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- PDB-5t5i: TUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE FROM METHANO... -

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Basic information

Entry
Database: PDB / ID: 5t5i
TitleTUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE FROM METHANOTHERMOBACTER WOLFEII, ORTHORHOMBIC FORM AT 1.9 A
Components
  • (Tungsten formylmethanofuran dehydrogenase subunit ...) x 5
  • Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
KeywordsOXIDOREDUCTASE / CO2 fixation / metallohydrolase / formate dehydrogenase / tungstopterin / methanogenesis / green house gas / methanothermobacter wolfeii / iron sulfur cluster / ferredoxin / beta helicoidal / channel / formate / CO2 / methanofuran / formylmethanofuran / nanomachine / binuclear center / tungsten / gate / coupling / enzyme / anaerobic / carboxylysine
Function / homology
Function and homology information


formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase activity / methanogenesis, from carbon dioxide / methanogenesis / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / molybdopterin cofactor binding / transition metal ion binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
FwdD/FmdC, molybdopterin dinucleotide-binding domain / Formylmethanofuran dehydrogenase, subunit D / Formylmethanofuran dehydrogenase, subunit B / Polyferredoxin MvhB-like / Formylmethanofuran dehydrogenase, subunit A / Formylmethanofuran dehydrogenase subunit C / Glutamate synthase, alpha subunit, C-terminal domain superfamily / Amidohydrolase 3 / Amidohydrolase family / 4Fe-4S binding domain ...FwdD/FmdC, molybdopterin dinucleotide-binding domain / Formylmethanofuran dehydrogenase, subunit D / Formylmethanofuran dehydrogenase, subunit B / Polyferredoxin MvhB-like / Formylmethanofuran dehydrogenase, subunit A / Formylmethanofuran dehydrogenase subunit C / Glutamate synthase, alpha subunit, C-terminal domain superfamily / Amidohydrolase 3 / Amidohydrolase family / 4Fe-4S binding domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Metal-dependent hydrolase, composite domain superfamily / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / 4Fe-4S dicluster domain / Metal-dependent hydrolase / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
HYDROSULFURIC ACID / : / Chem-MGD / IRON/SULFUR CLUSTER / : / 4Fe-4S binding protein / Protein fwdD / Tungsten formylmethanofuran dehydrogenase subunit fwdA / Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C / 4Fe-4S binding protein / Tungsten formylmethanofuran dehydrogenase subunit B
Similarity search - Component
Biological speciesMethanothermobacter wolfeii (archaea)
Methanothermobacter sp. CaT2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsWagner, T. / Ermler, U. / Shima, S.
Funding support Germany, Japan, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
PRESTO Japan
CitationJournal: Science / Year: 2016
Title: The methanogenic CO2 reducing-and-fixing enzyme is bifunctional and contains 46 [4Fe-4S] clusters.
Authors: Wagner, T. / Ermler, U. / Shima, S.
History
DepositionAug 31, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tungsten formylmethanofuran dehydrogenase subunit fwdA
B: Tungsten formylmethanofuran dehydrogenase subunit B
C: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
D: Tungsten formylmethanofuran dehydrogenase subunit fwdD
F: Tungsten formylmethanofuran dehydrogenase subunit fwdF
G: Tungsten formylmethanofuran dehydrogenase subunit fwdG
I: Tungsten formylmethanofuran dehydrogenase subunit fwdA
J: Tungsten formylmethanofuran dehydrogenase subunit B
K: Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C
L: Tungsten formylmethanofuran dehydrogenase subunit fwdD
N: Tungsten formylmethanofuran dehydrogenase subunit fwdF
P: Tungsten formylmethanofuran dehydrogenase subunit fwdG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)416,02082
Polymers402,84712
Non-polymers13,17270
Water45,1462506
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area67800 Å2
ΔGint-1012 kcal/mol
Surface area114750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.644, 174.576, 205.425
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Tungsten formylmethanofuran dehydrogenase subunit ... , 5 types, 10 molecules AIBJDLFNGP

#1: Protein Tungsten formylmethanofuran dehydrogenase subunit fwdA


Mass: 62806.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Native formylmethanofuran dehydrogenase subunit A containing the carboxylysine at position 178
Source: (natural) Methanothermobacter wolfeii (archaea) / References: UniProt: O74030*PLUS
#2: Protein Tungsten formylmethanofuran dehydrogenase subunit B


Mass: 48411.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanothermobacter sp. CaT2 (archaea) / References: UniProt: T2GJQ6*PLUS
#4: Protein Tungsten formylmethanofuran dehydrogenase subunit fwdD


Mass: 14408.779 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanothermobacter wolfeii (archaea) / References: UniProt: O74029*PLUS
#5: Protein Tungsten formylmethanofuran dehydrogenase subunit fwdF


Mass: 38618.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanothermobacter wolfeii (archaea) / References: UniProt: O74028*PLUS
#6: Protein Tungsten formylmethanofuran dehydrogenase subunit fwdG


Mass: 8564.948 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanothermobacter wolfeii (archaea) / References: UniProt: Q1MVD4*PLUS

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Protein , 1 types, 2 molecules CK

#3: Protein Tungsten-containing formylmethanofuran dehydrogenase 2 subunit C / Tungsten-containing formylmethanofuran dehydrogenase II subunit C


Mass: 28613.471 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanothermobacter wolfeii (archaea)
References: UniProt: O74031*PLUS, formylmethanofuran dehydrogenase

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Non-polymers , 11 types, 2576 molecules

