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- PDB-6za1: Structure of [NiFeSe] hydrogenase G491A variant from Desulfovibri... -

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Basic information

Entry
Database: PDB / ID: 6za1
TitleStructure of [NiFeSe] hydrogenase G491A variant from Desulfovibrio vulgaris Hildenborough pressurized with Oxygen gas - structure G491A-O2-hd
Components(Periplasmic [NiFeSe] hydrogenase, ...) x 2
KeywordsOXIDOREDUCTASE / Hydrogenase / Selenium / gas channels / high-pressure derivatization
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / ferredoxin 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
[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 ...[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
Similarity search - Domain/homology
oxygen-damaged SF4 / CARBONMONOXIDE-(DICYANO) IRON / : / HYDROSULFURIC ACID / NICKEL (II) ION / OXYGEN MOLECULE / IRON/SULFUR CLUSTER / Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing / cytochrome-c3 hydrogenase
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsZacarias, S. / Temporao, A. / Carpentier, P. / van der Linden, P. / Pereira, I.A.C. / Matias, P.M.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BBB-BEP/2885/2014 Portugal
Fundacao para a Ciencia e a TecnologiaLISBOA-01-0145-FEDER-007660 Portugal
CitationJournal: J.Biol.Inorg.Chem. / Year: 2020
Title: Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen.
Authors: Zacarias, S. / Temporao, A. / Carpentier, P. / van der Linden, P. / Pereira, I.A.C. / Matias, P.M.
History
DepositionJun 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)85,63617
Polymers83,6272
Non-polymers2,00915
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint-122 kcal/mol
Surface area24260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.156, 63.415, 110.044
Angle α, β, γ (deg.)90.000, 104.785, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

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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
Source: (gene. exp.) Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) (bacteria)
Gene: hysB, DVU_1917
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
References: UniProt: Q72AS4, ferredoxin hydrogenase
#2: Protein Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing


Mass: 53365.086 Da / Num. of mol.: 1 / Mutation: G491A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) (bacteria)
Gene: hysA, DVU_1918
Production host: Desulfovibrio vulgaris str. Hildenborough (bacteria)
References: UniProt: Q72AS3, ferredoxin hydrogenase

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Non-polymers , 9 types, 341 molecules

#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


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


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


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


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.05 Å3/Da / Density % sol: 39.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 20% PEG 1500 (w/v) and 0.1 mM Tris-HCl pH 7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.37→104.4 Å / Num. obs: 115312 / % possible obs: 77.8 % / Redundancy: 2.3 % / Biso Wilson estimate: 20.2 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.042 / Net I/σ(I): 9.8
Reflection shellResolution: 1.37→1.48 Å / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5766 / CC1/2: 0.566 / Rpim(I) all: 0.459

