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- PDB-4kn9: High-resolution structure of H2-activated anaerobically purified ... -

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Basic information

Entry
Database: PDB / ID: 4kn9
TitleHigh-resolution structure of H2-activated 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/PRODUCTION / NIFESE-SITE
Function / homology
Function and homology information


hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity ...hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / membrane / 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 ...: / 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: 1.4 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 9, 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 1.3Apr 9, 2014Group: Other
Revision 1.4Aug 6, 2014Group: Other
Revision 1.5Sep 20, 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_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

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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)175,58328
Polymers172,3324
Non-polymers3,25224
Water31,9771775
1
S: Periplasmic [NiFeSe] hydrogenase small subunit
L: Nickel-dependent hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,78914
Polymers86,1662
Non-polymers1,62312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8900 Å2
ΔGint-149 kcal/mol
Surface area24850 Å2
MethodPISA
2
T: Periplasmic [NiFeSe] hydrogenase small subunit
M: Nickel-dependent hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,79414
Polymers86,1662
Non-polymers1,62812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-144 kcal/mol
Surface area24530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.260, 108.730, 136.500
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: 55291.844 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, 1799 molecules

#3: Chemical
ChemComp-SF4 / 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.: 7 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


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


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


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


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


Mass: 18.015 Da / Num. of mol.: 1775 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHERE IS A SELENOCYSTEINE AT POSITIONS L 492 AND M 492. TWO MINOR CONFORMATIONS OF THE NIFESE SITE ...THERE IS A SELENOCYSTEINE AT POSITIONS L 492 AND M 492. TWO MINOR CONFORMATIONS OF THE NIFESE SITE CALLED D AND Q ARE ONLY PARTIALLY RESOLVED.

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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: 46.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 4000, 0.2M CaCl2, 0.1M Tris/HCl, 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: ID23-1 / Wavelength: 0.9465 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2011
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9465 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 309048 / Num. obs: 282740 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 21 Å2 / Rsym value: 0.072 / Net I/σ(I): 8.3
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 0.87 / Num. unique all: 28469 / Rsym value: 0.994 / % possible all: 60.5

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4KL8

4kl8


Resolution: 1.4→25 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.215 / SU ML: 0.037 / Isotropic thermal model: anisotropic temperature factors / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.059 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.16804 14302 5.1 %RANDOM
Rwork0.12698 ---
obs0.12906 268420 91.49 %-
all-309018 --
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: 18.912 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å20 Å2
2---0.75 Å20 Å2
3---0.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.057 Å0.059 Å
Refinement stepCycle: LAST / Resolution: 1.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11915 0 98 1775 13788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02212731
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.97717285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57851568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28424.429569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.504152163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5711565
X-RAY DIFFRACTIONr_chiral_restr0.0920.21911
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219591
X-RAY DIFFRACTIONr_mcbond_it2.3331.57769
X-RAY DIFFRACTIONr_mcangle_it3.3512.512631
X-RAY DIFFRACTIONr_scbond_it4.734962
X-RAY DIFFRACTIONr_scangle_it6.50354568
X-RAY DIFFRACTIONr_rigid_bond_restr2.471312731
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 669 -
Rwork0.32 11866 -
obs-12445 55.24 %

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