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- PDB-7qz1: Formate dehydrogenase from Starkeya novella -

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Basic information

Entry
Database: PDB / ID: 7qz1
TitleFormate dehydrogenase from Starkeya novella
ComponentsFormate dehydrogenase
KeywordsCYTOSOLIC PROTEIN / apo protein / formate dehydrogenase
Function / homology
Function and homology information


formate catabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / cytoplasm
Similarity search - Function
NAD-dependent formate dehydrogenase / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Formate dehydrogenase
Similarity search - Component
Biological speciesStarkeya novella DSM 506 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPontillo, N. / Slotboom, D.J. / Guskov, A.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)024.003.019 Netherlands
CitationJournal: Febs J. / Year: 2023
Title: Biochemical and structural insight into the chemical resistance and cofactor specificity of the formate dehydrogenase from Starkeya novella.
Authors: Partipilo, M. / Whittaker, J.J. / Pontillo, N. / Coenradij, J. / Herrmann, A. / Guskov, A. / Slotboom, D.J.
History
DepositionJan 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formate dehydrogenase
B: Formate dehydrogenase
C: Formate dehydrogenase
D: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,76128
Polymers185,8984
Non-polymers1,86324
Water9,026501
1
A: Formate dehydrogenase
C: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,15117
Polymers92,9492
Non-polymers1,20215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11150 Å2
ΔGint-71 kcal/mol
Surface area27170 Å2
MethodPISA
2
D: Formate dehydrogenase
hetero molecules

B: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,61011
Polymers92,9492
Non-polymers6609
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_544x,y-1,z-11
Buried area9540 Å2
ΔGint-64 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.255, 59.481, 122.673
Angle α, β, γ (deg.)79.894, 85.405, 63.153
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Formate dehydrogenase / FDH / NAD-dependent formate dehydrogenase


Mass: 46474.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Starkeya novella DSM 506 (bacteria)
Strain: ATCC 8093 / DSM 506 / JCM 20403 / CCM 1077 / IAM 12100 / NBRC 12443 / NCIMB 10456
Gene: Snov_3272 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: D7A8L2, formate dehydrogenase

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Non-polymers , 5 types, 525 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.04 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 5-20% PEG 3350, 0.1 M BIS-TRIS pH 5.8-7.2 / Temp details: 5.8-7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.99 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.1→52.87 Å / Num. obs: 79594 / % possible obs: 91.53 % / Redundancy: 3.8 % / Biso Wilson estimate: 37.96 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.89
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 7804 / CC1/2: 0.595

