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- PDB-4r0v: [FeFe]-hydrogenase Oxygen Inactivation is Initiated by the Modifi... -

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Basic information

Entry
Database: PDB / ID: 4r0v
Title[FeFe]-hydrogenase Oxygen Inactivation is Initiated by the Modification and Degradation of the H cluster 2Fe Subcluster
ComponentsFe-hydrogenase
KeywordsOXIDOREDUCTASE / HydA1 monomer / FES cluster / H-cluster / [FeFe]-hydrogenase / cys oxidation / S-hydroxycysteine / cysteine-S-dioxide / [2Fe2S] cluster
Function / homology
Function and homology information


1.18.99.1 / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
Rossmann fold - #1780 / Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 / Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 / Iron hydrogenase, small subunit / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain / Rossmann fold ...Rossmann fold - #1780 / Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 / Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 / Iron hydrogenase, small subunit / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ARSENIC / IRON/SULFUR CLUSTER / Fe-hydrogenase
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsSwanson, S.D. / Ratzloff, M.W. / Mulder, D.W. / Artz, J.H. / Ghose, S. / Hoffman, A. / White, S. / Zadvornyy, O.A. / Broderick, J.B. / Bothner, B. ...Swanson, S.D. / Ratzloff, M.W. / Mulder, D.W. / Artz, J.H. / Ghose, S. / Hoffman, A. / White, S. / Zadvornyy, O.A. / Broderick, J.B. / Bothner, B. / King, P.W. / Peters, J.W.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: [FeFe]-Hydrogenase Oxygen Inactivation Is Initiated at the H Cluster 2Fe Subcluster.
Authors: Swanson, K.D. / Ratzloff, M.W. / Mulder, D.W. / Artz, J.H. / Ghose, S. / Hoffman, A. / White, S. / Zadvornyy, O.A. / Broderick, J.B. / Bothner, B. / King, P.W. / Peters, J.W.
History
DepositionAug 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fe-hydrogenase
B: Fe-hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,56310
Polymers110,5682
Non-polymers9958
Water5,278293
1
A: Fe-hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7825
Polymers55,2841
Non-polymers4974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fe-hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7825
Polymers55,2841
Non-polymers4974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.645, 70.964, 94.686
Angle α, β, γ (deg.)90.00, 91.91, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-1, -0.000251, -0.000368), (-0.000251, 1, -0.00024), (0.000368, -0.00024, -1)37.24433, -5.0E-5, 47.31355

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Components

#1: Protein Fe-hydrogenase / Iron hydrogenase / Iron-hydrogenase HydA1


Mass: 55284.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLREDRAFT_183963, hyd1, hydA, hydA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FYU1, 1.18.99.1
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ARS / ARSENIC / Arsenic


Mass: 74.922 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: As
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 298 K / Method: small tubes / pH: 6.5
Details: 25.5% Polyethylene Glycol 8,000, 0.085 M Sodium Cacodylate, 0.17 M Sodium Acetate Trihydrate, 1mM Sodium Dithionite, pH 6.5, SMALL TUBES, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.7345 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2013
RadiationMonochromator: Liquid nitrogen-cooled crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7345 Å / Relative weight: 1
ReflectionResolution: 2.29→94.633 Å / Num. all: 46625 / Num. obs: 41114 / % possible obs: 88.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3
Reflection shellResolution: 2.29→2.41 Å / % possible all: 12

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.8.0073refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3lx4

3lx4


Resolution: 2.29→35 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.953 / SU B: 13.664 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.371 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25211 2097 5.1 %RANDOM
Rwork0.2065 ---
obs0.20882 39011 88.17 %-
all-46625 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.48 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å2-0.01 Å2
2---1.65 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.29→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6282 0 22 293 6597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196539
X-RAY DIFFRACTIONr_bond_other_d0.0010.026271
X-RAY DIFFRACTIONr_angle_refined_deg2.0931.9888874
X-RAY DIFFRACTIONr_angle_other_deg1.029314518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2985843
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33723.962260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.247151101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2331540
X-RAY DIFFRACTIONr_chiral_restr0.1150.2995
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217319
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021367
X-RAY DIFFRACTIONr_mcbond_it3.0233.3263360
X-RAY DIFFRACTIONr_mcbond_other3.0243.3263359
X-RAY DIFFRACTIONr_mcangle_it4.4914.9734195
X-RAY DIFFRACTIONr_mcangle_other4.4914.9734196
X-RAY DIFFRACTIONr_scbond_it3.9233.7173179
X-RAY DIFFRACTIONr_scbond_other3.9243.7173180
X-RAY DIFFRACTIONr_scangle_other5.5475.4124651
X-RAY DIFFRACTIONr_long_range_B_refined8.40115.027182
X-RAY DIFFRACTIONr_long_range_B_other8.34314.9367108
LS refinement shellResolution: 2.29→2.348 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 122 -
Rwork0.344 2375 -
obs--73.03 %
Refinement TLS params.

T11: 0.0142 Å2 / 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 °)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2102-0.3207-0.70531.40430.70043.15320.05470.0978-0.0085-0.09130.0158-0.06890.0739-0.0549-0.07060.0010.00110.05360.0120.009729.344-0.017741.8176
21.21270.32-0.68881.3944-0.68553.15470.0545-0.0963-0.01130.08750.01770.06980.07640.0548-0.0723-0.00040.0010.0529-0.01050.00957.9154-0.00985.4609
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A65 - 490
2X-RAY DIFFRACTION1A601 - 602
3X-RAY DIFFRACTION2B65 - 490
4X-RAY DIFFRACTION2B601 - 602

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