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- PDB-6vw8: Formate Dehydrogenase FdsABG subcomplex FdsBG from C. necator -

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Basic information

Entry
Database: PDB / ID: 6vw8
TitleFormate Dehydrogenase FdsABG subcomplex FdsBG from C. necator
Components(NAD-dependent formate dehydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / Rossmann fold / thioredoxin-like
Function / homology
Function and homology information


formate dehydrogenase / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region ...Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / Thioredoxin-like superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / : / IRON/SULFUR CLUSTER / NAD-dependent formate dehydrogenase beta subunit / NAD-dependent formate dehydrogenase gamma subunit
Similarity search - Component
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsYoung, T.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0010666 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Crystallographic and kinetic analyses of the FdsBG subcomplex of the cytosolic formate dehydrogenase FdsABG fromCupriavidus necator.
Authors: Young, T. / Niks, D. / Hakopian, S. / Tam, T.K. / Yu, X. / Hille, R. / Blaha, G.M.
History
DepositionFeb 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent formate dehydrogenase gamma subunit
B: NAD-dependent formate dehydrogenase beta subunit
C: NAD-dependent formate dehydrogenase gamma subunit
D: NAD-dependent formate dehydrogenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,56014
Polymers157,3224
Non-polymers2,23810
Water8,953497
1
A: NAD-dependent formate dehydrogenase gamma subunit
B: NAD-dependent formate dehydrogenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8768
Polymers78,6612
Non-polymers1,2156
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-78 kcal/mol
Surface area23910 Å2
MethodPISA
2
C: NAD-dependent formate dehydrogenase gamma subunit
D: NAD-dependent formate dehydrogenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6846
Polymers78,6612
Non-polymers1,0234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-63 kcal/mol
Surface area24010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.656, 127.050, 99.840
Angle α, β, γ (deg.)90.000, 123.500, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 52 through 54 or (resid 55...
21(chain C and (resid 52 through 54 or (resid 55...
12(chain B and (resid 4 through 38 or (resid 39...
22(chain D and (resid 4 through 38 or (resid 39...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 52 through 54 or (resid 55...A52 - 54
121(chain A and (resid 52 through 54 or (resid 55...A55
131(chain A and (resid 52 through 54 or (resid 55...A51 - 201
141(chain A and (resid 52 through 54 or (resid 55...A51 - 201
151(chain A and (resid 52 through 54 or (resid 55...A51 - 201
161(chain A and (resid 52 through 54 or (resid 55...A51 - 201
211(chain C and (resid 52 through 54 or (resid 55...C52 - 54
221(chain C and (resid 52 through 54 or (resid 55...C55
231(chain C and (resid 52 through 54 or (resid 55...C51 - 202
241(chain C and (resid 52 through 54 or (resid 55...C51 - 202
251(chain C and (resid 52 through 54 or (resid 55...C51 - 202
261(chain C and (resid 52 through 54 or (resid 55...C51 - 202
112(chain B and (resid 4 through 38 or (resid 39...B4 - 38
122(chain B and (resid 4 through 38 or (resid 39...B39
132(chain B and (resid 4 through 38 or (resid 39...B2 - 514
142(chain B and (resid 4 through 38 or (resid 39...B2 - 514
152(chain B and (resid 4 through 38 or (resid 39...B2 - 514
212(chain D and (resid 4 through 38 or (resid 39...D4 - 38
222(chain D and (resid 4 through 38 or (resid 39...D39
232(chain D and (resid 4 through 38 or (resid 39...D1 - 514

NCS ensembles :
ID
1
2

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Components

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NAD-dependent formate dehydrogenase ... , 2 types, 4 molecules ACBD

#1: Protein NAD-dependent formate dehydrogenase gamma subunit


Mass: 23368.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (bacteria) / Gene: fdsG, H16_A0640 / Plasmid: pTrc12HLB-FdsGBCD / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q0KDY3, formate dehydrogenase
#2: Protein NAD-dependent formate dehydrogenase beta subunit


Mass: 55292.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (bacteria) / Gene: fdsB, H16_A0641 / Plasmid: pTrc12HLB-FdsGBCD / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q0KDY2, formate dehydrogenase

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Non-polymers , 6 types, 507 molecules

#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2-propanol, ammonium sulfate, HEPES-NaOH, in an anaerobic chamber

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11931N
21931N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.110.9791
SYNCHROTRONAPS 24-ID-C21.7388
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELNov 6, 2018
ADSC QUANTUM 3152CCDJul 3, 2019
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
21.73881
ReflectionResolution: 2.3→48.534 Å / Num. obs: 61209 / % possible obs: 99.9 % / Redundancy: 6.1 % / CC1/2: 0.985 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.056 / Rrim(I) all: 0.141 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.365.20.4622342744970.9150.2230.5143.399.5
10.29-48.5360.06642257100.9940.0290.07217.799

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
HKL-3000data reduction
XDSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→48.534 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.31
RfactorNum. reflection% reflection
Rfree0.2231 1996 3.27 %
Rwork0.1817 --
obs0.183 61091 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.62 Å2 / Biso mean: 32.8316 Å2 / Biso min: 13.29 Å2
Refinement stepCycle: final / Resolution: 2.3→48.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9913 0 98 497 10508
Biso mean--28.69 34.31 -
Num. residues----1330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910205
X-RAY DIFFRACTIONf_angle_d1.05613866
X-RAY DIFFRACTIONf_dihedral_angle_d19.5813658
X-RAY DIFFRACTIONf_chiral_restr0.0581549
X-RAY DIFFRACTIONf_plane_restr0.0081828
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1196X-RAY DIFFRACTION6.214TORSIONAL
12C1196X-RAY DIFFRACTION6.214TORSIONAL
21B4550X-RAY DIFFRACTION6.214TORSIONAL
22D4550X-RAY DIFFRACTION6.214TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.35750.25941440.20124199100
2.3575-2.42130.25941440.19714186100
2.4213-2.49250.23661340.20274234100
2.4925-2.5730.2641460.19424210100
2.573-2.66490.25351390.19524199100
2.6649-2.77160.26691400.19414257100
2.7716-2.89770.22071480.18894190100
2.8977-3.05050.23491420.19424211100
3.0505-3.24160.27251410.19634212100
3.2416-3.49180.21831410.18744222100
3.4918-3.8430.21981440.17314210100
3.843-4.39880.18981460.1588421799
4.3988-5.54080.17791410.16354246100
5.5408-48.5340.21341460.17724302100
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)
11.28480.8149-0.52942.5819-0.8791.37310.0436-0.3332-0.08050.3273-0.1421-0.2892-0.08780.47930.08840.22930.03580.01790.39790.03530.176635.7809-28.609610.4574
20.8453-0.0869-0.30440.5253-0.02060.96580.107-0.05260.052-0.1525-0.0637-0.0822-0.06560.183-0.0370.2401-0.0030.0730.13930.0160.184427.5568-19.2093-8.6542
30.92280.5605-0.36691.8246-1.19021.9230.04740.00160.0406-0.163-0.0423-0.4003-0.05240.2125-0.00840.2652-0.03530.1170.2119-0.05760.276318.497321.756841.2844
40.62180.0404-0.35770.46560.20491.0927-0.01720.17190.01160.0609-0.05060.06560.1213-0.31580.0620.2428-0.09020.08430.268-0.05630.2258-2.82613.501541.256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA51 - 201
2X-RAY DIFFRACTION2chain BB2 - 514
3X-RAY DIFFRACTION3chain CC51 - 202
4X-RAY DIFFRACTION4chain DD1 - 514

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