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- PDB-6ru9: THE 3D STRUCTURE OF [NIFESE] HYDROGENASE G491A VARIANT FROM DESUL... -

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Basic information

Entry
Database: PDB / ID: 6ru9
TitleTHE 3D STRUCTURE OF [NIFESE] HYDROGENASE G491A VARIANT FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 1.36 ANGSTROM RESOLUTION
Components(Periplasmic [NiFeSe] hydrogenase, ...) x 2
KeywordsOXIDOREDUCTASE / NIFESE-SITE / H2 CLEAVAGE/PRODUCTION / O2 TOLERANCE
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / cell envelope / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding ...cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / cell envelope / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / metal ion binding / membrane
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 / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Cytochrome-c3 Hydrogenase; chain B ...: / 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 / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / : / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / 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
oxygen-damaged SF4 / CARBONMONOXIDE-(DICYANO) IRON / : / HYDROSULFURIC ACID / NICKEL (II) ION / IRON/SULFUR CLUSTER / Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing / cytochrome-c3 hydrogenase
Similarity search - Component
Biological speciesDesulfovibrio vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.355 Å
AuthorsMatias, P.M. / Zacarias, S. / Pereita, I.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BBB-BEP/2885/2014 Portugal
Fundacao para a Ciencia e a TecnologiaSFRH/BD/100314/2014 Portugal
CitationJournal: Acs Catalysis / Year: 2019
Title: A Hydrophilic Channel Is Involved in Oxidative Inactivation of a [NiFeSe] Hydrogenase
Authors: Zacarias, S. / Temporao, A. / del Barrio, M. / Fourmond, V. / Leger, C. / Matias, P.M. / Pereira, I.A.C.
History
DepositionMay 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
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.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic [NiFeSe] hydrogenase, small subunit
B: Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,51812
Polymers84,6692
Non-polymers1,84910
Water15,043835
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-125 kcal/mol
Surface area24110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.445, 98.664, 63.885
Angle α, β, γ (deg.)90.000, 105.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Periplasmic [NiFeSe] hydrogenase, ... , 2 types, 2 molecules AB

#1: Protein Periplasmic [NiFeSe] hydrogenase, small subunit


Mass: 30261.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Small subunit
Source: (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria)
Gene: hysB, DVU_1917 / Variant: Desulfovibrio vulgaris str. Hildenborough
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
References: UniProt: Q72AS4, ferredoxin hydrogenase
#2: Protein Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing


Mass: 54407.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria)
Gene: hysA, DVU_1918 / Variant: Desulfovibrio vulgaris str. Hildenborough
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
References: UniProt: Q72AS3, ferredoxin hydrogenase

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Non-polymers , 8 types, 845 molecules

#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-6ML / oxygen-damaged SF4


Mass: 383.639 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4O2S4
#5: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3FeN2O
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#8: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 835 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.32 % / Description: plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 1500 (w/v) and 0.1 mM Tris-HCl,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.355→61.6 Å / Num. obs: 112189 / % possible obs: 71.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 17.6 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.9
Reflection shellResolution: 1.355→1.51 Å / Num. unique obs: 5610 / CC1/2: 0.613

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å38.66 Å
Translation2.8 Å38.66 Å

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Processing

Software
NameVersionClassification
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JSH

