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

ID or keywords:

Entry

Database: PDB / ID: 3iqe

Title

Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methylene-tetrahydromethanopterin and coenzyme F420

Components

F420-dependent methylenetetrahydromethanopterin dehydrogenase

Keywords

OXIDOREDUCTASE / ternary complex of protein / substrate and co-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

Biological species

Methanopyrus kandleri (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Ceh, K.E. / Demmer, U. / Warkentin, E. / Moll, J. / Thauer, R.K. / Shima, S. / Ermler, U.

Citation

Journal: 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

Deposition	Aug 20, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Oct 6, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3iqe.cif.gz	353.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3iqe.ent.gz	286.9 KB	Display	PDB format
PDBx/mmJSON format	3iqe.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iq/3iqe ftp://data.pdbj.org/pub/pdb/validation_reports/iq/3iqe	HTTPS FTP

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Related structure data

Related structure data	3iqfC 3iqzC 1qv9S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3iqz-d 3iqf-2 1u6k-1 1u6i-2 3iqf-1 1u6j-1 1qv9-1 1u6i-1 1u6j-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

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

198 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	61.148, 165.539, 93.552
Angle α, β, γ (deg.)	90.00, 99.14, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
1	2	F
2	2	A
3	2	B
4	2	D
5	2	E
6	2	C

NCS domain segments:

Refine code: 3

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ALA	ALA	LYS	LYS	A	A	4 - 169	4 - 169
2	1	1	ALA	ALA	LYS	LYS	B	B	4 - 169	4 - 169
3	1	1	ALA	ALA	LYS	LYS	C	C	4 - 169	4 - 169
4	1	1	ALA	ALA	LYS	LYS	D	D	4 - 169	4 - 169
5	1	1	ALA	ALA	LYS	LYS	E	E	4 - 169	4 - 169
6	1	1	ALA	ALA	LYS	LYS	F	F	4 - 169	4 - 169
1	2	1	SER	SER	GLU	GLU	A	A	174 - 283	174 - 283
2	2	1	SER	SER	GLU	GLU	B	B	174 - 283	174 - 283
3	2	1	SER	SER	GLU	GLU	C	C	174 - 283	174 - 283
4	2	1	SER	SER	GLU	GLU	D	D	174 - 283	174 - 283
5	2	1	SER	SER	GLU	GLU	E	E	174 - 283	174 - 283
6	2	1	SER	SER	GLU	GLU	F	F	174 - 283	174 - 283
1	1	2	GLU	GLU	ILE	ILE	F	F	170 - 173	170 - 173
2	1	2	GLU	GLU	ILE	ILE	A	A	170 - 173	170 - 173
3	1	2	GLU	GLU	ILE	ILE	B	B	170 - 173	170 - 173
4	1	2	GLU	GLU	ILE	ILE	D	D	170 - 173	170 - 173
5	1	2	GLU	GLU	ILE	ILE	E	E	170 - 173	170 - 173
6	1	2	GLU	GLU	ILE	ILE	C	C	170 - 173	170 - 173

NCS ensembles :

ID
1
2

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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

#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, 653 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-F42 / COENZYME F420 / Coenzyme F420 Mass: 773.593 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₉H₃₆N₅O₁₈P
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#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 / Water Mass: 18.015 Da / Num. of mol.: 634 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.4 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9918 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 5, 2007
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9918 Å / Relative weight: 1
Reflection	Resolution: 1.8→92.5 Å / Num. obs: 169214 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / R_sym value: 0.074 / Net I/σ(I): 15.6
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 11198 / R_sym value: 0.411 / % possible all: 94.9

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Processing

Software

Name	Version	Classification
AMoRE		phasing
REFMAC	5.5.0066	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QV9

1qv9

Resolution: 1.8→92.45 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.941 / SU B: 6.858 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -0.3 / ESU R: 0.135 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22771	8157	5 %	RANDOM
R_work	0.18974	-	-	-
obs	0.19162	153747	95.68 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 20.67 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.83 Å²	0 Å²	-1 Å²
2-	-	0.78 Å²	0 Å²
3-	-	-	-0.27 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→92.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13092	0	457	634	14183

