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- PDB-4upe: Structure of the unready Ni-A state of the S499C mutant of D. fru... -

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Entry
Database: PDB / ID: 4upe
TitleStructure of the unready Ni-A state of the S499C mutant of D. fructosovorans NiFe-hydrogenase
Components
  • NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
  • NIFE-HYDROGENASE SMALL SUBUNIT
KeywordsOXIDOREDUCTASE / NIFE-SITE / NI-A STATE / SULFENATE
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / 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
FE3-S4 CLUSTER / CARBONMONOXIDE-(DICYANO) IRON / NICKEL (II) ION / PHOSPHATE ION / IRON/SULFUR CLUSTER / Periplasmic [NiFe] hydrogenase small subunit / Periplasmic [NiFe] hydrogenase large subunit
Similarity search - Component
Biological speciesDESULFOVIBRIO FRUCTOSOVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVolbeda, A. / Martin, L. / Barbier, E. / Gutierrez-Sanz, O. / DeLacey, A.L. / Liebgott, P.P. / Dementin, S. / Rousset, M. / Fontecilla-Camps, J.C.
Citation
Journal: J. Biol. Inorg. Chem. / Year: 2015
Title: Crystallographic studies of [NiFe]-hydrogenase mutants: towards consensus structures for the elusive unready oxidized states.
Authors: Volbeda, A. / Martin, L. / Barbier, E. / Gutierrez-Sanz, O. / De Lacey, A.L. / Liebgott, P.P. / Dementin, S. / Rousset, M. / Fontecilla-Camps, J.C.
#1: Journal: J.Biol.Inorg.Chem. / Year: 2005
Title: Structural Differences between the Ready and Unready Oxidized States of [Nife] Hydrogenases.
Authors: Volbeda, A. / Martin, L. / Cavazza, C. / Matho, M. / Faber, B.W. / Roseboom, W. / Albracht, S.P.J. / Garcin, E. / Rousset, M. / Fontecilla-Camps, J.C.
History
DepositionJun 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 2.0Jan 30, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Experimental preparation
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / exptl_crystal_grow / pdbx_struct_conn_angle / struct_conn
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] / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.ptnr2_label_atom_id
Revision 2.1Feb 27, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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
A: NIFE-HYDROGENASE SMALL SUBUNIT
B: NIFE-HYDROGENASE SMALL SUBUNIT
C: NIFE-HYDROGENASE SMALL SUBUNIT
Q: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
R: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
S: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,86233
Polymers264,2756
Non-polymers4,58727
Water36,6432034
1
A: NIFE-HYDROGENASE SMALL SUBUNIT
Q: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,60411
Polymers88,0922
Non-polymers1,5139
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-132.7 kcal/mol
Surface area25280 Å2
MethodPISA
2
B: NIFE-HYDROGENASE SMALL SUBUNIT
R: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,64512
Polymers88,0922
Non-polymers1,55310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9380 Å2
ΔGint-138.4 kcal/mol
Surface area25310 Å2
MethodPISA
3
C: NIFE-HYDROGENASE SMALL SUBUNIT
S: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,61310
Polymers88,0922
Non-polymers1,5218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9100 Å2
ΔGint-119.2 kcal/mol
Surface area25340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.430, 98.960, 184.950
Angle α, β, γ (deg.)90.00, 91.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 6 molecules ABCQRS

#1: Protein NIFE-HYDROGENASE SMALL SUBUNIT


Mass: 28418.389 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 53-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFOVIBRIO FRUCTOSOVORANS (bacteria)
Production host: DESULFOVIBRIO FRUCTOSOVORANS (bacteria) / References: UniProt: P18187, cytochrome-c3 hydrogenase
#2: Protein NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT / / NIFE-HYDROGENASE LARGE SUBUNIT


Mass: 59673.195 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 5-549 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFOVIBRIO FRUCTOSOVORANS (bacteria)
Production host: DESULFOVIBRIO FRUCTOSOVORANS (bacteria) / References: UniProt: P18188, cytochrome-c3 hydrogenase

