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- PDB-4s2a: Crystal structure of Caulobacter crescentus ThiC with Fe4S4 clust... -

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Basic information

Entry
Database: PDB / ID: 4s2a
TitleCrystal structure of Caulobacter crescentus ThiC with Fe4S4 cluster at remote site (holo form)
ComponentsPhosphomethylpyrimidine synthase
KeywordsLYASE / Alpha-Beta Barrel / Radical SAM superfamily / Iron-sulfur cluster / Thiamin / Vitamin B1 / Vitamin B12 / Domain swapping / AdoMet and Glutamate mutase
Function / homology
Function and homology information


phosphomethylpyrimidine synthase activity / phosphomethylpyrimidine synthase / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / 4 iron, 4 sulfur cluster binding / zinc ion binding / cytosol
Similarity search - Function
ThiC-associated domain / ThiC-associated domain / Radical SAM ThiC family, central domain / Phosphomethylpyrimidine synthase ThiC/5-hydroxybenzimidazole synthase BzaA/B / Phosphomethylpyrimidine synthase / ThiC/Bza, core domain / Radical SAM ThiC family / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / IRON/SULFUR CLUSTER / Phosphomethylpyrimidine synthase
Similarity search - Component
Biological speciesCaulobacter crescentus CB15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsFenwick, M.K. / Mehta, A.P. / Zhang, Y. / Abdelwahed, S. / Begley, T.P. / Ealick, S.E.
CitationJournal: Nat Commun
Title: Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.
Authors: Fenwick, M.K. / Mehta, A.P. / Zhang, Y. / Abdelwahed, S.H. / Begley, T.P. / Ealick, S.E.
History
DepositionJan 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_id / _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: Phosphomethylpyrimidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6983
Polymers68,2511
Non-polymers4472
Water00
1
A: Phosphomethylpyrimidine synthase
hetero molecules

A: Phosphomethylpyrimidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,3966
Polymers136,5032
Non-polymers8934
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area8790 Å2
ΔGint-136 kcal/mol
Surface area40000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.657, 68.922, 97.620
Angle α, β, γ (deg.)90.00, 120.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Phosphomethylpyrimidine synthase / Hydroxymethylpyrimidine phosphate synthase / HMP-P synthase / HMP-phosphate synthase / HMPP ...Hydroxymethylpyrimidine phosphate synthase / HMP-P synthase / HMP-phosphate synthase / HMPP synthase / Thiamine biosynthesis protein ThiC


Mass: 68251.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus CB15 (bacteria) / Strain: ATCC 19089 / CB15 / Gene: thiC, CC_2029 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q9A6Q5, phosphomethylpyrimidine synthase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.2
Details: 140 mM HEPES, pH 9.2, and 7.5% (w/v) PEG8000, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.93→50 Å / Num. all: 13706 / Num. obs: 13613 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 33.76 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 5.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.93-3.032.40.517197.3
3.03-3.162.40.428196.6
3.16-3.32.40.305196.2
3.3-3.472.30.218195.4
3.47-3.692.20.176190.3
3.69-3.982.50.134196.6
3.98-4.382.50.103194.9
4.38-5.012.40.092194.4
5.01-6.312.40.095190.8
6.31-502.40.072189.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EPN

3epn


Resolution: 2.93→45.55 Å / SU ML: 0.41 / σ(F): 1.37 / Phase error: 25.04 / Stereochemistry target values: ML
Details: WEAK RESIDUAL ACTIVE SITE ELECTRON DENSITY IS CONSISTENT WITH LOW OCCUPANCYHMP-P, WHICH WAS NOT ADDED DURING CRYSTALLIZATION BUT WHICH COPURIFIES WITH THE ENZYME. A PHOSPHATE WAS INCLUDED IN ...Details: WEAK RESIDUAL ACTIVE SITE ELECTRON DENSITY IS CONSISTENT WITH LOW OCCUPANCYHMP-P, WHICH WAS NOT ADDED DURING CRYSTALLIZATION BUT WHICH COPURIFIES WITH THE ENZYME. A PHOSPHATE WAS INCLUDED IN THE MODEL, BUT NOT THE PYRIMIDINE
RfactorNum. reflection% reflection
Rfree0.246 682 5.01 %
Rwork0.194 --
obs0.197 13613 93.5 %
all-13706 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.97 Å2
Refinement stepCycle: LAST / Resolution: 2.93→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4527 0 13 0 4540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024658
X-RAY DIFFRACTIONf_angle_d0.9596338
X-RAY DIFFRACTIONf_dihedral_angle_d10.6991675
X-RAY DIFFRACTIONf_chiral_restr0.023690
X-RAY DIFFRACTIONf_plane_restr0.003836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.93-3.15630.35511360.26692641X-RAY DIFFRACTION96
3.1563-3.47380.26571340.21482609X-RAY DIFFRACTION95
3.4738-3.97620.27251320.1882573X-RAY DIFFRACTION93
3.9762-5.00860.19141440.15832571X-RAY DIFFRACTION94
5.0086-45.55840.22581360.18392537X-RAY DIFFRACTION90

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