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Entry
Database: PDB / ID: 1u6k
TitleTLS refinement of the structure of Se-methionine labelled Coenzyme f420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) from Methanopyrus kandleri
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: 1.55 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: Derived calculations / Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7377
Polymers96,6393
Non-polymers974
Water10,449580
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 area29870 Å2
ΔGint-214 kcal/mol
Surface area51280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)120.100, 151.200, 110.000
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 / 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.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: ESRF / Beamline: ID14-4 / Wavelength: 0.9792, 0.9797, 0.95
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 11, 2002
RadiationMonochromator: diamond / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97971
30.951
ReflectionResolution: 1.54→20 Å / 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: 1.54→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

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.372 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.071
RfactorNum. reflection% reflectionSelection details
Rfree0.19546 7207 5 %RANDOM
Rwork0.17829 ---
all-135825 --
obs-135825 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.914 Å2
Baniso -1Baniso -2Baniso -3
1-2.48 Å20 Å20 Å2
2---1.72 Å20 Å2
3----0.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6546 0 4 580 7130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226759
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.9939112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.0985843
X-RAY DIFFRACTIONr_chiral_restr0.1330.21032
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025044
X-RAY DIFFRACTIONr_nbd_refined0.2360.23397
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2504
X-RAY DIFFRACTIONr_metal_ion_refined0.070.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.2295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.263
X-RAY DIFFRACTIONr_mcbond_it0.5881.54262
X-RAY DIFFRACTIONr_mcangle_it1.14826890
X-RAY DIFFRACTIONr_scbond_it2.35232497
X-RAY DIFFRACTIONr_scangle_it3.7334.52222
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 526 -
Rwork0.222 10052 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 55.7813 Å / Origin y: 43.7867 Å / Origin z: 32.3101 Å
111213212223313233
T0.0023 Å20.0022 Å20.0137 Å2-0.1224 Å20.0088 Å2--0.0818 Å2
L0.196 °20.0531 °20.0142 °2-1.2359 °20.1035 °2--0.5923 °2
S-0.0095 Å °-0.0224 Å °-0.0656 Å °0.1053 Å °0.0089 Å °0.0964 Å °0.0626 Å °-0.0641 Å °0.0007 Å °

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