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NAC
Resolution: 2.1→52.87 Å / SU ML: 0.2572 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.4749
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.224 3958 5.03 %
Rwork0.1756 74661 -
obs0.178 78619 91.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.62 Å2
Refinement stepCycle: LAST / Resolution: 2.1→52.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11622 0 117 501 12240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007312041
X-RAY DIFFRACTIONf_angle_d0.883916364
X-RAY DIFFRACTIONf_chiral_restr0.05251795
X-RAY DIFFRACTIONf_plane_restr0.00852116
X-RAY DIFFRACTIONf_dihedral_angle_d7.72811679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.35611540.30232686X-RAY DIFFRACTION90.79
2.13-2.150.371250.28962636X-RAY DIFFRACTION91.21
2.15-2.180.3071500.27942596X-RAY DIFFRACTION90.96
2.18-2.210.28971440.25712695X-RAY DIFFRACTION90.64
2.21-2.240.28241470.23932580X-RAY DIFFRACTION91.11
2.24-2.280.26651450.23612690X-RAY DIFFRACTION90.78
2.28-2.310.29521720.23282591X-RAY DIFFRACTION90.15
2.31-2.350.28311630.21962594X-RAY DIFFRACTION90.81
2.35-2.390.31071540.22122662X-RAY DIFFRACTION90.58
2.39-2.430.28591530.21412567X-RAY DIFFRACTION90.61
2.43-2.480.31221320.21532730X-RAY DIFFRACTION91.18
2.48-2.530.27211540.21172629X-RAY DIFFRACTION92.34
2.53-2.590.2831480.19832788X-RAY DIFFRACTION92.59
2.59-2.650.24741310.19372619X-RAY DIFFRACTION93.13
2.65-2.710.25191210.18922783X-RAY DIFFRACTION92.78
2.71-2.790.25011040.17612702X-RAY DIFFRACTION92.94
2.79-2.870.2281290.16982740X-RAY DIFFRACTION92.85
2.87-2.960.23931210.17652742X-RAY DIFFRACTION92.62
2.96-3.070.23061270.17562653X-RAY DIFFRACTION91.9
3.07-3.190.24211540.16752642X-RAY DIFFRACTION91.46
3.19-3.330.22921640.16272646X-RAY DIFFRACTION91
3.33-3.510.1971210.15982667X-RAY DIFFRACTION90.52
3.51-3.730.2061190.15342639X-RAY DIFFRACTION89.98
3.73-4.020.20261250.15362615X-RAY DIFFRACTION89.95
4.02-4.420.17681510.13992626X-RAY DIFFRACTION89.73
4.42-5.060.18341770.14222648X-RAY DIFFRACTION92.53
5.06-6.370.19981420.18262776X-RAY DIFFRACTION95.48
6.37-52.870.17921310.15472719X-RAY DIFFRACTION92.59
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.227342494610.412383178026-0.6721057478611.887564096680.0607791454642.87754632269-0.02338574789730.1849064530180.0762809159944-0.2903188218580.1045016468820.104658719219-0.168834550264-0.18240536459-0.0545330257660.2459999091390.0587754052133-0.01124346120160.2093968831210.02340801451940.241060927629-2.455873462611.6480495605-11.3336190895
21.515388420480.2960471037840.4551481751861.589901243310.6530772907752.80912718634-0.0368493081872-0.09436240475440.1546480697430.05312498820360.033643916622-0.176737852315-0.3239759360420.03042713739710.02673079164010.2966594350440.0427007382019-0.02547201754380.2659036030190.0244432600040.3463616789051.4119194179516.56733744682.44823173005
30.4576963187440.233383069696-0.3851703917921.687540189360.1904675477552.2885723647-0.02266027189250.0214846464312-0.109541964519-0.1487285674240.0203196228352-0.001254237547110.1592734008390.0638892937778-0.008858144114630.2223425410420.0195600420951-0.02166516288390.2238830849570.001067284811280.2142945952281.60269115641-14.222200445-14.0252505826
45.85222362397-2.91363697243-3.375445141135.8514278334.346704649849.89771464751-0.39467423469-0.15099732537-0.1885522350910.2223869035460.2633062495120.7093409805230.453063641623-0.379366175180.1180126264490.302801670967-0.06301209440970.04199057081020.3134847666450.0692131409480.425555407952-14.7467817564-16.12601708150.74535760226
53.055572854681.371188240350.6155770911121.752624795840.1144386492062.92088370206-0.0373193528975-0.422530242094-0.07630987515430.3573731679430.03632646352180.09477319019260.3241575684440.02668449918170.0527772972080.4092982527660.0548007603773-0.002172901561520.2932946425490.02272336159980.3314068515320.149974836242-17.71631935234.08349259618
