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- PDB-4pde: Crystal structure of FdhD in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 4pde
TitleCrystal structure of FdhD in complex with GDP
ComponentsProtein FdhD
KeywordsHYDROLASE / GDP / Mo-bisPGD sulfuration
Function / homology
Function and homology information


sulfur carrier activity / sulfurtransferase activity / Mo-molybdopterin cofactor biosynthetic process / molybdopterin cofactor binding / positive regulation of catalytic activity / cytosol / cytoplasm
Similarity search - Function
Sulfur carrier protein FdhD / FdhD/NarQ family / Cytidine deaminase-like
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Sulfur carrier protein FdhD / Sulfur carrier protein FdhD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsArnoux, P. / Walburger, A. / Magalon, A. / Pignol, D.
CitationJournal: Nat Commun / Year: 2015
Title: Sulphur shuttling across a chaperone during molybdenum cofactor maturation.
Authors: Arnoux, P. / Ruppelt, C. / Oudouhou, F. / Lavergne, J. / Siponen, M.I. / Toci, R. / Mendel, R.R. / Bittner, F. / Pignol, D. / Magalon, A. / Walburger, A.
History
DepositionApr 18, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein FdhD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1112
Polymers31,6681
Non-polymers4431
Water28816
1
A: Protein FdhD
hetero molecules

A: Protein FdhD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2234
Polymers63,3362
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area4810 Å2
ΔGint-15 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.430, 98.430, 120.411
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Protein FdhD / FdhD


Mass: 31668.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fdhD, BN17_38461 / Production host: Escherichia coli (E. coli) / References: UniProt: J7QY30, UniProt: P32177*PLUS
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2M NaNO3, 2.2 M AmSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.8→85 Å / Num. obs: 8948 / % possible obs: 99.8 % / Redundancy: 8.4 % / Net I/σ(I): 12.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6_289) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1pw9

1pw9


Resolution: 2.8→69.573 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2763 418 4.72 %
Rwork0.1895 --
obs0.1934 8848 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.814 Å2 / ksol: 0.369 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.0827 Å20 Å2-0 Å2
2--11.0827 Å20 Å2
3----22.1655 Å2
Refinement stepCycle: LAST / Resolution: 2.8→69.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1891 0 28 16 1935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081957
X-RAY DIFFRACTIONf_angle_d1.1782656
X-RAY DIFFRACTIONf_dihedral_angle_d19.636723
X-RAY DIFFRACTIONf_chiral_restr0.077298
X-RAY DIFFRACTIONf_plane_restr0.004343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-3.20520.33191440.23152700X-RAY DIFFRACTION98
3.2052-4.03820.30131250.18092780X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.84210.54540.30611.3579-0.74063.43940.6115-0.38020.0597-0.1531-0.2062-0.02160.9813-0.2248-0.26440.3824-0.1592-0.02370.2368-0.00480.1877-18.837436.285529.653
21.0494-0.15810.88060.2859-0.1020.7472-0.05320.4213-0.1023-0.0995-0.0902-0.20890.0397-0.04060.14510.0489-0.02150.00030.40820.00020.26576.272243.44457.521
33.0868-0.8147-1.54010.9513-0.9913.4240.49040.05630.0445-0.14130.4616-0.22620.8686-0.5287-0.96770.73680.045-0.31170.9091-0.10740.62976.098755.3942-2.0442
41.07620.01760.83220.8816-0.20031.4319-0.08430.5102-0.1316-0.046800.00680.12640.22330.05410.0801-0.0810.03660.2791-0.07710.1411-12.871539.3283-3.2611
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 15:38)
2X-RAY DIFFRACTION2(chain A and resid 39:109)
3X-RAY DIFFRACTION3(chain A and resid 110:135)
4X-RAY DIFFRACTION4(chain A and resid 136:277)

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