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Non-polymers , 9 types, 2061 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-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3FeN2O
#6: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#10: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2034 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE: S499C MUTATION IN LARGE SUBUNIT ACTIVE SITE DETAILS: IN THE UNREADY NI-A STATE NI(III) IS ...SEQUENCE: S499C MUTATION IN LARGE SUBUNIT ACTIVE SITE DETAILS: IN THE UNREADY NI-A STATE NI(III) IS BOUND TO CYS72-SG, CSX75-OD (SULFENATE), CYS543-SG, O2001 AND CYS546-SG IN A DISTORTED SQUARE PYRAMIDAL COORDINATION (CHAINS Q, R AND S). THIS STATE IS ISOSTRUCTURAL WITH THE UNREADY DIAMAGNETIC NI-SU STATE (WITH NI(II)) THIS STATE IS SENSITIVE TO PHOTOREDUCTION (INDUCED BY X-RAYS)

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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: 2.22 Å3/Da / Density % sol: 44.6 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.2
Details: VAPOR DIFFUSION, UNDER AIR, 298 K, PEG 6000, MES, TRIS/HCL, PH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 9, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→29.83 Å / Num. obs: 209473 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 4.21 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 6.14
Reflection shellResolution: 1.8→1.92 Å / Redundancy: 3.11 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 1.74 / % possible all: 82.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YQW

1yqw


Resolution: 1.8→29.83 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.639 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.18977 10529 5 %RANDOM
Rwork0.1509 ---
obs0.15284 198944 96.13 %-
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: 19.994 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å20 Å2-0.16 Å2
2---0.47 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18424 0 149 2034 20607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01919389
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.98426365
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9652482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00924.505788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.039153126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3981573
X-RAY DIFFRACTIONr_chiral_restr0.0980.22880
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02114663
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.2041.0719747
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7511.59812195
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0181.2189642
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
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 621 -
Rwork0.26 11509 -
obs--75.86 %
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)
10.1946-0.0077-0.03150.3189-0.07770.6945-0.0177-0.01020.00120.04220.0067-0.0130.04390.02290.01110.0290.01410.00070.00790.00490.05549.6630.27911.617
20.3419-0.1069-0.10730.4240.06920.6262-0.0429-0.0154-0.03730.03890.01460.04440.0699-0.01540.02830.01530.00930.01530.03040.00310.0763-25.273-36.950.523
30.36870.096-0.11470.4668-0.06830.75310.0768-0.07140.02710.0278-0.07030.0416-0.03520.0101-0.00650.03440.00450.00470.0427-0.01420.0518-8.17814.39872.886
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 264
2X-RAY DIFFRACTION1A1265 - 1267
3X-RAY DIFFRACTION1A2001 - 2223
4X-RAY DIFFRACTION1Q5 - 549
5X-RAY DIFFRACTION1Q1550 - 1552
6X-RAY DIFFRACTION1Q1561 - 1564
7X-RAY DIFFRACTION1Q2001 - 2396
8X-RAY DIFFRACTION2B3 - 264
9X-RAY DIFFRACTION2B1265 - 1267
10X-RAY DIFFRACTION2B2001 - 2153
11X-RAY DIFFRACTION2R6 - 549
12X-RAY DIFFRACTION2R1550 - 1552
13X-RAY DIFFRACTION2R1561 - 1564
14X-RAY DIFFRACTION2R2001 - 2365
15X-RAY DIFFRACTION3C4 - 264
16X-RAY DIFFRACTION3C1265 - 1267
17X-RAY DIFFRACTION3C2001 - 2189
18X-RAY DIFFRACTION3S6 - 549
19X-RAY DIFFRACTION3S1550 - 1552
20X-RAY DIFFRACTION3S1561 - 1562
21X-RAY DIFFRACTION3S2001 - 2306

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