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- PDB-5zby: Crystal structure of a [NiFe] hydrogenase maturation protease Hyc... -

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Basic information

Entry
Database: PDB / ID: 5zby
TitleCrystal structure of a [NiFe] hydrogenase maturation protease HycI from Thermococcus kodakarensis KOD1
ComponentsHydrogenase maturation protease HycI
KeywordsHYDROLASE / Maturation protease / HycI / [NiFe] hydrogenase / C-terminal cleavage
Function / homologyPeptidase A31, hydrogenase maturation protease HycI / Hydrogenase maturation protease / Peptidase A31 family / Peptidase HybD-like domain superfamily / enzyme activator activity / protein processing / endopeptidase activity / Hydrogenase maturation protease HycI
Function and homology information
Biological speciesThermococcus kodakarensis KOD1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.591 Å
AuthorsKwon, 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: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structure of a [NiFe] hydrogenase maturation protease HycI provides insights into its substrate selectivity
Authors: Kwon, S. / Nishitani, Y. / Hirao, Y. / Kanai, T. / Atomi, H. / Miki, K.
History
DepositionFeb 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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: Hydrogenase maturation protease HycI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2952
Polymers17,0571
Non-polymers2381
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint6 kcal/mol
Surface area8130 Å2
Unit cell
Length a, b, c (Å)50.377, 50.377, 146.167
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Hydrogenase maturation protease HycI


Mass: 17056.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea)
Strain: KOD1 / Gene: TK2004 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JIH7
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: HEPES (pH 7.5), 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.591→47.628 Å / Num. obs: 25807 / % possible obs: 98.1 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 35.4
Reflection shellResolution: 1.591→1.63 Å / Rmerge(I) obs: 0.623 / Num. unique obs: 1300

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIXmodel building
HKL-2000data scaling
PHASERphasing
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 2.0E+85 / Resolution: 1.591→47.628 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2233 1254 4.88 %
Rwork0.2021 --
obs0.2032 25672 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.591→47.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1170 0 15 102 1287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151201
X-RAY DIFFRACTIONf_angle_d1.6321626
X-RAY DIFFRACTIONf_dihedral_angle_d13.44450
X-RAY DIFFRACTIONf_chiral_restr0.088197
X-RAY DIFFRACTIONf_plane_restr0.009208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.591-1.65470.33691150.30612234X-RAY DIFFRACTION83
1.6547-1.730.32941390.27142687X-RAY DIFFRACTION99
1.73-1.82120.31351220.25382724X-RAY DIFFRACTION100
1.8212-1.93530.251340.22912719X-RAY DIFFRACTION99
1.9353-2.08480.23451370.21182734X-RAY DIFFRACTION100
2.0848-2.29460.22231480.212752X-RAY DIFFRACTION100
2.2946-2.62660.19691540.21112758X-RAY DIFFRACTION100
2.6266-3.30910.22881590.20322805X-RAY DIFFRACTION100
3.3091-47.64890.20731460.18153005X-RAY DIFFRACTION100

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