), (-0.300846, 0.175794, 0.93733)87.74722, -41.97642, 17.66459
6given(-0.8805, -0.47058, 0.057222), (-0.469581, 0.849297, -0.241223), (0.064916, -0.239267, -0.968781)78.18453, 16.24388, -31.66574
7given(0.03276, -0.99781, -0.057456), (0.970227, 0.017947, 0.241531), (-0.239972, -0.063658, 0.968691)21.80578, -64.80766, 9.51802
8given(-0.499293, 0.866433, 7.1E-5), (0.866433, 0.499292, 0.000958), (0.000795, 0.00054, -1)90.33633, -52.17899, -23.58238

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Components

#1: Protein
Putative ribose 1,5-bisphosphate isomerase / Ribulose 1 / 5-bisphosphate synthase / RuBP synthase


Mass: 31371.217 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ0601 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: Q58018, ribose-1,5-bisphosphate isomerase
#2: Chemical
ChemComp-48F / [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R)-2,3,5-tris(oxidanyl)-4-oxidanylidene-pentyl] hydrogen phosphate


Mass: 559.316 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Chemical
ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 9.5
Details: 1.05 M Potassium/sodium tartrate, 0.1 M CHES/ Sodium hydroxide pH 9.5, 0.2 M Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 72800 / % possible obs: 99.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/av σ(I): 2.3 / Net I/σ(I): 13.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RP0

1rp0


Resolution: 2.71→40 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / ESU R: 0.787 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20311 3646 5 %RANDOM
Rwork0.17708 ---
obs0.17841 68627 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.853 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20.4 Å20 Å2
2--0.81 Å20 Å2
3----2.62 Å2
Refinement stepCycle: LAST / Resolution: 2.71→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15270 0 353 21 15644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01915879
X-RAY DIFFRACTIONr_bond_other_d00.0215492
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.99921553
X-RAY DIFFRACTIONr_angle_other_deg3.659335590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05452057
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.60824.497567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.322152606
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2021572
X-RAY DIFFRACTIONr_chiral_restr0.0760.22536
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217662
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023250
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9635.2678252
X-RAY DIFFRACTIONr_mcbond_other2.9625.2678251
X-RAY DIFFRACTIONr_mcangle_it4.5257.89510301
X-RAY DIFFRACTIONr_mcangle_other4.5257.89510302
X-RAY DIFFRACTIONr_scbond_it4.1435.8367627
X-RAY DIFFRACTIONr_scbond_other4.1435.8367628
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6138.56811252
X-RAY DIFFRACTIONr_long_range_B_refined9.97143.30517265
X-RAY DIFFRACTIONr_long_range_B_other9.97143.30417264
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3747 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Auth asym-IDRms dev position (Å)
A5.59
B5.93
C7.08
D7.14
E5.88
F4.35
G4.29
H5.85
LS refinement shellResolution: 2.71→2.777 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 257 -
Rwork0.274 4862 -
obs--95.84 %

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