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JSK

5jsk


Resolution: 1.37→50.95 Å / SU ML: 0.1188 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.9533
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.163 5698 4.94 %
Rwork0.1431 109593 -
obs0.1441 115291 77.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.18 Å2
Refinement stepCycle: LAST / Resolution: 1.37→50.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5845 0 61 326 6232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00556147
X-RAY DIFFRACTIONf_angle_d1.26778380
X-RAY DIFFRACTIONf_chiral_restr0.0786911
X-RAY DIFFRACTIONf_plane_restr0.00581086
X-RAY DIFFRACTIONf_dihedral_angle_d15.83672298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.540220.23549X-RAY DIFFRACTION1.04
1.39-1.40.3746100.2514187X-RAY DIFFRACTION4
1.4-1.420.3464290.256535X-RAY DIFFRACTION11.56
1.42-1.440.2461600.2471020X-RAY DIFFRACTION21.58
1.44-1.460.2818620.24881256X-RAY DIFFRACTION27.4
1.46-1.480.2496860.2441668X-RAY DIFFRACTION35.02
1.48-1.50.22381340.2452363X-RAY DIFFRACTION51.47
1.5-1.520.22491590.23253158X-RAY DIFFRACTION67.36
1.52-1.540.25851760.22753732X-RAY DIFFRACTION79.03
1.54-1.570.24482190.21834072X-RAY DIFFRACTION88.2
1.57-1.60.23732510.20824380X-RAY DIFFRACTION93.8
1.6-1.620.21722290.20344555X-RAY DIFFRACTION96.01
1.62-1.660.20912520.18694454X-RAY DIFFRACTION96.36
1.66-1.690.19382440.17294531X-RAY DIFFRACTION96.97
1.69-1.730.18492310.16594563X-RAY DIFFRACTION96.97
1.73-1.770.17522490.15384512X-RAY DIFFRACTION96.2
1.77-1.810.19082350.14314477X-RAY DIFFRACTION95.77
1.81-1.860.172260.1394526X-RAY DIFFRACTION96.74
1.86-1.910.15442260.13494537X-RAY DIFFRACTION97.12
1.91-1.980.14432280.12824603X-RAY DIFFRACTION97.34
1.98-2.050.12372260.1214624X-RAY DIFFRACTION98.04
2.05-2.130.12912580.11594606X-RAY DIFFRACTION98.42
2.13-2.230.13092270.11934594X-RAY DIFFRACTION97.41
2.23-2.340.1422490.11824558X-RAY DIFFRACTION97.47
2.34-2.490.14832400.11694622X-RAY DIFFRACTION98.18
2.49-2.680.12811940.12044717X-RAY DIFFRACTION98.95
2.68-2.950.15292550.12314647X-RAY DIFFRACTION98.41
2.95-3.380.14612320.12824654X-RAY DIFFRACTION98.55
3.38-4.260.15572450.13724692X-RAY DIFFRACTION98.48
4.26-50.950.19022640.1724701X-RAY DIFFRACTION97.14
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)
11.57336571810.0297353041534-0.1454362234841.22333168188-0.1270952015841.2181798082-0.0138373976270.0122158621858-0.0609070265451-0.005422169578780.00497899410584-0.01799087862710.1034094813670.147274801514-0.004630766192820.1496123250030.02528783082860.0006494528832910.153188346057-0.01009372129970.1210361078927.2005885927-29.4389409592139.594321695
22.287180128130.6524385982420.01898166012981.60341254654-0.3934370289311.2619843308-0.03172956111770.160652267218-0.178446974067-0.1878368180010.01035993127-0.09018128605330.2448642502520.1927731397510.01857140870690.2245496775730.05122190859170.006852476427950.189380240834-0.05273311903960.1451005141910.6099880584-33.2746772728127.054225509
34.34684486957-0.437329474959-2.115353792853.58572231691-1.119830153487.157725454090.1359846586030.337560179412-0.353960667407-0.390638005589-0.07259139679040.1034656286970.652445099939-0.125703764884-0.06720749795640.2352632777380.0283557577241-0.006820276928310.148718332858-0.07384270749610.1728976234677.20471192933-39.3749128575127.929700077
46.9662349646-4.855297763710.07352446984496.27048913138-1.07195913561.58203832008-0.0790280864897-0.0428523831643-0.02454447652080.147206241032-0.027074400117-0.4646579753810.1591352437620.1708313899360.09576743992860.1621802719130.02997597192550.00316444583410.204021281165-0.02912309049610.15361018845918.039345634-33.6505908683149.992528592
51.51729820663-1.37245855232-0.3521416204482.0516910636-0.1343379605711.70229887678-0.190443474523-0.279798704794-0.0732026626610.3476201739350.2094621357160.207507491016-0.0664883150262-0.0714225814423-0.01507353690180.1811955600680.02693242117990.03716305737150.2288577301630.004302658154740.160601007049-5.09017095999-21.8385567179161.077165288
