PDB-8eac: Thermus thermophilus methylenetetrahydrofolate reductase

ID or keywords:

Entry

Database: PDB / ID: 8eac

Title

Thermus thermophilus methylenetetrahydrofolate reductase

Components

Methylenetetrahydrofolate reductase

Keywords

OXIDOREDUCTASE / TIM barrel / flavin

Function / homology

Function and homology information

methylenetetrahydrofolate reductase (NADH) / methylenetetrahydrofolate reductase (NADH) activity / methionine biosynthetic process / tetrahydrofolate interconversion / FAD binding / cytosol
Similarity search - Function

Biological species

Thermus thermophilus HB8 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Yamada, K. / Koutmos, M.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2022
Title: 5-Formyltetrahydrofolate promotes conformational remodeling in a methylenetetrahydrofolate reductase active site and inhibits its activity.
Authors: Yamada, K. / Mendoza, J. / Koutmos, M.

History

Deposition	Aug 28, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 18, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 8, 2023	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8eac.cif.gz	238.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8eac.ent.gz	184.9 KB	Display	PDB format
PDBx/mmJSON format	8eac.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8eac_validation.pdf.gz	737.7 KB	Display	wwPDB validaton report
Full document	8eac_full_validation.pdf.gz	742.4 KB	Display
Data in XML	8eac_validation.xml.gz	23.6 KB	Display
Data in CIF	8eac_validation.cif.gz	34.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ea/8eac ftp://data.pdbj.org/pub/pdb/validation_reports/ea/8eac	HTTPS FTP

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Related structure data

Related structure data	7th4C 7th5C 3aptS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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: Methylenetetrahydrofolate reductase

B: Methylenetetrahydrofolate reductase

hetero molecules

66.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	44.284, 89.055, 161.207
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Methylenetetrahydrofolate reductase Mass: 33050.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: ATCC 27634 / DSM 579 / HB8 / Gene: TTHA0327 / Production host: Escherichia coli (E. coli) References: UniProt: Q5SLG6, methylenetetrahydrofolate reductase [NAD(P)H]
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.84 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion / pH: 7.8 / Details: 0.1M Hepes pH7.8, 1M LiCl, 20% PEG6k

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1271 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 2, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1271 Å / Relative weight: 1
Reflection	Resolution: 1.9→89.06 Å / Num. obs: 49988 / % possible obs: 97.7 % / Redundancy: 6.5 % / CC_1/2: 0.996 / Net I/σ(I): 12.7
Reflection shell	Resolution: 1.9→1.94 Å / Num. unique obs: 2948 / CC_1/2: 0.965

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
DIALS		data reduction
DIALS		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3apt

3apt

Resolution: 1.9→80.734 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.918 / SU B: 3.585 / SU ML: 0.107 / Cross valid method: FREE R-VALUE / ESU R: 0.165 / ESU R Free: 0.155
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2501	2534	5.076 %
R_work	0.2065	47388	-
all	0.209	-	-
obs	-	49922	97.354 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 30.143 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.602 Å²	-0 Å²	0 Å²
2-	-	-0.995 Å²	-0 Å²
3-	-	-	-1.608 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→80.734 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4489	0	53	231	4773

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	4651
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.014	4488
X-RAY DIFFRACTION	r_angle_refined_deg	1.594	1.653	6292
X-RAY DIFFRACTION	r_angle_other_deg	1.318	1.574	10286
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.31	5	559
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.09	19.291	282
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.624	15	768
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.208	15	58
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	569
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	5215
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1150
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	914
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.182	0.2	4143
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	2221
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	2270
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	172
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.063	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.285	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.213	0.2	33
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.339	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	2.668	2.842	2254
X-RAY DIFFRACTION	r_mcbond_other	2.669	2.841	2253
X-RAY DIFFRACTION	r_mcangle_it	3.939	4.243	2807
X-RAY DIFFRACTION	r_mcangle_other	3.939	4.244	2808
X-RAY DIFFRACTION	r_scbond_it	3.462	3.41	2397
X-RAY DIFFRACTION	r_scbond_other	3.461	3.411	2398
X-RAY DIFFRACTION	r_scangle_it	5.374	4.92	3485
X-RAY DIFFRACTION	r_scangle_other	5.373	4.921	3486
X-RAY DIFFRACTION	r_lrange_it	7.362	33.409	5070
X-RAY DIFFRACTION	r_lrange_other	7.353	33.326	5035

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9-1.949	0.277	196	0.232	3203	X-RAY DIFFRACTION	91.004
1.949-2.003	0.258	176	0.224	3296	X-RAY DIFFRACTION	95.3846
2.003-2.061	0.265	175	0.213	3308	X-RAY DIFFRACTION	98.8085
2.061-2.124	0.286	159	0.211	3214	X-RAY DIFFRACTION	97.4011
2.124-2.194	0.284	172	0.208	3125	X-RAY DIFFRACTION	99.3671
2.194-2.271	0.25	150	0.207	3035	X-RAY DIFFRACTION	98.151
2.271-2.357	0.283	155	0.212	2915	X-RAY DIFFRACTION	97.8642
2.357-2.453	0.265	143	0.219	2835	X-RAY DIFFRACTION	98.7401
2.453-2.562	0.276	145	0.213	2732	X-RAY DIFFRACTION	99.3096
2.562-2.687	0.299	109	0.221	2429	X-RAY DIFFRACTION	91.7902
2.687-2.832	0.252	117	0.213	2500	X-RAY DIFFRACTION	98.643
2.832-3.004	0.204	110	0.203	2381	X-RAY DIFFRACTION	99.164
3.004-3.211	0.259	113	0.216	2237	X-RAY DIFFRACTION	99.198
3.211-3.468	0.265	111	0.201	2085	X-RAY DIFFRACTION	99.4115
3.468-3.799	0.239	114	0.202	1916	X-RAY DIFFRACTION	99.4611
3.799-4.247	0.243	92	0.172	1748	X-RAY DIFFRACTION	99.5671
4.247-4.904	0.209	96	0.172	1521	X-RAY DIFFRACTION	96.7105
4.904-6.004	0.214	73	0.22	1252	X-RAY DIFFRACTION	93.5074
6.004-8.486	0.234	77	0.213	1040	X-RAY DIFFRACTION	99.1127
8.486-80.734	0.262	51	0.238	616	X-RAY DIFFRACTION	98.5229

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