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- PDB-3vyt: Crystal structure of the HypC-HypD-HypE complex (form I inward) -

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Basic information

Entry
Database: PDB / ID: 3vyt
TitleCrystal structure of the HypC-HypD-HypE complex (form I inward)
Components(Hydrogenase expression/formation protein ...) x 3
KeywordsMETAL BINDING PROTEIN/TRANSFERASE / [NiFe] hydrogenase maturation / METAL BINDING PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


carbon dioxide binding / carbon monoxide binding / protein maturation / 4 iron, 4 sulfur cluster binding / iron ion binding / ATP binding / metal 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 / Carbamoyl dehydratase HypE / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / Arc Repressor Mutant, subunit A / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / SH3 type barrels. - #140 / 60s Ribosomal Protein L30; Chain: A; / Helix non-globular / Special / SH3 type barrels. / Roll / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Hydrogenase expression/formation protein HypC / hydrogenase expression/formation protein HypD / Hydrogenase expression/formation protein HypE
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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
C: Hydrogenase expression/formation protein HypE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,52210
Polymers86,0143
Non-polymers5097
Water2,756153
1
A: Hydrogenase expression/formation protein HypC
B: Hydrogenase expression/formation protein HypD
C: Hydrogenase expression/formation protein HypE
hetero molecules

A: Hydrogenase expression/formation protein HypC
B: Hydrogenase expression/formation protein HypD
C: Hydrogenase expression/formation protein HypE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,04420
Polymers172,0276
Non-polymers1,01714
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area17400 Å2
ΔGint-272 kcal/mol
Surface area50890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.333, 99.412, 103.923
Angle α, β, γ (deg.)90.00, 97.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Hydrogenase expression/formation protein ... , 3 types, 3 molecules ABC

#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: Protein Hydrogenase expression/formation protein HypE


Mass: 35954.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: TK1993 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JII7

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Non-polymers , 4 types, 160 molecules

#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 50mM MES, 12-16% PEG400, 10mM magnesium chloride, pH 6.4, 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: RAYONIX MX225HE / Detector: CCD / Date: Jun 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 34520 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 50.7 Å2 / Rsym value: 0.039 / Net I/σ(I): 23.2
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 2 % / Mean I/σ(I) obs: 22.3 / % possible all: 80.4

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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: 2Z1C, 2Z1D, 2Z1E

2z1c

2z1d

2z1e


Resolution: 2.25→34.79 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3484493.99 / 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
Rfree0.253 1698 4.9 %RANDOM
Rwork0.207 ---
obs0.207 34500 92.1 %-
all-37475 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.2869 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 58.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.14 Å20 Å2-1.23 Å2
2--12.27 Å20 Å2
3----7.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.25→34.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5673 0 14 153 5840
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d5.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.871.5
X-RAY DIFFRACTIONc_mcangle_it5.382
X-RAY DIFFRACTIONc_scbond_it5.692
X-RAY DIFFRACTIONc_scangle_it7.362.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 236 4.6 %
Rwork0.303 4847 -
obs--82.2 %
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

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