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- PDB-3iqz: Structure of F420 dependent methylene-tetrahydromethanopterin deh... -

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Basic information

Entry
Database: PDB / ID: 3iqz
TitleStructure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methylene-tetrahydromethanopterin
ComponentsF420-dependent methylenetetrahydromethanopterin dehydrogenase
KeywordsOXIDOREDUCTASE / binary complex of protein and substrate / Methanogenesis / One-carbon metabolism
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
5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN / F420-dependent methylenetetrahydromethanopterin dehydrogenase
Similarity search - Component
Biological speciesMethanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCeh, K.E. / Demmer, U. / Warkentin, E. / Moll, J. / Thauer, R.K. / Shima, S. / Ermler, U.
CitationJournal: Biochemistry / Year: 2009
Title: Structural basis of the hydride transfer mechanism in F(420)-dependent methylenetetrahydromethanopterin dehydrogenase
Authors: Ceh, K. / Demmer, U. / Warkentin, E. / Moll, J. / Thauer, R.K. / Shima, S. / Ermler, U.
History
DepositionAug 21, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,42917
Polymers188,4956
Non-polymers4,93311
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36420 Å2
ΔGint-223 kcal/mol
Surface area49520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.810, 167.700, 95.860
Angle α, β, γ (deg.)90.00, 101.25, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
31C
41D
51F
13D
23A
33C
43E
53F
12B
22E

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRARGARGBB2 - 842 - 84
211THRTHRARGARGAA2 - 842 - 84
311THRTHRARGARGCC2 - 842 - 84
411THRTHRARGARGDD2 - 842 - 84
511THRTHRARGARGFF2 - 842 - 84
121SERSERGLUGLUBB90 - 28390 - 283
221SERSERGLUGLUAA90 - 28390 - 283
321SERSERGLUGLUCC90 - 28390 - 283
421SERSERGLUGLUDD90 - 28390 - 283
521SERSERGLUGLUFF90 - 28390 - 283
112THRTHRPROPROBB2 - 462 - 46
212THRTHRPROPROEE2 - 462 - 46
122ALAALAARGARGBB51 - 8451 - 84
222ALAALAARGARGEE51 - 8451 - 84
132SERSERGLUGLUBB90 - 28390 - 283
232SERSERGLUGLUEE90 - 28390 - 283
113GLUGLUASPASPDD85 - 8985 - 89
213GLUGLUASPASPAA85 - 8985 - 89
313GLUGLUASPASPCC85 - 8985 - 89
413GLUGLUASPASPEE85 - 8985 - 89
513GLUGLUASPASPFF85 - 8985 - 89

NCS ensembles :
ID
1
3
2

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 31415.885 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea) / Gene: mtd / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P94951, EC: 1.5.99.9

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Non-polymers , 5 types, 283 molecules

#2: Chemical
ChemComp-H4M / 5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN


Mass: 788.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H45N6O16P
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG400, 0.1M MES, 0.1M sodium acetate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.008 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 27, 2009
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.1→94 Å / Num. all: 113106 / Num. obs: 109528 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rsym value: 0.048 / Net I/σ(I): 16.1
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 7651 / Rsym value: 0.53 / % possible all: 96.4

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Processing

Software
NameVersionClassification
MAR345data collection
AMoREphasing
REFMAC5.5.0066refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QV9

1qv9


Resolution: 2.1→94 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 14.659 / SU ML: 0.172 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.226 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22647 5502 5 %RANDOM
Rwork0.19841 ---
all0.19981 103990 --
obs0.19981 103990 96.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.288 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å22.2 Å2
2---1.78 Å20 Å2
3---1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.1→94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13092 0 280 272 13644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02213628
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.572.02218454
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46451697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15625.598627
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.134152447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1181584
X-RAY DIFFRACTIONr_chiral_restr0.1040.22075
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110228
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6571.58495
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.202213666
X-RAY DIFFRACTIONr_scbond_it2.27835133
X-RAY DIFFRACTIONr_scangle_it3.7944.54784
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11B2117tight positional0.060.05
12A2117tight positional0.050.05
13C2117tight positional0.060.05
14D2117tight positional0.050.05
15F2117tight positional0.060.05
31D38tight positional0.020.05
32A38tight positional0.030.05
33C38tight positional0.040.05
34E38tight positional0.050.05
35F38tight positional0.050.05
11B2117tight thermal0.270.5
12A2117tight thermal0.180.5
13C2117tight thermal0.230.5
14D2117tight thermal0.170.5
15F2117tight thermal0.230.5
31D38tight thermal0.080.5
32A38tight thermal0.090.5
33C38tight thermal0.140.5
34E38tight thermal0.120.5
35F38tight thermal0.10.5
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 411 -
Rwork0.297 7651 -
obs--96.29 %
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)
11.14640.00161.03880.8238-0.19232.75520.55540.2928-0.4969-0.1640.00470.00961.61370.4323-0.56011.22880.2607-0.49340.5071-0.07070.4359-4.825-27.71924.89
20.96050.11270.4740.7286-0.14182.2543-0.03980.09390.21010.1692-0.0122-0.0677-0.22780.4770.05210.2647-0.0437-0.23050.56330.0630.27166.58914.07442.636
30.90070.03330.67470.8498-0.0682.4983-0.07440.46830.1325-0.23880.05240.0743-0.01880.40180.02190.2971-0.0549-0.24020.75980.17840.2431-12.13911.055-0.361
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 283
2X-RAY DIFFRACTION1D2 - 283
3X-RAY DIFFRACTION2B2 - 283
4X-RAY DIFFRACTION2F2 - 283
5X-RAY DIFFRACTION3C2 - 283
6X-RAY DIFFRACTION3E2 - 283

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