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- PDB-4c3o: Structure and function of an oxygen tolerant NiFe hydrogenase fro... -

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Basic information

Entry
Database: PDB / ID: 4c3o
TitleStructure and function of an oxygen tolerant NiFe hydrogenase from Salmonella
Components(HYDROGENASE-1 ...) x 2
KeywordsOXIDOREDUCTASE / HYDROGEN METABOLISM / NIFE HYDROGENASE
Function / homology
Function and homology information


hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space ...hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / membrane / metal ion binding / plasma membrane
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 ...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
FE3-S4 CLUSTER / FE4-S3 CLUSTER / Chem-NFU / IRON/SULFUR CLUSTER / hydrogenase (acceptor) / Uptake hydrogenase large subunit
Similarity search - Component
Biological speciesSALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM STR. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBowman, L. / Flanagan, L. / Fyfe, P.K. / Parkin, A. / Hunter, W.N. / Sargent, F.
Citation
Journal: Biochem.J. / Year: 2014
Title: How the Structure of the Large Subunit Controls Function in an Oxygen-Tolerant [Nife]-Hydrogenase.
Authors: Bowman, L. / Flanagan, L. / Fyfe, P.K. / Parkin, A. / Hunter, W.N. / Sargent, F.
#1: Journal: FEBS Lett. / Year: 2012
Title: How Salmonella Oxidises H(2) Under Aerobic Conditions.
Authors: Parkin, A. / Bowman, L. / Roessler, M.M. / Davies, R.A. / Palmer, T. / Armstrong, F.A. / Sargent, F.
History
DepositionAug 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Source and taxonomy
Revision 2.0Jun 27, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _struct_site.details / _struct_site.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYDROGENASE-1 LARGE SUBUNIT
B: HYDROGENASE-1 SMALL SUBUNIT
C: HYDROGENASE-1 LARGE SUBUNIT
D: HYDROGENASE-1 SMALL SUBUNIT
E: HYDROGENASE-1 LARGE SUBUNIT
F: HYDROGENASE-1 SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,38029
Polymers288,4156
Non-polymers3,96623
Water2,054114
1
E: HYDROGENASE-1 LARGE SUBUNIT
F: HYDROGENASE-1 SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,49210
Polymers96,1382
Non-polymers1,3548
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-98.7 kcal/mol
Surface area25700 Å2
MethodPISA
2
A: HYDROGENASE-1 LARGE SUBUNIT
B: HYDROGENASE-1 SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,56312
Polymers96,1382
Non-polymers1,42510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9430 Å2
ΔGint-115.5 kcal/mol
Surface area25740 Å2
MethodPISA
3
C: HYDROGENASE-1 LARGE SUBUNIT
D: HYDROGENASE-1 SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3257
Polymers96,1382
Non-polymers1,1875
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-90.4 kcal/mol
Surface area25730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.460, 122.210, 227.820
Angle α, β, γ (deg.)90.00, 95.56, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13B
23D
14B
24F
15C
25E
16D
26F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRHISHISAA3 - 5853 - 585
21TYRTYRHISHISCC3 - 5853 - 585
12TYRTYRHISHISAA3 - 5853 - 585
22TYRTYRHISHISEE3 - 5853 - 585
13PROPROSERSERBB5 - 2655 - 265
23PROPROSERSERDD5 - 2655 - 265
14PROPROSERSERBB5 - 2655 - 265
24PROPROSERSERFF5 - 2655 - 265
15TYRTYRHISHISCC3 - 5853 - 585
25TYRTYRHISHISEE3 - 5853 - 585
16PROPROSERSERDD5 - 2655 - 265
26PROPROSERSERFF5 - 2655 - 265

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(-0.9936, 0.0585, -0.09689), (0.05635, -0.4867, -0.8718), (-0.09815, -0.8716, 0.4803)-23.96, 260.1, 151.7
2given(0.9977, 0.05598, 0.03892), (-0.06199, 0.5071, 0.8597), (0.02839, -0.8601, 0.5094)-8.12, -307.2, 146.1
3given(-0.9975, 0.05736, -0.04014), (0.06371, 0.5061, -0.8601), (-0.02902, -0.8606, -0.5085)-47.19, 281.9, 490.3
4given(-0.9938, 0.05559, -0.09581), (0.05659, -0.4887, -0.8706), (-0.09522, -0.8707, 0.4826)-24.23, 259.9, 151.1
5given(0.9975, 0.05962, 0.03825), (-0.06312, 0.5029, 0.862), (0.03216, -0.8623, 0.5054)-7.889, -307.9, 147.7
6given(-0.998, 0.05131, -0.03735), (0.05829, 0.5083, -0.8592), (-0.0251, -0.8597, -0.5103)-48.04, 281.4, 491.1

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Components

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HYDROGENASE-1 ... , 2 types, 6 molecules ACEBDF

