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- PDB-5lad: Crystal Structure of apo HydF from thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 5lad
TitleCrystal Structure of apo HydF from thermotoga maritima
ComponentsPutative GTP-binding proteinG protein
KeywordsOXIDOREDUCTASE / [FEFE]-HYDROGENASE MATURASE
Function / homology
Function and homology information


tRNA wobble uridine modification / tRNA methylation / GTP binding / cytoplasm
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
Uncharacterized protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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: PDBE / 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 1.4Jan 10, 2024Group: 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: Putative GTP-binding protein


Theoretical massNumber of molelcules
Total (without water)45,1491
Polymers45,1491
Non-polymers00
Water0
1
A: Putative GTP-binding protein

A: Putative GTP-binding protein


Theoretical massNumber of molelcules
Total (without water)90,2992
Polymers90,2992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_875-x+3,-y+2,z1
Buried area2880 Å2
ΔGint-21 kcal/mol
Surface area35120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.140, 126.140, 68.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Putative GTP-binding protein / G protein


Mass: 45149.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0445, Tmari_0442 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYS6

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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: 3.03 Å3/Da / Density % sol: 59.44 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 5
Details: 0.3 M sodium malonate dibasic monohydrate, 0.1M sodium acetate pH 5.0, 8% w/v gamma poly glutamic acid Anaerobic glovebox <1 ppm O2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2016
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3→44.6 Å / Num. obs: 10940 / % possible obs: 97.4 % / Redundancy: 4.5 % / Biso Wilson estimate: 125.23 Å2 / Rrim(I) all: 0.051 / Net I/σ(I): 17.48
Reflection shellCC1/2: 0.524 / Rrim(I) all: 0.1567

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSVERSION Oct 15, 2015data reduction
XDSVERSION Oct 15, 2015data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQ5

3qq5


Resolution: 3→44.6 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.897 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.415
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1050 9.83 %RANDOM
Rwork0.244 ---
obs0.248 10683 97.4 %-
Displacement parametersBiso mean: 115.15 Å2
Baniso -1Baniso -2Baniso -3
1-1.6723 Å20 Å20 Å2
2--1.6723 Å20 Å2
3----3.3446 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å
Refinement stepCycle: LAST / Resolution: 3→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2775 0 0 0 2775
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112815HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.193809HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1001SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes68HARMONIC2
X-RAY DIFFRACTIONt_gen_planes405HARMONIC5
X-RAY DIFFRACTIONt_it2815HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.31
X-RAY DIFFRACTIONt_other_torsion21.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion369SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3369SEMIHARMONIC4
LS refinement shellResolution: 3→3.35 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.258 261 9.31 %
Rwork0.243 2542 -
all0.245 2803 -
obs--91.1 %

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