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Basic information

Entry
Database: PDB / ID: 4kl8
TitleHigh-resolution structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air
Components
  • Nickel-dependent hydrogenase large subunit
  • Periplasmic [NiFeSe] hydrogenase small subunit
KeywordsOXIDOREDUCTASE / O2-resistance / H2-cleavage and production / SELENINATE
Function / homology
Function and homology information


hydrogenase (acceptor) / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / metal ion binding
Similarity search - Function
Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 2. ...Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Few Secondary Structures / Irregular / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CARBONMONOXIDE-(DICYANO) IRON / HYDROSULFURIC ACID / NICKEL (II) ION / IRON/SULFUR CLUSTER / Nickel-dependent hydrogenase large subunit / Periplasmic [NiFeSe] hydrogenase small subunit
Similarity search - Component
Biological speciesDesulfomicrobium baculatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsVolbeda, A. / Cavazza, C. / Fontecilla-Camps, J.C.
Citation
Journal: Chem.Commun.(Camb.) / Year: 2013
Title: Structural foundations for the O2 resistance of Desulfomicrobium baculatum [NiFeSe]-hydrogenase.
Authors: Volbeda, A. / Amara, P. / Iannello, M. / De Lacey, A.L. / Cavazza, C. / Fontecilla-Camps, J.C.
#1: Journal: Structure / Year: 1999
Title: The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center.
Authors: Garcin, E. / Vernede, X. / Hatchikian, E.C. / Volbeda, A. / Frey, M. / Fontecilla-Camps, J.C.
History
DepositionMay 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Dec 25, 2013Group: Other
Revision 1.4Apr 9, 2014Group: Other
Revision 1.5Aug 6, 2014Group: Other
Revision 1.6Jun 15, 2016Group: Non-polymer description
Revision 2.0May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_distant_solvent_atoms ...entity_poly / pdbx_distant_solvent_atoms / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Oct 26, 2022Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Non-polymer description
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 3.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: Periplasmic [NiFeSe] hydrogenase small subunit
L: Nickel-dependent hydrogenase large subunit
T: Periplasmic [NiFeSe] hydrogenase small subunit
M: Nickel-dependent hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,68829
Polymers172,3964
Non-polymers3,29225
Water33,2201844
1
S: Periplasmic [NiFeSe] hydrogenase small subunit
L: Nickel-dependent hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,82114
Polymers86,1982
Non-polymers1,62312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-148 kcal/mol
Surface area24780 Å2
MethodPISA
2
T: Periplasmic [NiFeSe] hydrogenase small subunit
M: Nickel-dependent hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,86615
Polymers86,1982
Non-polymers1,66813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-157 kcal/mol
Surface area24490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.200, 108.720, 136.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules STLM

#1: Protein Periplasmic [NiFeSe] hydrogenase small subunit / NiFeSe hydrogenlyase small chain


Mass: 30874.131 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Desulfomicrobium baculatum (bacteria) / References: UniProt: P13063, hydrogenase (acceptor)
#2: Protein Nickel-dependent hydrogenase large subunit / / NiFeSe hydrogenlyase large chain


Mass: 55323.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Desulfomicrobium baculatum (bacteria) / Strain: DSM 4028 / VKM B-1378 / References: UniProt: C7LN88, hydrogenase (acceptor)

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Non-polymers , 8 types, 1869 molecules

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


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3FeN2O
#8: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#9: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1844 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUES L 492 AND M 492 HAVE THREE STATES: SE7 = OXIDIZED TO SELENINATE (O=SE-O, CONFORMATION ...RESIDUES L 492 AND M 492 HAVE THREE STATES: SE7 = OXIDIZED TO SELENINATE (O=SE-O, CONFORMATION LABELED O); SEC = NON-OXIDIZED SELENOATE (CONFORMATION R, WITH NI-SE BOND); UOX = SELENENATE (SE-O, CONFORMATION P, WITH NI-SE AND FE-O BOND). CONFORMATION P CONTAINS A PUTATIVE SS-BOND BETWEEN CYS70 AND CYS73.

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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: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 22-27% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, under air, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2010
RadiationMonochromator: two crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.52→30 Å / Num. all: 242003 / Num. obs: 226689 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.057 / Net I/σ(I): 11.3
Reflection shellResolution: 1.52→1.6 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 22885 / Rsym value: 0.375 / % possible all: 66.9

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Processing

Software
NameVersionClassification
Xnemodata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CC1

1cc1


Resolution: 1.52→25 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.629 / SU ML: 0.043 / Isotropic thermal model: anisotropic temperature factors / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17109 11463 5.1 %RANDOM
Rwork0.12179 ---
obs0.12429 215209 93.68 %-
all-241973 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.769 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0 Å20 Å2
2---0.72 Å2-0 Å2
3---0.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.069 Å0.077 Å
Refinement stepCycle: LAST / Resolution: 1.52→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11944 0 99 1844 13887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02212693
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.97717190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66351546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62724.417566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.816152152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5361565
X-RAY DIFFRACTIONr_chiral_restr0.0910.21902
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219517
X-RAY DIFFRACTIONr_mcbond_it2.1281.57736
X-RAY DIFFRACTIONr_mcangle_it3.0242.512563
X-RAY DIFFRACTIONr_scbond_it4.35234957
X-RAY DIFFRACTIONr_scangle_it5.93254549
X-RAY DIFFRACTIONr_rigid_bond_restr2.281312693
LS refinement shellResolution: 1.52→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 525 -
Rwork0.187 10340 -
obs-10758 61.47 %

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