60.44322051825-0.432596498616-0.3499775376252.816828716090.5753663191071.45821483744-0.0395564241527-0.1518467923120.1186510676770.1159753934330.0576626310014-0.2265761520550.03400694130670.0216632164833-0.01235755970120.1969499074230.0124179577393-0.02215458152460.264308605636-0.008035828403790.2301598307093.084614218840.105662675702-1.52766716672
71.279066622090.009431008601040.08796364202131.68640014931-0.06494705795322.89463115349-0.06358440253820.0803334920988-0.222297216550.0828859289510.0614858615531-0.3816951700990.02215370052110.745907849977-0.02483793142290.2338471178080.0414581613618-0.006153417369260.494346143328-0.0545244545660.37475205556337.12085375348.5035159048328.8115491278
81.775839961830.48366114109-1.478933199984.371409314881.490732513383.430813854760.07463141102990.713258733527-0.229128150944-0.556565397373-0.0601887114647-0.2153830014630.1288877561630.307332906063-0.03367483601030.3139475493730.02229736544920.03209884456270.559717240401-0.07554163193830.34188314946532.71807525353.6561223917212.3281304835
91.098326630610.4068186531051.357837024351.247787953870.4943160919981.780252365520.1446202036020.143924798293-0.164105079087-0.114015272709-0.1936188661380.2472872682710.0963192438533-0.1216271077510.04849248488360.3333127939620.0498939234038-0.001457764101790.432325924034-0.1049410050430.40395294771922.437866393-0.76606615963119.3812451081
100.680168897304-0.01412831712830.1228800719182.687959524180.9905440750030.9689181220120.0210901324461-0.049930049037-0.0149887527521-0.03906072658-0.06602503614350.168314242226-0.0724635304842-0.0163465745460.05114924087510.270722562901-0.0298227364915-0.006596165319390.334226293307-0.01132724569550.27171797723817.737360555922.23877392844.5036695274
112.777993255810.408531790349-0.4546407813576.359548891030.1837403018990.356656004661-0.000384874335873-0.100850874809-0.2975771143050.1543565741590.1700682473940.3889191360.05786645375910.0451920455837-0.1173430613010.302895109537-0.04820777309370.0434646813890.4182418858240.04087857238720.34814498038811.02305075542.2329574325749.7587487566
122.063597976530.4612015713860.1340509531821.77829911069-0.1632617572712.516668967940.0966702906038-0.0286563997187-0.03633877751280.049964152113-0.07771987809580.5583546687150.303348176097-0.335078593462-0.01901868561360.263900081838-0.0639508932620.02806541828340.35842759081-0.02962754017240.3933920419935.0071828382711.318360396438.5084745133
130.817458484768-0.347402096241-0.02530091034882.463581132690.9311619996951.469878388930.007120207060740.08337580021250.0106152410429-0.202045863014-0.007920315722450.113566024166-0.05132469697080.086755202367-0.006447610095510.232795282142-0.0225061024205-0.01370355196450.3565680227230.009873086210440.24939415597818.682317827115.846460852229.4017293764
147.13151865843-3.496892716550.5999515647487.487300845071.502339107919.077458492930.1700350909920.155864903065-0.6524516496650.376114577261-0.0107279444847-0.322865811461.620550922930.0520570084174-0.1630638397150.5700873277490.0455348208877-0.07873413440610.361108972794-0.04776419037520.39427465631627.6019531536-10.371104585127.7473526293
151.745565565920.262754047380.5705079251521.458917899250.5956159292272.65934178901-0.02190352186390.132873277283-0.373766896309-0.01338756799090.116246641841-0.08567513545320.8180855698220.137905132715-0.08294961629030.5582014183140.0160020879760.01322383014990.286625737643-0.006006153982470.3351312470574.74415943924-35.7417760762-31.942441288
160.8315861427570.255832778126-0.1624266613232.311519158520.3590533214981.55549222708-0.130905462970.2889581379860.00784929168468-0.6172541415280.1333594936670.1383170473250.0925890679623-0.180001513426-0.0111786796890.395758686061-0.0574992316531-0.01058175666510.2889279581290.02392287730590.222633174951-2.97030153512-11.8537693597-28.2925173271
