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- PDB-5yy0: Crystal structure of the HyhL-HypA complex (form II) -

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Basic information

Entry
Database: PDB / ID: 5yy0
TitleCrystal structure of the HyhL-HypA complex (form II)
Components
  • Cytosolic NiFe-hydrogenase, alpha subunit
  • Probable hydrogenase nickel incorporation protein HypA
KeywordsMETAL BINDING PROTEIN / Hydrogenase / Maturation / HyhL / HypA
Function / homology
Function and homology information


ferredoxin hydrogenase activity / nickel cation binding / protein maturation / catalytic complex / protein modification process / zinc ion binding
Similarity search - Function
hypothetical protein PF0899 fold - #50 / Hydrogenase maturation factor HypA/HybF / Hydrogenase nickel incorporation protein HypA/HybF, conserved site / Hydrogenase/urease nickel incorporation, metallochaperone, hypA / Hydrogenases expression/synthesis hypA family signature. / hypothetical protein PF0899 fold / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase ...hypothetical protein PF0899 fold - #50 / Hydrogenase maturation factor HypA/HybF / Hydrogenase nickel incorporation protein HypA/HybF, conserved site / Hydrogenase/urease nickel incorporation, metallochaperone, hypA / Hydrogenases expression/synthesis hypA family signature. / hypothetical protein PF0899 fold / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / [NiFe]-hydrogenase, large subunit / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Hydrogenase maturation factor HypA / Cytosolic NiFe-hydrogenase, alpha subunit
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.243 Å
AuthorsKwon, S. / Watanabe, S. / Nishitani, Y. / Miki, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)26291012 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)17H03642 Japan
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Crystal structures of a [NiFe] hydrogenase large subunit HyhL in an immature state in complex with a Ni chaperone HypA.
Authors: Kwon, S. / Watanabe, S. / Nishitani, Y. / Kawashima, T. / Kanai, T. / Atomi, H. / Miki, K.
History
DepositionDec 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 27, 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: Cytosolic NiFe-hydrogenase, alpha subunit
B: Probable hydrogenase nickel incorporation protein HypA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1303
Polymers64,0642
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-9 kcal/mol
Surface area25220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.046, 132.046, 132.046
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23

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Components

#1: Protein Cytosolic NiFe-hydrogenase, alpha subunit / Sulfhydrogenase alpha subunit


Mass: 48352.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: hydA, TK2069 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NKS2
#2: Protein Probable hydrogenase nickel incorporation protein HypA


Mass: 15711.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: hypA, TK2008 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5JIH3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 2.99 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1M NaCl, 0.1M MgCl2, 12% PEG 3350, 0.1M imidazole-HCl (pH 6.2)

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.243→44.015 Å / Num. obs: 12459 / % possible obs: 100 % / Redundancy: 20.2 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 23.6
Reflection shellResolution: 3.243→3.36 Å / Rmerge(I) obs: 1.622

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.243→44.015 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 47.36 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3137 625 5.02 %
Rwork0.29 --
obs0.2918 12451 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.243→44.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3721 0 1 0 3722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033782
X-RAY DIFFRACTIONf_angle_d0.7935158
X-RAY DIFFRACTIONf_dihedral_angle_d9.9521264
X-RAY DIFFRACTIONf_chiral_restr0.032618
X-RAY DIFFRACTIONf_plane_restr0.004676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2429-3.56910.4371650.36662917X-RAY DIFFRACTION95
3.5691-4.08520.37461450.35962919X-RAY DIFFRACTION95
4.0852-5.14570.361540.31592940X-RAY DIFFRACTION95
5.1457-44.01940.25571610.24883050X-RAY DIFFRACTION95

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