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- PDB-2z1c: Crystal structure of HypC from Thermococcus kodakaraensis KOD1 -

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Basic information

Entry
Database: PDB / ID: 2z1c
TitleCrystal structure of HypC from Thermococcus kodakaraensis KOD1
ComponentsHydrogenase expression/formation protein HypC
KeywordsCHAPERONE / METAL BINDING PROTEIN / [NiFe] hydrogenase maturation / OB-fold
Function / homology
Function and homology information


carbon dioxide binding / protein maturation / iron ion binding
Similarity search - Function
Hydrogenase assembly chaperone, conserved site / Hydrogenases expression/synthesis hupF/hypC family signature. / Hydrogenase expression/formation protein, HupF/HypC / HupF/HypC family / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Hydrogenase expression/formation protein HypC
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.8 Å
AuthorsWatanabe, S. / Matsumi, R. / Arai, T. / Atomi, H. / Imanaka, T. / Miki, K.
CitationJournal: Mol.Cell / Year: 2007
Title: Crystal Structures of [NiFe] Hydrogenase Maturation Proteins HypC, HypD, and HypE: Insights into Cyanation Reaction by Thiol Redox Signaling
Authors: Watanabe, S. / Matsumi, R. / Arai, T. / Atomi, H. / Imanaka, T. / Miki, K.
History
DepositionMay 8, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydrogenase expression/formation protein HypC
B: Hydrogenase expression/formation protein HypC
C: Hydrogenase expression/formation protein HypC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0805
Polymers24,7943
Non-polymers2862
Water1,910106
1
A: Hydrogenase expression/formation protein HypC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3572
Polymers8,2651
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hydrogenase expression/formation protein HypC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4592
Polymers8,2651
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hydrogenase expression/formation protein HypC


Theoretical massNumber of molelcules
Total (without water)8,2651
Polymers8,2651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.237, 59.130, 53.973
Angle α, β, γ (deg.)90.00, 109.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-235-

HOH

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Components

#1: Protein Hydrogenase expression/formation protein HypC


Mass: 8264.673 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: hypC / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JII0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M citrate acid, pH 4.3-4.5, 100-600mM NaBr, 17-20% PEG4000, 20% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 28, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 21035 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 31.7 Å2 / Rsym value: 0.035 / Net I/σ(I): 31.3
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 4.3 / Rsym value: 0.213 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.8→46.18 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.145 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.134
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1045 5 %RANDOM
Rwork0.222 ---
obs0.223 21030 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.431 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20.57 Å2
2--2.52 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1601 0 19 106 1726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221647
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.9752229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.115211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40425.51758
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60815269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.393155
X-RAY DIFFRACTIONr_chiral_restr0.0850.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021200
X-RAY DIFFRACTIONr_nbd_refined0.210.2725
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21110
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2104
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.214
X-RAY DIFFRACTIONr_mcbond_it0.7491.51087
X-RAY DIFFRACTIONr_mcangle_it1.2221706
X-RAY DIFFRACTIONr_scbond_it2.2683629
X-RAY DIFFRACTIONr_scangle_it3.74.5523
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 74 -
Rwork0.234 1380 -
obs--93.15 %
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)
15.051-2.6275-2.08123.09670.70085.8446-0.0437-0.0392-0.26440.0544-0.15930.00960.3890.42160.203-0.16180.0706-0.0277-0.22890.0022-0.250624.86818.3735.8536
211.1879-4.46561.00084.915-1.85644.3541-0.35540.09120.61650.28890.0525-0.5431-0.37550.23460.3028-0.17760.0111-0.0491-0.26550.0411-0.163611.482629.877730.7015
316.9249-2.2908-8.523112.26957.477218.1589-0.9975-3.0185-1.05791.61230.22680.22811.2010.78030.77070.37790.45190.23680.76430.65330.1148-5.371720.581751.8628
418.19313.2311-6.195715.8413-9.981512.5089-0.1617-1.6843-2.45820.48680.42971.26080.524-0.1522-0.2679-0.10660.03170.0665-0.07160.30640.36332.474514.979335.5922
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 723 - 72
2X-RAY DIFFRACTION2BB2 - 752 - 75
3X-RAY DIFFRACTION3CC3 - 513 - 51
4X-RAY DIFFRACTION4CC53 - 7553 - 75

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