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	13805
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	12605
X-RAY DIFFRACTION	r_angle_refined_deg	1.627	2.037	18722
X-RAY DIFFRACTION	r_angle_other_deg	2.342	3	29483
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.75	5	1694
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.789	25.591	626
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.185	15	2444
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.78	15	84
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	2091
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	15080
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	2448
X-RAY DIFFRACTION	r_mcbond_it	0.82	1.5	8490
X-RAY DIFFRACTION	r_mcbond_other	0.243	1.5	3390
X-RAY DIFFRACTION	r_mcangle_it	1.384	2	13658
X-RAY DIFFRACTION	r_scbond_it	2.407	3	5315
X-RAY DIFFRACTION	r_scangle_it	3.854	4.5	5062

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1612	tight positional	0.16	0.05
1	2	B	1612	tight positional	0.13	0.05
1	3	C	1612	tight positional	0.12	0.05
1	4	D	1612	tight positional	0.14	0.05
1	5	E	1612	tight positional	0.13	0.05
1	6	F	1612	tight positional	0.13	0.05
2	1	F	24	tight positional	0.03	0.05
2	2	A	24	tight positional	0.02	0.05
2	3	B	24	tight positional	0.03	0.05
2	4	D	24	tight positional	0.02	0.05
2	5	E	24	tight positional	0.03	0.05
2	6	C	24	tight positional	0.05	0.05
1	1	A	2496	loose positional	0.47	5
1	2	B	2496	loose positional	0.43	5
1	3	C	2496	loose positional	0.47	5
1	4	D	2496	loose positional	0.42	5
1	5	E	2496	loose positional	0.46	5
1	6	F	2496	loose positional	0.43	5
2	1	F	37	loose positional	0.02	5
2	2	A	37	loose positional	0.01	5
2	3	B	37	loose positional	0.02	5
2	4	D	37	loose positional	0.01	5
2	5	E	37	loose positional	0.01	5
2	6	C	37	loose positional	0.02	5
1	1	A	1612	tight thermal	1.55	0.5
1	2	B	1612	tight thermal	1.23	0.5
1	3	C	1612	tight thermal	1.37	0.5
1	4	D	1612	tight thermal	1.27	0.5
1	5	E	1612	tight thermal	1.77	0.5
1	6	F	1612	tight thermal	1.46	0.5
2	1	F	24	tight thermal	0.14	0.5
2	2	A	24	tight thermal	0.08	0.5
2	3	B	24	tight thermal	0.05	0.5
2	4	D	24	tight thermal	0.09	0.5
2	5	E	24	tight thermal	0.09	0.5
2	6	C	24	tight thermal	0.06	0.5
1	1	A	2496	loose thermal	1.61	10
1	2	B	2496	loose thermal	1.59	10
1	3	C	2496	loose thermal	1.77	10
1	4	D	2496	loose thermal	1.65	10
1	5	E	2496	loose thermal	1.9	10
1	6	F	2496	loose thermal	1.67	10
2	1	F	37	loose thermal	0.03	10
2	2	A	37	loose thermal	0.03	10
2	3	B	37	loose thermal	0.05	10
2	4	D	37	loose thermal	0.02	10
2	5	E	37	loose thermal	0.04	10
2	6	F	37	loose thermal	0.04	10

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.339	617	-
R_work	0.327	11198	-
obs	-	-	94.6 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.4027	0.0343	0.0639	0.5829	-0.1402	0.498	0.027	0.0106	-0.1674	-0.0646	0.0549	0.0226	0.1697	-0.0228	-0.0819	0.1585	-0.0073	0.0012	0.0062	0.0009	0.0868	-4.68	-26.433	25.311
2	0.4248	-0.0087	0.0825	0.3745	-0.0293	0.4421	-0.0303	-0.0127	0.0334	0.0767	0.0286	-0.0315	-0.0573	0.0368	0.0016	0.0919	0.011	0.0094	0.0232	-0.0066	0.0111	9.972	14.704	41.205
3	0.4065	0.0218	0.1065	0.3582	-0.1177	0.507	-0.0291	0.0828	0.0191	-0.0909	0.052	0.0232	-0.0243	-0.0166	-0.0229	0.0999	-0.0217	0.0159	0.0843	0.0252	0.0155	-9.535	11.809	-0.919

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 283
2	X-RAY DIFFRACTION	1	D	2 - 283
3	X-RAY DIFFRACTION	2	B	2 - 283
4	X-RAY DIFFRACTION	2	F	2 - 283
5	X-RAY DIFFRACTION	3	C	2 - 283
6	X-RAY DIFFRACTION	3	E	2 - 283

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