5jsh


Resolution: 1.355→49.332 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0.78 / Phase error: 19.02
Details: REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.355 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.332 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.78 REMARK 3 ...Details: REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.355 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.332 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.78 REMARK 3 COMPLETENESS FOR RANGE (%) : 67.51 REMARK 3 NUMBER OF REFLECTIONS : 208549 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 112183
RfactorNum. reflection% reflection
Rfree0.1628 10214 4.9 %
Rwork0.1441 --
obs0.145 112183 67.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.42 Å2 / Biso mean: 21.6249 Å2 / Biso min: 9.12 Å2
Refinement stepCycle: final / Resolution: 1.355→49.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5824 0 73 835 6732
Biso mean--17 32.58 -
Num. residues----759
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3555-1.37090.321790.27242202292
1.3709-1.3870.2968310.28742452763
1.387-1.40390.3378210.25723453664
1.4039-1.42170.3077240.27484634875
1.4217-1.44040.2998530.29957558088
1.4404-1.46020.3576770.28791287136413
1.4602-1.4810.31031340.29462102223622
1.481-1.50310.27931600.27293072323231
1.5031-1.52660.28142410.27134311455244
1.5266-1.55170.29052820.26136013629561
1.5517-1.57840.30373780.25627321769976
1.5784-1.60710.27244620.25028310877284
1.6071-1.6380.2764460.24258770921689
1.638-1.67150.25894490.2248592904188
1.6715-1.70780.24064150.21998991940692
1.7078-1.74750.21644850.20229336982195
1.7475-1.79120.20964850.18269239972495
1.7912-1.83970.18374700.17159398986895
1.8397-1.89380.18385220.15829174969695
1.8938-1.95490.16184530.14319205965894
1.9549-2.02480.1554640.13538963942791
2.0248-2.10590.15124380.12659370980895
2.1059-2.20170.14574250.11899345977095
2.2017-2.31780.13025230.11649224974795
2.3178-2.4630.13723820.11649291967394
2.463-2.65320.1425000.12088897939791
2.6532-2.92020.14324910.1249211970294
2.9202-3.34260.1354170.12489156957393
3.3426-4.2110.12674540.11398861931590
4.211-49.36470.14515230.13198868939191
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)
10.5920.14030.05590.5754-0.07650.4883-0.02330.0382-0.0705-0.04570.0038-0.04220.0920.01370.01850.1233-0.00160.01120.1212-0.00690.1337125.4787-37.475379.0395
20.34-0.0747-0.32390.9775-0.39520.92520.00120.1616-0.0223-0.2334-0.01010.00260.1075-0.0260.0090.1755-0.020.00160.1857-0.00180.134117.7755-31.726865.1678
32.9561-1.7463-2.07322.44970.10482.36740.10040.1379-0.2248-0.2258-0.11910.20.1253-0.1038-0.00380.1861-0.0251-0.01510.1794-0.01570.146117.8091-38.711565.6599
41.0332-0.913-1.03421.32971.21382.4491-0.0030.2733-0.0673-0.2935-0.0023-0.34220.11420.3980.01920.23790.01730.08650.3031-0.01850.2302141.363-31.009769.9585
50.5448-0.1140.15150.56780.19641.0329-0.0138-0.02120.00040.14320.0214-0.16790.07060.11830.00040.1338-0.0059-0.03160.14880.01070.1818138.877-30.22498.1541
60.713-0.12780.17830.7430.25040.5483-0.0045-0.03920.01420.02690.0004-0.0679-0.0020.0537-0.00180.114-0.0093-0.00830.11810.00420.1201133.0494-28.587193.8523
71.9846-0.32370.48151.4936-0.35981.6841-0.00070.1552-0.1599-0.2290.00440.16610.057-0.2189-0.01310.1559-0.0114-0.02180.1896-0.00570.1334101.4053-23.582366.9592
80.5031-0.06940.12650.40990.01670.4718-0.02380.03010.0501-0.0373-0.01430.011-0.0566-0.02660.03280.1223-0.0069-0.00190.12020.00110.1241113.1108-18.621481.9001
90.3346-0.06860.12340.4153-0.20780.7309-0.0611-0.03320.14880.0747-0.0144-0.0681-0.14330.04030.07030.1544-0.0218-0.02980.1405-0.0020.181126.6741-9.863993.2123
100.88450.17140.1150.8159-0.18930.6952-0.0165-0.06590.11910.061-0.03670.0292-0.1617-0.05470.05370.18280.0041-0.02160.1378-0.00690.153106.0129-6.125783.3815
110.5014-0.0788-0.10861.09890.2030.7981-0.0207-0.0339-0.05930.1207-0.03120.18270.0487-0.13030.05850.1114-0.02150.01450.1781-0.0120.166896.6421-26.641387.7864
120.3406-0.3058-0.00250.4756-0.28270.4753-0.07920.00410.14790.09020.00340.0271-0.1799-0.03040.07490.20420.0015-0.0310.1349-0.0010.1884106.6338-0.710484.1125
130.6213-0.10140.20560.4634-0.24880.5776-0.0325-0.14470.00510.10350.03160.0149-0.0068-0.0972-0.00760.1503-0.00030.00540.16440.00410.1236113.4534-22.2071102.1504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resid 5 through 46 ) or (resid 112 through 162 ) or (resid 286 through 287))A0
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 96 )A47 - 96
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 111 )A97 - 111
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 192 )A163 - 192
5X-RAY DIFFRACTION5chain 'A' and (resid 193 through 242 )A193 - 242
6X-RAY DIFFRACTION6chain 'A' and ((resid 243 through 283 ) or (resid 284 through 285))A0
7X-RAY DIFFRACTION7chain 'B' and (resid 15 through 49 )B15 - 49
8X-RAY DIFFRACTION8chain 'B' and ((resid 50 through 180 ) or (resid 433 through 495 ) or (resid 500 through 504))B0
9X-RAY DIFFRACTION9chain 'B' and (resid 181 through 219 )B181 - 219
10X-RAY DIFFRACTION10chain 'B' and (resid 220 through 262 )B220 - 262
11X-RAY DIFFRACTION11chain 'B' and (resid 263 through 329 )B263 - 329
12X-RAY DIFFRACTION12chain 'B' and (resid 330 through 395 )B330 - 395
13X-RAY DIFFRACTION13chain 'B' and (resid 396 through 432 )B396 - 432

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