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Basic information

Entry
Database: PDB / ID: 4ko4
TitleHigh X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air
Components
  • Nickel-dependent hydrogenase large subunit
  • Periplasmic [NiFeSe] hydrogenase small subunit
KeywordsOXIDOREDUCTASE / NIFESE-SITE / H2 CLEAVAGE/PRODUCTION / SELENINATE
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: 2 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 11, 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 8, 2016Group: Atomic model
Revision 1.7May 8, 2019Group: Advisory / Data collection
Category: pdbx_distant_solvent_atoms / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Revision 2.0Oct 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 2.1Sep 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)175,62429
Polymers172,3324
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)87,78914
Polymers86,1662
Non-polymers1,62312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8750 Å2
ΔGint-149 kcal/mol
Surface area24790 Å2
MethodPISA
2
T: Periplasmic [NiFeSe] hydrogenase small subunit
M: Nickel-dependent hydrogenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,83415
Polymers86,1662
Non-polymers1,66813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9360 Å2
ΔGint-157 kcal/mol
Surface area24510 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


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, 1.18.99.1

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Non-polymers , 8 types, 1869 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.: 8 / 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.: 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: SEC = NON-OXIDIZED SELENOATE (CONFORMATION R); UOX = ...RESIDUES L 492 AND M 492 HAVE THREE STATES: SEC = NON-OXIDIZED SELENOATE (CONFORMATION R); UOX = SELENENATE (SE-O, CONFORMATION P, WITH NI-SE AND FE-O BOND); SE7 = SELENINATE (O=SE-O, CONFORMATION O, BOTH O'S ARE BOUND TO NI).

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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: 46.25 %
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: BM30A / Wavelength: 1.7394 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7394 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 107173 / Num. obs: 105522 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 18.2 Å2 / Rsym value: 0.087 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.12 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 16976 / Rsym value: 0.26 / % possible all: 91.9

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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 4KL8

4kl8


Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.691 / SU ML: 0.084 / Isotropic thermal model: isotropic temperature factors / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: use of 4 TLS groups (1/subunit)
RfactorNum. reflection% reflectionSelection details
Rfree0.17188 5315 5 %RANDOM
Rwork0.14837 ---
obs0.14955 100181 98.79 %-
all-107143 --
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: 15.008 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2---0.84 Å2-0 Å2
3---0.86 Å2
Refine analyzeLuzzati coordinate error obs: 0.173 Å / Luzzati d res low obs: 0.132 Å
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11944 0 99 1844 13887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02212693
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.97717190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60451546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60424.417566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.749152152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6591565
X-RAY DIFFRACTIONr_chiral_restr0.0860.21902
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219517
X-RAY DIFFRACTIONr_mcbond_it0.8871.57736
X-RAY DIFFRACTIONr_mcangle_it1.5132.512563
X-RAY DIFFRACTIONr_scbond_it2.25534957
X-RAY DIFFRACTIONr_scangle_it3.61754549
LS refinement shellResolution: 2→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 383 -
Rwork0.2 6678 -
obs-7069 90.76 %
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)
10.3263-0.0226-0.060.05640.03360.1144-0.00040.0439-0.0058-0.0064-0.0115-0.02160.0110.00750.01190.0235-0.00040.00510.03990.00050.016932.49911.680.803
20.2844-0.0117-0.05560.1096-0.0230.13140.0094-0.02520.02650.0222-0.00270.0275-0.0086-0.0001-0.00670.0266-0.00170.00810.0269-0.01010.013217.13419.50319.98
30.17180.13570.05580.34390.15870.1351-0.01090.0025-0.0264-0.0122-0.00490.0462-0.0085-0.03440.01570.0292-0.0070.00980.0246-0.00770.03611.465-44.30920.063
40.14430.0854-0.01780.51090.00030.1474-0.0081-0.0016-0.00950.02260.0322-0.1201-0.02760.0067-0.02410.0195-0.0056-0.00010.0119-0.020.050933.349-32.01424.724
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1S5 - 283
2X-RAY DIFFRACTION1S301 - 303
3X-RAY DIFFRACTION2L10 - 498
4X-RAY DIFFRACTION2L501 - 504
5X-RAY DIFFRACTION2L606 - 611
6X-RAY DIFFRACTION3T5 - 283
7X-RAY DIFFRACTION3T301 - 303
8X-RAY DIFFRACTION4M10 - 498
9X-RAY DIFFRACTION4M501 - 504
10X-RAY DIFFRACTION4M623 - 629

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