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- PDB-5kh0: Crystal Structure of HydF from thermosipho melanesiensis in compl... -

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Basic information

Entry
Database: PDB / ID: 5kh0
TitleCrystal Structure of HydF from thermosipho melanesiensis in complex with a [4Fe-4S] cluster
ComponentsSmall GTP-binding protein
KeywordsOXIDOREDUCTASE / [FEFE]-HYDROGENASE MATURASE OXIDOREDUCTASE
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / GTP binding / metal ion binding
Similarity search - Function
Rossmann fold - #11410 / Rossmann fold - #11420 / [FeFe]-hydrogenase H-cluster maturation GTPase HydF / Hydrogen maturase F, tetramerization domain / Hydrogen maturase F dimerization domain / Hydrogen maturase F dimerization domain / Hydrogen maturase F tetramerization domain / 50S ribosome-binding GTPase / GTP binding domain / Small GTP-binding protein domain ...Rossmann fold - #11410 / Rossmann fold - #11420 / [FeFe]-hydrogenase H-cluster maturation GTPase HydF / Hydrogen maturase F, tetramerization domain / Hydrogen maturase F dimerization domain / Hydrogen maturase F dimerization domain / Hydrogen maturase F tetramerization domain / 50S ribosome-binding GTPase / GTP binding domain / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Small GTP-binding protein
Similarity search - Component
Biological speciesThermosipho melanesiensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCaserta, G. / Pecqueur, L. / Fontecave, M.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Structural and functional characterization of the hydrogenase-maturation HydF protein.
Authors: Caserta, G. / Pecqueur, L. / Adamska-Venkatesh, A. / Papini, C. / Roy, S. / Artero, V. / Atta, M. / Reijerse, E. / Lubitz, W. / Fontecave, M.
History
DepositionJun 14, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Jun 7, 2017Group: Database references
Revision 1.3Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Small GTP-binding protein
B: Small GTP-binding protein
C: Small GTP-binding protein
D: Small GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,8268
Polymers177,4194
Non-polymers1,4074
Water0
1
A: Small GTP-binding protein
B: Small GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4134
Polymers88,7102
Non-polymers7032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-58 kcal/mol
Surface area32780 Å2
MethodPISA
2
C: Small GTP-binding protein
D: Small GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4134
Polymers88,7102
Non-polymers7032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-59 kcal/mol
Surface area32310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.010, 173.480, 89.320
Angle α, β, γ (deg.)90.00, 110.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Small GTP-binding protein


Mass: 44354.867 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosipho melanesiensis (strain DSM 12029 / CIP 104789 / BI429) (bacteria)
Gene: Tmel_1361 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: A6LMQ7
#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4

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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: 2.94 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5
Details: Hepes 25 mM pH 7.5, PEG 8K 1.5% w/v Anaerobic glovebox <1 ppm O2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2015
RadiationMonochromator: Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.8→47.62 Å / Num. obs: 48183 / % possible obs: 95.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 92.27 Å2 / Rrim(I) all: 0.067 / Net I/σ(I): 11.86
Reflection shellHighest resolution: 2.8 Å / CC1/2: 0.549 / Rrim(I) all: 0.806

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSNovember 3, 2014data reduction
XDSNovember 3, 2014data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→47.62 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.887 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.357 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.928 / SU Rfree Blow DPI: 0.345 / SU Rfree Cruickshank DPI: 0.361
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1948 4.04 %RANDOM
Rwork0.233 ---
obs0.234 48177 95.2 %-
Displacement parametersBiso mean: 86.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.326 Å20 Å20.0897 Å2
2---1.8252 Å20 Å2
3---1.4992 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: 1 / Resolution: 2.8→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11339 0 32 0 11371
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00911561HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1415630HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4214SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes274HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1617HARMONIC5
X-RAY DIFFRACTIONt_it11561HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion20.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1567SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance20HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13085SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 126 4.39 %
Rwork0.222 2746 -
all0.223 2872 -
obs--76.6 %

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