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- PDB-3vyr: Crystal structure of the HypC-HypD complex -

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Basic information

Entry
Database: PDB / ID: 3vyr
TitleCrystal structure of the HypC-HypD complex
Components
  • Hydrogenase expression/formation protein HypC
  • Hydrogenase expression/formation protein HypD
KeywordsMETAL BINDING PROTEIN / [NiFe] hydrogenase maturation
Function / homology
Function and homology information


carbon dioxide binding / carbon monoxide binding / protein maturation / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
HypD, alpha/beta domain 2 / HypD, alpha/beta domain 1 / Arc Repressor Mutant, subunit A - #100 / Hydrogenase formation HypD protein / HypD, domain 1 / HypD, domain 2 / Hydrogenase formation hypA family / Hydrogenase assembly chaperone, conserved site / Hydrogenases expression/synthesis hupF/hypC family signature. / Hydrogenase expression/formation protein, HupF/HypC ...HypD, alpha/beta domain 2 / HypD, alpha/beta domain 1 / Arc Repressor Mutant, subunit A - #100 / Hydrogenase formation HypD protein / HypD, domain 1 / HypD, domain 2 / Hydrogenase formation hypA family / Hydrogenase assembly chaperone, conserved site / Hydrogenases expression/synthesis hupF/hypC family signature. / Hydrogenase expression/formation protein, HupF/HypC / HupF/HypC family / Arc Repressor Mutant, subunit A / SH3 type barrels. - #140 / Helix non-globular / Special / SH3 type barrels. / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / IRON/SULFUR CLUSTER / Hydrogenase expression/formation protein HypC / hydrogenase expression/formation protein HypD
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsWatanabe, S. / Miki, K.
CitationJournal: Structure / Year: 2012
Title: Crystal structures of the HypCD complex and the HypCDE ternary complex: transient intermediate complexes during [NiFe] hydrogenase maturation
Authors: Watanabe, S. / Matsumi, R. / Atomi, H. / Imanaka, T. / Miki, K.
History
DepositionOct 2, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_id / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,75610
Polymers50,0592
Non-polymers1,6978
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-33 kcal/mol
Surface area18750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.179, 181.179, 49.433
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Hydrogenase expression/formation protein HypC


Mass: 8133.478 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: Tk-hypC / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JII0
#2: Protein Hydrogenase expression/formation protein HypD


Mass: 41925.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: Tk-hypD / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JII1
#3: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 4.68 Å3/Da / Density % sol: 73.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 1.4M (NH4)3 citrate/citric acid(pH 4.5-4.7), 0.7% 2-methyl-2,4-pentandiol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 30506 / Num. obs: 30506 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 45.5 Å2 / Rsym value: 0.077 / Net I/σ(I): 23.1
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.482 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z2C, 2Z1D

2z2c

2z1d


Resolution: 2.55→45.3 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1746755.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1545 5.1 %RANDOM
Rwork0.17 ---
obs0.17 30494 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.7863 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 50 Å2
Baniso -1Baniso -2Baniso -3
1-8.74 Å20 Å20 Å2
2--8.74 Å20 Å2
3----17.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.55→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3430 0 99 138 3667
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d7.07
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.131.5
X-RAY DIFFRACTIONc_mcangle_it7.552
X-RAY DIFFRACTIONc_scbond_it9.962
X-RAY DIFFRACTIONc_scangle_it11.522.5
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 240 4.8 %
Rwork0.256 4773 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4hypd_fs10.paramhypd_fs4.top
X-RAY DIFFRACTION5cit_xplor_par4.paramcit_xplor_top2.top

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