#1: Protein HYDROGENASE-1 LARGE SUBUNIT / OXYGEN TOLERANT NIFE HYDROGENASE


Mass: 65148.836 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-585
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM STR. LT2 (bacteria)
Variant: LT2A
Production host: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
References: UniProt: Q8ZPH0, ferredoxin hydrogenase
#2: Protein HYDROGENASE-1 SMALL SUBUNIT / OXYGEN TOLERANT NIFE HYDROGENASE


Mass: 30989.432 Da / Num. of mol.: 3 / Fragment: RESIDUES 46-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM STR. LT2 (bacteria)
Variant: LT2A
Production host: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
References: UniProt: Q8ZPG9, ferredoxin hydrogenase

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Non-polymers , 8 types, 137 molecules

#3: Chemical ChemComp-NFU / formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) / NI-FE REDUCED ACTIVE CENTER


Mass: 195.591 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3HFeN2NiO
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#7: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe3S4
#8: Chemical ChemComp-F4S / FE4-S3 CLUSTER / T-CLUSTER


Mass: 319.575 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S3
#9: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence details15 RESIDUES FROM C-TERMINUS OF LARGE SUBUNIT PROTEOLYTICALLY PROCESSED 54 RESIDUES FROM C-TERMINUS ...15 RESIDUES FROM C-TERMINUS OF LARGE SUBUNIT PROTEOLYTICALLY PROCESSED 54 RESIDUES FROM C-TERMINUS OF SMALL SUBUNIT REMOVED IN TRUNCATED CONSTRUCT AND C-TERMINAL HEXA-HIS TAG ADDED. 45 RESIDUES FROM N-TERMINUS PROTEOLYTICALLY PROCESSED.

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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: 3.98 Å3/Da / Density % sol: 69.13 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.2→29.5 Å / Num. obs: 51795 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 83.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.7
Reflection shellResolution: 3.2→3.38 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.8 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RGW

3rgw


Resolution: 3.2→29.52 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 43.429 / SU ML: 0.328 / Cross valid method: THROUGHOUT / ESU R Free: 0.427 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.20467 2639 5.1 %RANDOM
Rwork0.15811 ---
obs0.1605 49122 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.343 Å2
Baniso -1Baniso -2Baniso -3
1-3.09 Å20 Å2-2.73 Å2
2---1.99 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 3.2→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19828 0 109 114 20051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01920576
X-RAY DIFFRACTIONr_bond_other_d0.0050.0219122
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.95928121
X-RAY DIFFRACTIONr_angle_other_deg1.3313.00243956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63452531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91423.73917
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.558153228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.16515123
X-RAY DIFFRACTIONr_chiral_restr0.0830.23007
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02123260
X-RAY DIFFRACTIONr_gen_planes_other0.0040.024791
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3485.3810142
X-RAY DIFFRACTIONr_mcbond_other3.3475.3810141
X-RAY DIFFRACTIONr_mcangle_it5.2688.07212667
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7235.64210433
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A361660.08
12C361660.08
21A362040.08
22E362040.08
31B157860.02
32D157860.02
41B157320.03
42F157320.03
51C364080.08
52E364080.08
61D157860.03
62F157860.03
LS refinement shellResolution: 3.203→3.285 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 190 -
Rwork0.27 3512 -
obs--97.37 %
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)
11.00380.09020.25581.34920.28612.2145-0.03640.1141-0.0586-0.29290.2727-0.5282-0.10360.7072-0.23630.3065-0.07940.16820.2528-0.14670.22522.1037.806282.692
21.49870.3282-0.13931.92770.41612.1970.1441-0.38520.1138-0.04860.0725-0.1787-0.07280.2302-0.21660.1784-0.03840.02280.152-0.0790.0585-10.52412.771302.498
31.99390.1575-0.34991.32870.46331.37750.09860.2574-0.0406-0.2768-0.22480.3937-0.1285-0.59940.12610.16130.0835-0.09450.2837-0.07810.1287-53.02910.149280.284
41.2829-0.1698-0.11871.29860.51851.49070.1197-0.0073-0.408-0.0326-0.1630.20330.4552-0.26110.04330.314-0.1636-0.03930.1426-0.05030.182-42.146-10.255286.926
51.6802-0.0212-0.07321.13880.12522.4713-0.1124-0.17160.1133-0.01180.1947-0.3014-0.83941.0483-0.08220.4579-0.3860.03190.5109-0.09750.0949-5.85942.88340.515
61.74050.10130.21291.01050.36893.5348-0.0323-0.4084-0.31930.15610.0829-0.0284-0.31590.599-0.05060.1817-0.00520.00370.28320.05870.0619-17.7927.41354.491
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 585
2X-RAY DIFFRACTION2B4 - 266
3X-RAY DIFFRACTION3C3 - 585
4X-RAY DIFFRACTION4D5 - 266
5X-RAY DIFFRACTION5E3 - 585
6X-RAY DIFFRACTION6F5 - 267

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