#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: K
#10: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#11: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#12: Chemical...
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Fe4S4
#13: Chemical ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: W
#14: Chemical
ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#15: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S
#16: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2506 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.65 %
Description: About 500 x 200 um size with a brown color and a brick shape
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tricine/NaOH, pH 8.0, 30% (v/v) pentaerythritol propoxylate 426 (5/4 PO/OH), and 400 mM KCl. The crystallized sample has to be anoxic and extremely fresh (crystallized after 3 days of ...Details: 100 mM Tricine/NaOH, pH 8.0, 30% (v/v) pentaerythritol propoxylate 426 (5/4 PO/OH), and 400 mM KCl. The crystallized sample has to be anoxic and extremely fresh (crystallized after 3 days of purification) without any freezing step. The optimal protein concentration is 30 mg/mL. Drops are made by mixing 1 uL protein and 1 uL precipitant. Crystals appeared usually after 7-10 days.
PH range: 7.5-8.5 / Temp details: Only one temperature has been tested

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.21372 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.21372 Å / Relative weight: 1
ReflectionResolution: 1.9→49.26 Å / Num. obs: 339028 / % possible obs: 99.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 24.97 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Rsym value: 0.054 / Net I/σ(I): 9.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.726 / % possible all: 96.9

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALA3.3.22data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→48.49 Å / Cor.coef. Fo:Fc: 0.9545 / Cor.coef. Fo:Fc free: 0.9474 / SU R Cruickshank DPI: 0.156 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.109 / SU Rfree Blow DPI: 0.098 / SU Rfree Cruickshank DPI: 0.098
Details: The structure was refined by REFMAC after the initial building. For the two last refinement steps, BUSTER was used to improve the stereochemistry of the model.
RfactorNum. reflection% reflectionSelection details
Rfree0.1721 16949 5 %RANDOM
Rwork0.1522 ---
obs0.1532 338906 99.15 %-
Displacement parametersBiso mean: 30.97 Å2
Baniso -1Baniso -2Baniso -3
1--5.6414 Å20 Å20 Å2
2---0.4168 Å20 Å2
3---6.0582 Å2
Refine analyzeLuzzati coordinate error obs: 0.181 Å
Refinement stepCycle: 1 / Resolution: 1.9→48.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55205 0 3163 2506 60874
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0156516HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.22102562HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d12552SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes753HARMONIC2
X-RAY DIFFRACTIONt_gen_planes8198HARMONIC5
X-RAY DIFFRACTIONt_it56482HARMONIC20
X-RAY DIFFRACTIONt_nbd30SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.95
X-RAY DIFFRACTIONt_other_torsion13.97
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3838SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact57784SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2631 1120 4.75 %
Rwork0.2425 22458 -
all0.2435 23578 -
obs--99.15 %
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)
10.4676-0.16320.0190.48210.01830.45990.0025-0.0326-0.11190.01260.01060.01730.13380.0436-0.0132-0.0155-0.0038-0.0183-0.05580.0204-0.052820.7548116.88630.175
20.4534-0.01880.03120.2054-0.00690.28740.01980.00480.0117-0.0113-0.01430.05140.0001-0.0518-0.0055-0.016-0.0109-0.0094-0.02830.0095-0.0308-2.5611141.40519.8482
30.8090.245-0.31850.6668-0.08930.50190.00470.1796-0.0504-0.1365-0.042-0.00010.0737-0.06630.0373-0.00660.025-0.0255-0.0057-0.0076-0.09998.0403131.529-11.2226
40.5121-0.09410.03620.6489-0.30150.74830.03450.09190.0969-0.089-0.02950.09-0.1215-0.1365-0.005-0.01360.0289-0.0197-0.0130.0173-0.0283-13.4987156.1478.8815
50.17990.05710.05270.25380.40330.73520.006-0.06060.051-0.0794-0.00840.0674-0.22740.06790.00230.0297-0.0026-0.0276-0.1232-0.0263-0.027424.3424184.44429.5412
60.9350.24260.33010.69850.31340.6936-0.0033-0.16140.15660.0869-0.07360.12110.0074-0.09830.0769-0.01240.00450.0091-0.0183-0.0443-0.0075-1.1358163.13440.5684
70.31790.0786-0.03160.4641-0.09810.40850.01280.00360.04380.0148-0.0241-0.04-0.11820.03380.01140.00810.00890.0046-0.07820.0129-0.035914.0268232.231-30.0235
80.31980.0131-0.02850.27860.01820.32670.0055-0.0066-0.02790.014-0.02290.0407-0.0248-0.04890.0174-0.01080.01140.0037-0.05430.0015-0.0121-8.8879207.621-19.2914
90.6858-0.21550.12070.6286-0.05950.5607-0.0127-0.09940.03040.1383-0.0117-0.0138-0.10170.00490.02440.0178-0.02580.0028-0.0520.0057-0.07720.6811218.80911.556
100.48530.08820.01770.6202-0.1650.67540.0231-0.0564-0.09630.1038-0.02730.10030.0907-0.09910.0042-0.0087-0.01710.032-0.04890.01060.0066-19.6488192.907-8.2018
110.2212-0.03760.11660.17870.16160.5470.04890.0076-0.00990.0817-0.02780.02050.05480.0482-0.02110.0086-0.020.0084-0.0923-0.0067-0.018121.8307165.277-27.4145
120.4936-0.4126-0.27941.430.36390.8185-0.00050.1066-0.1324-0.1173-0.06490.1274-0.0007-0.07370.0654-0.0150.004-0.0081-0.0473-0.03350.0163-6.3499184.939-39.1973
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ F|* }
6X-RAY DIFFRACTION6{ G|* }
7X-RAY DIFFRACTION7{ I|* }
8X-RAY DIFFRACTION8{ J|* }
9X-RAY DIFFRACTION9{ K|* }
10X-RAY DIFFRACTION10{ L|* }
11X-RAY DIFFRACTION11{ N|* }
12X-RAY DIFFRACTION12{ P|* }

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