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- PDB-1qv9: Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrog... -

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Basic information

Entry
Database: PDB / ID: 1qv9
TitleCoenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd) from Methanopyrus kandleri: A methanogenic enzyme with an unusual quarternary structure
ComponentsF420-dependent methylenetetrahydromethanopterin dehydrogenase
KeywordsOXIDOREDUCTASE / monomer: alpha/beta domain / helix bundle / trimer of dimers
Function / homology
Function and homology information


methylenetetrahydromethanopterin dehydrogenase / methylenetetrahydromethanopterin dehydrogenase activity / methanogenesis, from carbon dioxide / ferredoxin hydrogenase activity / one-carbon metabolic process
Similarity search - Function
F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) / Helix Hairpins - #120 / F420-dependent methylenetetrahydromethanopterin dehydrogenase / F420-dependent methylenetetrahydromethanopterin dehydrogenase superfamily / methylene-5,6,7,8-tetrahydromethanopterin dehydrogenase / Helix Hairpins / Helix non-globular / Special / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
F420-dependent methylenetetrahydromethanopterin dehydrogenase
Similarity search - Component
Biological speciesMethanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.54 Å
AuthorsHagemeier, C.H. / Shima, S. / Thauer, R.K. / Bourenkov, G. / Bartunik, H.D. / Ermler, U.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd) from Methanopyrus kandleri: a methanogenic enzyme with an unusual quarternary structure
Authors: Hagemeier, C.H. / Shima, S. / Thauer, R.K. / Bourenkov, G. / Bartunik, H.D. / Ermler, U.
History
DepositionAug 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F420-dependent methylenetetrahydromethanopterin dehydrogenase
B: F420-dependent methylenetetrahydromethanopterin dehydrogenase
C: F420-dependent methylenetetrahydromethanopterin dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7377
Polymers96,6393
Non-polymers974
Water10,467581
1
A: F420-dependent methylenetetrahydromethanopterin dehydrogenase
B: F420-dependent methylenetetrahydromethanopterin dehydrogenase
C: F420-dependent methylenetetrahydromethanopterin dehydrogenase
hetero molecules

A: F420-dependent methylenetetrahydromethanopterin dehydrogenase
B: F420-dependent methylenetetrahydromethanopterin dehydrogenase
C: F420-dependent methylenetetrahydromethanopterin dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,47314
Polymers193,2796
Non-polymers1948
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area29880 Å2
ΔGint-214 kcal/mol
Surface area51230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)120.1, 151.2, 110.0
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-4581-

HOH

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Components

#1: Protein F420-dependent methylenetetrahydromethanopterin dehydrogenase / MTD / Coenzyme F420 dependent N5 / N10- methylenetetrahydromethanopterin dehydrogenase


Mass: 32213.100 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea) / Gene: MTD OR MK0011 / Production host: Escherichia coli (E. coli) / References: UniProt: P94951, EC: 1.5.99.9
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Mops/KOH, MPD, Mg acetate, Na phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
210 mMMOPS-KCH1droppH7.0
313 %(v/v)MPD1reservoir
40.1 Msodium phosphate1reservoirpH8.0
50.2 Mmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 11, 2002
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.54→20 Å / Num. all: 145808 / Num. obs: 145808 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 17.7
Reflection shellResolution: 1.55→1.62 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 3.9 / Num. unique all: 15700 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 1.6 Å

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.54→19.92 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 5165889.15 / Data cutoff high rms absF: 5165889.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 7349 5 %RANDOM
Rwork0.201 ---
obs0.201 145808 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.0075 Å2 / ksol: 0.406286 e/Å3
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1-9.78 Å20 Å20 Å2
2---6.59 Å20 Å2
3----3.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.54→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6546 0 4 581 7131
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.14
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.54→1.64 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.314 1218 5 %
Rwork0.293 23061 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.14

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