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- PDB-6vw7: Formate Dehydrogenase FdsABG subcomplex FdsBG from C. necator - N... -

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Basic information

Entry
Database: PDB / ID: 6vw7
TitleFormate Dehydrogenase FdsABG subcomplex FdsBG from C. necator - NADH bound
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
NADP-reducing hydrogenase subunit HndA / NADH-ubiquinone oxidoreductase 51kDa subunit / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Ubiquitin-like (UB roll) - #600 / de novo design (two linked rop proteins) / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. ...NADP-reducing hydrogenase subunit HndA / NADH-ubiquinone oxidoreductase 51kDa subunit / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Ubiquitin-like (UB roll) - #600 / de novo design (two linked rop proteins) / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-quinone oxidoreductase subunit E, N-terminal / 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 / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Nuo51 FMN-binding domain / Glutaredoxin / Glutaredoxin / Ubiquitin-like (UB roll) / Thioredoxin-like superfamily / Roll / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / Formate dehydrogenase beta subunit / Formate dehydrogenase subunit gamma
Similarity search - Component
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)151,37912
Polymers148,0804
Non-polymers3,2988
Water12,845713
1
A: NAD-dependent formate dehydrogenase gamma subunit
B: NAD-dependent formate dehydrogenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6896
Polymers74,0402
Non-polymers1,6494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-66 kcal/mol
Surface area23570 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)75,6896
Polymers74,0402
Non-polymers1,6494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-66 kcal/mol
Surface area23640 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-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ILEILEARGARG(chain A and (resid 52 through 54 or (resid 55...AA52 - 5453 - 55
121ALAALAALAALA(chain A and (resid 52 through 54 or (resid 55...AA5556
131ALAALAARGARG(chain A and (resid 52 through 54 or (resid 55...AA11 - 16012 - 161
141ALAALAARGARG(chain A and (resid 52 through 54 or (resid 55...AA11 - 16012 - 161
151ALAALAARGARG(chain A and (resid 52 through 54 or (resid 55...AA11 - 16012 - 161
161ALAALAARGARG(chain A and (resid 52 through 54 or (resid 55...AA11 - 16012 - 161
211ILEILEARGARG(chain C and (resid 52 through 54 or (resid 55...CC52 - 5453 - 55
221ALAALAALAALA(chain C and (resid 52 through 54 or (resid 55...CC5556
231ASPASPSERSER(chain C and (resid 52 through 54 or (resid 55...CC12 - 16213 - 163
241ASPASPSERSER(chain C and (resid 52 through 54 or (resid 55...CC12 - 16213 - 163
251ASPASPSERSER(chain C and (resid 52 through 54 or (resid 55...CC12 - 16213 - 163
261ASPASPSERSER(chain C and (resid 52 through 54 or (resid 55...CC12 - 16213 - 163
112ILEILEVALVAL(chain B and (resid 4 through 38 or (resid 39...BB4 - 384 - 38
122ARGARGARGARG(chain B and (resid 4 through 38 or (resid 39...BB3939
132ILEILEALAALA(chain B and (resid 4 through 38 or (resid 39...BB2 - 5132 - 513
142ILEILEALAALA(chain B and (resid 4 through 38 or (resid 39...BB2 - 5132 - 513
152ILEILEALAALA(chain B and (resid 4 through 38 or (resid 39...BB2 - 5132 - 513
212ILEILEVALVAL(chain D and (resid 4 through 38 or (resid 39...DD4 - 384 - 38
222ARGARGARGARG(chain D and (resid 4 through 38 or (resid 39...DD3939
232METMETSERSER(chain D and (resid 4 through 38 or (resid 39...DD1 - 5141 - 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: 18747.148 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 (E. coli) / 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-FdsBGCD / Production host: Escherichia coli (E. coli) / References: UniProt: Q0KDY2, formate dehydrogenase

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Non-polymers , 5 types, 721 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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#6: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 713 / 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: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 287 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 5.0.211.00001
SYNCHROTRONAPS 24-ID-E21
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELDec 4, 2019
DECTRIS EIGER X 16M2PIXELNov 6, 2019
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.000011
211
ReflectionResolution: 2→48.56 Å / Num. obs: 93063 / % possible obs: 99.9 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.031 / Rrim(I) all: 0.072 / Net I/σ(I): 15.4 / Num. measured all: 475014 / Scaling rejects: 35
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
2-2.035.30.4262434146070.9360.2070.4743.9100
10.95-48.565.10.03930275900.9980.0180.04339.498.8

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
CRANK2phasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→48.534 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1991 2982 3.22 %
Rwork0.1586 89617 -
obs0.1598 92599 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.57 Å2 / Biso mean: 35.4504 Å2 / Biso min: 16.61 Å2
Refinement stepCycle: final / Resolution: 2→48.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9907 0 140 713 10760
Biso mean--44.14 41.64 -
Num. residues----1327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810387
X-RAY DIFFRACTIONf_angle_d0.96814146
X-RAY DIFFRACTIONf_dihedral_angle_d15.6676128
X-RAY DIFFRACTIONf_chiral_restr0.0561577
X-RAY DIFFRACTIONf_plane_restr0.0071862
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1128X-RAY DIFFRACTION6.048TORSIONAL
12C1128X-RAY DIFFRACTION6.048TORSIONAL
21B4466X-RAY DIFFRACTION6.048TORSIONAL
22D4466X-RAY DIFFRACTION6.048TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.03280.24721370.2073410597
2.0328-2.06780.25141520.19744257100
2.0678-2.10540.22371420.18764262100
2.1054-2.14590.21251500.17534257100
2.1459-2.18970.23981490.17354281100
2.1897-2.23740.19651400.16514266100
2.2374-2.28940.20591290.16644247100
2.2894-2.34670.22721540.15634245100
2.3467-2.41010.20231450.16424265100
2.4101-2.4810.18871300.16184277100
2.481-2.56110.20381490.16324260100
2.5611-2.65260.20171480.16194271100
2.6526-2.75880.24741500.174274100
2.7588-2.88440.20951380.17114277100
2.8844-3.03640.21081150.16994284100
3.0364-3.22660.2011420.174273100
3.2266-3.47570.20731490.16464270100
3.4757-3.82530.2071470.14644300100
3.8253-4.37860.15721290.13054314100
4.3786-5.51530.16281390.13974287100
5.5153-48.5340.1911480.15624345100
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)
10.68050.1391-0.30131.1622-0.47311.10360.0432-0.3566-0.1220.2658-0.1493-0.1339-0.00050.37770.05710.26460.0197-0.01120.34370.06140.241635.7192-28.630710.2905
20.9438-0.1044-0.32580.61960.0870.9390.0684-0.00960.0121-0.1394-0.0443-0.1079-0.05760.17980.0530.31350.00410.02320.17280.02180.270227.5499-19.1543-8.7665
30.91370.3829-0.44282.2009-0.63161.39720.13980.03870.1297-0.0553-0.0368-0.469-0.2370.2891-0.05530.3208-0.0520.07410.242-0.04830.349918.448421.276541.5565
40.8777-0.0075-0.68650.54380.3641.98430.03440.23870.05550.0697-0.0190.06590.0657-0.4438-0.03240.2149-0.04720.01480.2471-0.01050.246-2.690213.453341.4722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA11 - 160
2X-RAY DIFFRACTION2chain BB2 - 513
3X-RAY DIFFRACTION3chain CC12 - 162
4X-RAY DIFFRACTION4chain DD1 - 514

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