60.6072626470090.3406245346440.5553032684381.807665937650.284393744762.00504696841-0.0482522890761-0.117614444883-0.04192046971030.06081834260370.07168069676120.0506102006862-0.0373020026652-0.095552362968-0.01475150587650.1383586260120.02928657405920.02133017948880.179795470259-0.002437537687330.142494232679-3.90586307389-21.3705969338153.766559081
72.07527658222-0.335250228105-0.5200255908281.561795454830.171521375743.493678334990.041336124770.20567144065-0.0576536233527-0.196231534735-0.0492230670009-0.05887686273510.114587978375-0.0644225215929-0.003566634923380.1677573531290.0119774476909-0.006536537554510.148884259921-0.03064332895740.1186242899084.98683024175-23.0879226183112.559785788
80.42668690319-0.0612482060109-0.007166301430190.524033788933-0.01815324113060.727973712356-0.001188925964050.04677431471730.0101198185684-0.06500676350940.008019201290650.0110040138908-0.03569582165130.0276304359629-0.002526901909130.1560769884320.00170652961853-0.004694640165380.154547149107-0.0109900370890.150824442830.359631206346-14.4881312389129.951822656
92.761120044330.337451417242-1.799269285720.661737766005-0.08317031543852.29795704540.0695551169546-0.09851545263560.2389453549730.1115022241080.03303856218260.0632725069141-0.2572830773610.0470177863434-0.08876750319030.1428991589830.0297126467614-0.02797208044470.11764193417-0.01871393057110.1239056186871.2345561148-3.59832801639146.298675525
102.553951038230.208109438425-0.4048826316910.9196137612210.1458212363343.300739796290.02056211389560.05774360255410.133631087728-0.0529678395918-2.0615995469E-5-0.0325613766278-0.281019819474-0.0377923465054-0.05916050717390.1993178822520.0127424330345-0.01352505523630.04131253058520.03870814690740.151281729790.929268633966-1.46656409545123.29981045
111.02342414389-0.0657781758724-0.09478153958313.01085138297-0.53106046450.742023275920.04499981564630.151311975052-0.12894690197-0.2034973125170.03491032512640.276370040120.0625817296334-0.163352775897-0.08933635203760.1655832389220.00244805392815-0.06190428557790.214902958639-0.01594423938510.168773996714-15.0601707012-17.5030693761118.807180381
121.75357028971-0.369469759292-0.8915730514070.717836209124-0.2544299159212.558665214930.03581719473450.1486585094090.215219475346-0.0994013926545-0.0201207004521-0.0538767057565-0.2609850792380.0577167976914-0.04162456678550.212328137838-0.0170130579747-0.0005924242095150.1252341634420.01858019889760.1900309128542.666044878593.68293598791124.098385733
132.656539849180.352880593286-0.3854599760340.5485040557740.07888245706321.92306124821-0.08767466031690.0684665015802-0.036821800616-0.004677896604250.01475241501940.185099250019-0.0728998341179-0.2657362192960.0767569972380.1328563084330.06153753970140.0009039893426590.1253439843080.02536556546520.201352893651-17.1096504948-10.1211535683139.886935039
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and ((resid 5 through 46 ) or (resid 112 through 162 ) or (resid 286 through 287))AA - E5 - 2871
22chain 'A' and (resid 47 through 96 )AA47 - 9646 - 98
33chain 'A' and (resid 97 through 111 )AA97 - 11199 - 116
44chain 'A' and (resid 163 through 192 )AA163 - 192168 - 197
55chain 'A' and (resid 193 through 242 )AA193 - 242198 - 249
66chain 'A' and ((resid 243 through 283 ) or (resid 284 through 285))AA - C243 - 285250
77chain 'B' and (resid 14 through 49 )BF14 - 491 - 41
88chain 'B' and ((resid 50 through 180 ) or (resid 433 through 495 ) or (resid 500 through 504))BF - K50 - 50442
99chain 'B' and (resid 181 through 219 )BF181 - 219177 - 215
1010chain 'B' and (resid 220 through 262 )BF220 - 262216 - 258
1111chain 'B' and (resid 263 through 329 )BF263 - 329259 - 325
1212chain 'B' and (resid 330 through 395 )BF330 - 395326 - 393
1313chain 'B' and (resid 396 through 432 )BF396 - 432394 - 432

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