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- PDB-1u6j: The Structure of native coenzyme F420-dependent methylenetetrahyd... -

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Basic information

Entry
Database: PDB / ID: 1u6j
TitleThe Structure of native coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase at 2.4A resolution
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 / Resolution: 2.4 Å
AuthorsWarkentin, E. / Hagemeier, C.H. / Shima, S. / Thauer, R.K. / Ermler, U.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: The structure of F420-dependent methylenetetrahydromethanopterin dehydrogenase: a crystallographic 'superstructure' of the selenomethionine-labelled protein crystal structure.
Authors: Warkentin, E. / Hagemeier, C.H. / Shima, S. / Thauer, R.K. / Ermler, U.
#1: Journal: 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
DepositionJul 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: F420-dependent methylenetetrahydromethanopterin dehydrogenase
B: F420-dependent methylenetetrahydromethanopterin dehydrogenase
C: F420-dependent methylenetetrahydromethanopterin dehydrogenase
D: F420-dependent methylenetetrahydromethanopterin dehydrogenase
E: F420-dependent methylenetetrahydromethanopterin dehydrogenase
F: F420-dependent methylenetetrahydromethanopterin dehydrogenase
G: F420-dependent methylenetetrahydromethanopterin dehydrogenase
H: F420-dependent methylenetetrahydromethanopterin dehydrogenase
I: F420-dependent methylenetetrahydromethanopterin dehydrogenase
J: F420-dependent methylenetetrahydromethanopterin dehydrogenase
K: F420-dependent methylenetetrahydromethanopterin dehydrogenase
L: F420-dependent methylenetetrahydromethanopterin dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)377,18520
Polymers376,99112
Non-polymers1948
Water10,106561
1
A: F420-dependent methylenetetrahydromethanopterin dehydrogenase
B: F420-dependent methylenetetrahydromethanopterin dehydrogenase
C: F420-dependent methylenetetrahydromethanopterin dehydrogenase
D: F420-dependent methylenetetrahydromethanopterin dehydrogenase
E: F420-dependent methylenetetrahydromethanopterin dehydrogenase
F: F420-dependent methylenetetrahydromethanopterin dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,59310
Polymers188,4956
Non-polymers974
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29550 Å2
ΔGint-190 kcal/mol
Surface area49960 Å2
MethodPISA
2
G: F420-dependent methylenetetrahydromethanopterin dehydrogenase
H: F420-dependent methylenetetrahydromethanopterin dehydrogenase
I: F420-dependent methylenetetrahydromethanopterin dehydrogenase
J: F420-dependent methylenetetrahydromethanopterin dehydrogenase
K: F420-dependent methylenetetrahydromethanopterin dehydrogenase
L: F420-dependent methylenetetrahydromethanopterin dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,59310
Polymers188,4956
Non-polymers974
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29480 Å2
ΔGint-192 kcal/mol
Surface area50030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.900, 118.900, 219.200
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 31415.885 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea) / Gene: mtd / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P94951, EC: 1.5.99.9
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.6 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MOPS, KOH, MPD, PEG 400, Mg acetate, Na phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 19, 2002
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 144106 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.065 / Net I/σ(I): 14.2
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 5.9 / Num. unique all: 22231 / Rsym value: 0.264 / % possible all: 88.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
XDSdata scaling
CNSphasing
RefinementStarting model: Selenomethionine-labelled METHYLENETETRAHYDROMETHANOPTERIN DEHYDROGENASE (MTD), PDB-ID 1QV9

1qv9


Resolution: 2.4→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 9513287.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Description of the kMtd(Se) structure (PDB-ID 1QV9; space group C2221) in C2, a subgroup of C2221.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 7031 4.7 %random with hemihedral twinning
Rwork0.175 ---
obs-143042 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.7 Å2 / ksol: 0.33114 e/Å3
Displacement parametersBiso mean: 43.5 Å2
Baniso -1Baniso -2Baniso -3
1-11.8 Å20 Å20 Å2
2---18.4 Å20 Å2
3---6.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26184 0 8 561 26753
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.25
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.87
Refine LS restraints NCSNCS model details: THE MAIN-CHAIN ATOMS OF THE 2ND HEXAMER WERE STRONGLY TIED TO THE FIRST, THE SIDE-CHAIN ATOMS LESS TIGHT. IN ADDITION THE (PSEUDO) TWO-FOLD ALONG THE A AXIS WAS WEAKLY IMPOSED.
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.276 603 4.5 %
Rwork0.263 12672 -
obs--88.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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