171.842793102090.2256164889391.794764717162.72630282960.3791599694153.27263913133-0.143166243785-0.1470411005660.1862368052710.0976964336885-0.1365864419220.542609923663-0.0557457052475-0.5823843619360.2432699459970.2732861669830.03087515260760.06417312460990.478728883442-0.1029504695630.437707678057-27.8061647431-37.7262002832-63.4492834954
181.987024967260.13073206614-0.1854471568451.898583894670.1726379232022.8409458033-0.0108382857701-0.2020540868240.5829352571330.293279909859-0.09403382115460.418497130975-0.449905874091-0.3674918675080.1032015906990.4300276105390.111062541069-0.05796440396720.486806582835-0.1417968362110.473151600235-27.9268613302-26.0180498237-57.4872563005
192.259135909951.551091172940.8723878846951.40612584996-0.212025000952.16287881882-0.179252196335-0.2454267899550.345159127844-0.0872018515149-0.08408527737270.203891009127-0.50414842023-0.1554750147940.2618081035420.4949467135410.0100618388657-0.02071672361980.439916882158-0.1083882646170.377050800845-15.1476594161-27.4141490055-52.0809869681
200.983619447598-0.1704310873790.8239828008781.309240571631.164351402311.99504255617-0.030214958830.07935178507030.005022959385810.03316203686010.00610320217215-0.118621646262-0.137208873350.2686594147810.008273399598360.260049455527-0.07252820472720.004627696002320.317954895090.004824415884170.259795703641-9.46260824051-50.7952268345-77.4683577695
213.798129325470.205290750024-0.09727116027683.85106425806-1.375726040964.362279353-0.00201804246772-0.468341905133-0.05912230780760.629493500255-0.0491582966272-0.466664745129-0.03058398870930.7356312908150.03416155181560.4573420117160.0121639470082-0.09214043673490.446175471257-0.005368247269940.3472495225551.1653094872-54.852828822-61.3946093347
221.4356580048-0.617029159831-0.2132895609731.712656090420.4653661424361.982713032050.0345993673692-0.158378330080.3051687911080.04687037809540.0469720850277-0.347753938958-0.3978689415750.649550382647-0.09156764212610.374231821167-0.1507483946120.01070099002230.513224245613-0.04383475694110.352329565299-1.1193523711-38.147098382-72.7742429052
231.61631820748-0.316864090632-0.504807225431.755757338040.5729056140552.52133916405-0.153128702672-0.5743581272410.07291388887590.525125270095-0.3316798284190.4840380771170.148909237904-0.5953475601810.4809873881010.460703408875-0.0568264478470.07761867518270.521588108193-0.1011373951290.426156680359-24.7703044492-36.7193362571-49.5522005294
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 38 )AA2 - 381 - 37
22chain 'A' and (resid 39 through 148 )AA39 - 14838 - 147
33chain 'A' and (resid 149 through 215 )AA149 - 215148 - 214
44chain 'A' and (resid 216 through 235 )AA216 - 235215 - 234
55chain 'A' and (resid 236 through 283 )AA236 - 283235 - 282
66chain 'A' and (resid 284 through 373 )AA284 - 373283 - 372
77chain 'B' and (resid 2 through 61 )BD2 - 611 - 60
88chain 'B' and (resid 62 through 97 )BD62 - 9761 - 96
99chain 'B' and (resid 98 through 148 )BD98 - 14897 - 147
1010chain 'B' and (resid 149 through 215 )BD149 - 215148 - 214
1111chain 'B' and (resid 216 through 234 )BD216 - 234215 - 233
1212chain 'B' and (resid 235 through 291 )BD235 - 291234 - 290
1313chain 'B' and (resid 292 through 358 )BD292 - 358291 - 357
1414chain 'B' and (resid 359 through 376 )BD359 - 376358 - 375
1515chain 'C' and (resid 2 through 148 )CF2 - 1481 - 147
1616chain 'C' and (resid 149 through 371 )CF149 - 371148 - 370
1717chain 'D' and (resid 2 through 38 )DI2 - 381 - 37
1818chain 'D' and (resid 39 through 97 )DI39 - 9738 - 96
1919chain 'D' and (resid 98 through 148 )DI98 - 14897 - 147
2020chain 'D' and (resid 149 through 215 )DI149 - 215148 - 214
2121chain 'D' and (resid 216 through 255 )DI216 - 255215 - 254
2222chain 'D' and (resid 256 through 339 )DI256 - 339255 - 338
2323chain 'D' and (resid 340 through 372 )DI340 - 372339 - 371

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