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- PDB-4ucw: Structure of the T18V small subunit mutant of D. fructosovorans N... -

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Basic information

Entry
Database: PDB / ID: 4ucw
TitleStructure of the T18V small subunit mutant of D. fructosovorans NiFe- hydrogenase
Components
  • HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
  • NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
KeywordsOXIDOREDUCTASE / NIFE-HYDROGENASE MUTANT / UNREADY STATE
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / cell envelope / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding ...cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / cell envelope / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / periplasmic space / 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 / : / [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. ...Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / : / [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 / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / 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 / IRON/SULFUR CLUSTER / Nickel-dependent hydrogenase large subunit / cytochrome-c3 hydrogenase / Periplasmic [NiFe] hydrogenase small subunit / Periplasmic [NiFe] hydrogenase large subunit
Similarity search - Component
Biological speciesDESULFOVIBRIO FRUCTOSIVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAbou-Hamdan, A. / Ceccaldi, P. / Lebrette, H. / Guttierez-Sanz, O. / Richaud, P. / Cournac, L. / Guigliarelli, B. / deLacey, A.L. / Leger, C. / Volbeda, A. ...Abou-Hamdan, A. / Ceccaldi, P. / Lebrette, H. / Guttierez-Sanz, O. / Richaud, P. / Cournac, L. / Guigliarelli, B. / deLacey, A.L. / Leger, C. / Volbeda, A. / Burlat, B. / Dementin, S.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: A Threonine Stabilizes the Nic and Nir Catalytic Intermediates of [Nife]-Hydrogenase.
Authors: Abou-Hamdan, A. / Ceccaldi, P. / Lebrette, H. / Gutierrez-Sanz, O. / Richaud, P. / Cournac, L. / Guigliarelli, B. / De Lacey, A.L. / Leger, C. / Volbeda, A. / Burlat, B. / Dementin, S.
History
DepositionDec 4, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 2019Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.5Dec 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_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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
Revision 1.6Nov 20, 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 (NIFE) SMALL SUBUNIT HYDA
B: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
C: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
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)272,75329
Polymers268,6386
Non-polymers4,11423
Water10,233568
1
A: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
Q: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,04011
Polymers89,5462
Non-polymers1,4949
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-125.4 kcal/mol
Surface area25390 Å2
MethodPISA
2
C: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
S: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8569
Polymers89,5462
Non-polymers1,3107
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9000 Å2
ΔGint-123.8 kcal/mol
Surface area25000 Å2
MethodPISA
3
B: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
R: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8569
Polymers89,5462
Non-polymers1,3107
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
ΔGint-121.9 kcal/mol
Surface area24870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.200, 99.590, 181.840
Angle α, β, γ (deg.)90.00, 92.47, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.340556, -0.769058, -0.540898), (0.751587, -0.568326, 0.334848), (-0.564924, -0.292498, 0.771561)-0.191, 3.95, 68.218
2given(0.494384, -0.625003, 0.604116), (-0.635423, -0.734093, -0.23947), (0.593146, -0.265479, -0.760065)-36.273, -28.477, 53.939
3given(-0.333731, -0.771781, -0.541274), (0.755175, -0.562557, 0.336512), (-0.564211, -0.296452, 0.770572)-0.242, 3.977, 68.256
4given(0.492842, -0.625397, 0.604968), (-0.635704, -0.733537, -0.240426), (0.594128, -0.266088, -0.759085)-36.244, -28.476, 53.902

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Components

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Protein , 2 types, 6 molecules ABCQRS

#1: Protein HYDROGENASE (NIFE) SMALL SUBUNIT HYDA / NIFE-HYDROGENASE SMALL SUBUNIT


Mass: 28345.338 Da / Num. of mol.: 3 / Fragment: RESIDUES 51-314 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFOVIBRIO FRUCTOSIVORANS (bacteria)
Production host: DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria)
References: UniProt: E1K248, UniProt: P18187*PLUS, cytochrome-c3 hydrogenase
#2: Protein NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT / NIFE-HYDROGENASE LARGE SUBUNIT


Mass: 61200.785 Da / Num. of mol.: 3 / Fragment: RESIDUES 2-549
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFOVIBRIO FRUCTOSIVORANS (bacteria)
Production host: DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria)
References: UniProt: E1K247, UniProt: P18188*PLUS, cytochrome-c3 hydrogenase

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Non-polymers , 7 types, 591 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-F3S / FE3-S4 CLUSTER


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


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


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsT18V MUTANT N-TERMINAL STREP TAG

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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: 2.08 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: VAPOR DIFFUSION, PH 6.0, 293K, PEG 6000, MES, INSIDE A GLOVEBOX

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 92096 / % possible obs: 93.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.5
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.88 / % possible all: 67.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YQW

1yqw


Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.891 / SU B: 17.081 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.609 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23552 4581 5 %RANDOM
Rwork0.19185 ---
obs0.19398 87451 93.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.486 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å20 Å20.91 Å2
2---0.95 Å20 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18409 0 126 568 19103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01919142
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.96725959
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18352412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84624.452775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.239153038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8131572
X-RAY DIFFRACTIONr_chiral_restr0.0980.22837
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02114456
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_it0.6411.0659666
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0091.49412072
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8811.1159476
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: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 264 -
Rwork0.249 4700 -
obs--69.49 %
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)
11.5696-0.3361-0.32560.7338-0.32451.4131-0.00620.1620.32730.06670.0212-0.1442-0.18150.0439-0.0150.0351-0.0188-0.04290.0410.05930.187312.31114.40894.8837
21.075-0.177-0.0410.9277-0.07410.9209-0.05070.0228-0.06020.09950.03890.00030.13210.00560.01190.04320.0036-0.02890.00270.00190.1017.9351-6.747715.0779
30.71940.138-0.66971.2141-0.19631.78060.05050.1825-0.09830.04-0.04920.14080.0455-0.3506-0.00130.07730.0235-0.05450.1408-0.05430.1194-17.83946.580760.6887
41.03250.2368-0.54761.0935-0.23981.5960.2364-0.17950.08470.2659-0.14420.03-0.27770.1486-0.09220.2363-0.0572-0.01240.0756-0.02990.0848-5.872518.836677.4514
52.465-0.8678-0.32321.1798-0.01841.6242-0.402-0.5215-0.92050.30140.26310.55520.4931-0.10430.13880.3140.10770.16980.24740.23360.5563-36.3583-47.875953.8164
62.3829-0.8381-0.71261.43020.22831.8888-0.2757-0.4661-0.0810.13180.261-0.05670.08810.30660.01470.07510.101-0.03430.23510.01460.1186-18.9438-32.197848.9326
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 264
2X-RAY DIFFRACTION1A1265 - 1267
3X-RAY DIFFRACTION2Q6 - 549
4X-RAY DIFFRACTION2Q1550 - 1553
5X-RAY DIFFRACTION3B5 - 264
6X-RAY DIFFRACTION3B1265 - 1267
7X-RAY DIFFRACTION4R5 - 549
8X-RAY DIFFRACTION4R1550 - 1553
9X-RAY DIFFRACTION5C4 - 264
10X-RAY DIFFRACTION5C1265 - 1267
11X-RAY DIFFRACTION6S5 - 549
12X-RAY DIFFRACTION6S1550 - 1553

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