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- PDB-8hlg: Crystal structure of MoaE -

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Basic information

Entry
Database: PDB / ID: 8hlg
TitleCrystal structure of MoaE
ComponentsMolybdenum cofactor biosynthesis protein D/E
KeywordsTRANSFERASE / cofactor / biosynthesis
Function / homology
Function and homology information


Mo-molybdopterin cofactor biosynthetic process / cytosol
Similarity search - Function
Molybdopterin biosynthesis MoaE / Molybdopterin biosynthesis MoaE subunit superfamily / MoaE protein / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain superfamily
Similarity search - Domain/homology
Molybdenum cofactor biosynthesis protein D/E
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCai, J. / Zhao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2017YFA0503900 China
CitationJournal: Int J Mol Sci / Year: 2023
Title: MoaE Is Involved in Response to Oxidative Stress in Deinococcus radiodurans.
Authors: Cai, J. / Zhang, M. / Chen, Z. / Zhao, Y. / Xu, H. / Tian, B. / Wang, L. / Hua, Y.
History
DepositionNov 30, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Refinement description / Structure summary
Category: pdbx_entry_details / pdbx_initial_refinement_model
Item: _pdbx_entry_details.has_protein_modification / _pdbx_initial_refinement_model.accession_code ..._pdbx_entry_details.has_protein_modification / _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molybdenum cofactor biosynthesis protein D/E
B: Molybdenum cofactor biosynthesis protein D/E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4114
Polymers38,2192
Non-polymers1922
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-47 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.020, 94.950, 101.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

21A-334-

HOH

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Components

#1: Protein Molybdenum cofactor biosynthesis protein D/E


Mass: 19109.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Gene: DR_2607 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RR88
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.95 Å3/Da / Density % sol: 36.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Lithium Sulfate, Tris-HCl, PEG 3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 20539 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.062 / Net I/σ(I): 16.56
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2-2.050.5614770.9090.6081
2.05-2.110.44314780.930.4791
2.11-2.170.38314130.940.4151
2.17-2.240.2913750.9670.3151
2.24-2.310.26113400.9690.2851
2.31-2.390.21113040.980.2291
2.39-2.480.16912460.9860.1831
2.48-2.580.13512230.990.1461
2.58-2.70.10711690.9940.1171
2.7-2.830.09211070.9950.11
2.83-2.980.06910620.9970.0751
2.98-3.160.06110060.9970.0661
3.16-3.380.0559400.9970.0611
3.38-3.650.0468810.9980.0511
3.65-40.0478280.9980.0511
4-4.470.0437420.9980.0461
4.47-5.160.046680.9980.0441
5.16-6.320.045710.9980.0431
6.32-8.940.0364450.9990.0391
8.94-300.0282640.9990.0311

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Processing

Software
NameVersionClassification
XSCALEdata scaling
XDSdata reduction
BALBESphasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.65 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2356 1011 4.93 %
Rwork0.1944 --
obs0.1965 20510 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2121 0 10 77 2208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052185
X-RAY DIFFRACTIONf_angle_d0.7222973
X-RAY DIFFRACTIONf_dihedral_angle_d16.73783
X-RAY DIFFRACTIONf_chiral_restr0.054321
X-RAY DIFFRACTIONf_plane_restr0.009387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.110.28161440.25452745X-RAY DIFFRACTION100
2.11-2.240.26171240.22692748X-RAY DIFFRACTION100
2.24-2.410.25921420.22222751X-RAY DIFFRACTION100
2.41-2.650.27541330.22252783X-RAY DIFFRACTION100
2.65-3.040.27161670.23212752X-RAY DIFFRACTION100
3.04-3.820.2371500.19952810X-RAY DIFFRACTION100
3.82-29.650.19931510.15882910X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 12.5328 Å / Origin y: 63.1665 Å / Origin z: 35.8742 Å
111213212223313233
T0.3106 Å2-0.0446 Å20.005 Å2-0.3391 Å2-0.0396 Å2--0.2976 Å2
L1.0401 °2-0.087 °2-0.0577 °2-0.9056 °2-0.2817 °2--1.359 °2
S0.0884 Å °-0.0948 Å °0.0122 Å °-0.0518 Å °-0.0163 Å °0.0491 Å °-0.0799 Å °0.2674 Å °0 Å °
Refinement TLS groupSelection details: all

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