PDB-5ume: Crystal Structure of 5,10-Methylenetetrahydrofolate Reductase Met...

ID or keywords:

Entry

Database: PDB / ID: 5ume

Title

Crystal Structure of 5,10-Methylenetetrahydrofolate Reductase MetF from Haemophilus influenzae

Components

5,10-methylenetetrahydrofolate reductase

Keywords

OXIDOREDUCTASE / alpha-beta structure / TIM barrel / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

methylenetetrahydrofolate reductase [NAD(P)H] / methylenetetrahydrofolate reductase (NAD(P)H) activity / methionine biosynthetic process / tetrahydrofolate interconversion / FAD binding / one-carbon metabolic process / cytosol
Similarity search - Function

Biological species

Haemophilus influenzae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Kim, Y. / Mulligan, R. / Maltseva, N. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of 5,10-Methylenetetrahydrofolate Reductase MetF from Haemophilus influenzae
Authors: Kim, Y. / Mulligan, R. / Maltseva, N. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Jan 27, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 22, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Apr 13, 2022	Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3	Oct 4, 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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PDBx/mmCIF format	5ume.cif.gz	702.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5ume.ent.gz	589 KB	Display	PDB format
PDBx/mmJSON format	5ume.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/um/5ume ftp://data.pdbj.org/pub/pdb/validation_reports/um/5ume	HTTPS FTP

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Related structure data

Related structure data	3fstS S: Starting model for refinement
Similar structure data	1zrq-2 1zrq-1 1zp3-3 6pey-5 1zp3-1 1zp3-2 6pey-4 2d5c-d 1xdl-4 6wx8-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

3fstS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: 5,10-methylenetetrahydrofolate reductase

B: 5,10-methylenetetrahydrofolate reductase

C: 5,10-methylenetetrahydrofolate reductase

D: 5,10-methylenetetrahydrofolate reductase

E: 5,10-methylenetetrahydrofolate reductase

F: 5,10-methylenetetrahydrofolate reductase

hetero molecules

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

1

A: 5,10-methylenetetrahydrofolate reductase

D: 5,10-methylenetetrahydrofolate reductase

hetero molecules

defined by author&software
68.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 5,10-methylenetetrahydrofolate reductase

F: 5,10-methylenetetrahydrofolate reductase

hetero molecules

defined by author&software
68.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: 5,10-methylenetetrahydrofolate reductase

E: 5,10-methylenetetrahydrofolate reductase

hetero molecules

defined by author&software
68.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	90.065, 134.960, 182.985
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein	5,10-methylenetetrahydrofolate reductase Mass: 33338.113 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria) Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: metF, HI_1444 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold References: UniProt: P45208, methylenetetrahydrofolate reductase [NAD(P)H]

#1: Protein

5,10-methylenetetrahydrofolate reductase

Mass: 33338.113 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: metF, HI_1444 / Plasmid: pMCSG68 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold
References: UniProt: P45208, methylenetetrahydrofolate reductase [NAD(P)H]

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Non-polymers , 6 types, 71 molecules

#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₄O₂
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH₂O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.78 Å³/Da / Density % sol: 55.75 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M calcium acetate, 0.1M 0.1 M imidazole, pH 8.0, 20 %(w/v) PEG1000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97914 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 29, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97914 Å / Relative weight: 1
Reflection	Resolution: 2.7→43.728 Å / Num. obs: 61981 / % possible obs: 98.6 % / Redundancy: 7.1 % / R_sym value: 0.121 / Net I/σ(I): 17.04
Reflection shell	Resolution: 2.7→2.75 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2984 / CC_1/2: 0.667 / R_sym value: 0.968 / % possible all: 95.8

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3fst

3fst

Resolution: 2.7→43.728 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / Phase error: 26.42

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2284	3025	4.95 %	random
R_work	0.1692	-	-	-
obs	0.1721	61077	98.51 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.7→43.728 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13515	0	384	48	13947

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	14224
X-RAY DIFFRACTION	f_angle_d	1.004	19305
X-RAY DIFFRACTION	f_dihedral_angle_d	17.591	8407
X-RAY DIFFRACTION	f_chiral_restr	0.056	2142
X-RAY DIFFRACTION	f_plane_restr	0.006	2433

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 (%)
2.6997-2.7419	0.3618	125	0.2946	2496	X-RAY DIFFRACTION	94
2.7419-2.7868	0.3186	132	0.2606	2519	X-RAY DIFFRACTION	96
2.7868-2.8349	0.2674	133	0.245	2603	X-RAY DIFFRACTION	99
2.8349-2.8864	0.3465	137	0.2527	2629	X-RAY DIFFRACTION	99
2.8864-2.9419	0.3456	125	0.2435	2637	X-RAY DIFFRACTION	99
2.9419-3.002	0.3259	139	0.2474	2641	X-RAY DIFFRACTION	99
3.002-3.0672	0.334	129	0.2561	2602	X-RAY DIFFRACTION	99
3.0672-3.1386	0.3214	151	0.2357	2640	X-RAY DIFFRACTION	99
3.1386-3.217	0.3574	134	0.2195	2633	X-RAY DIFFRACTION	99
3.217-3.304	0.2753	143	0.1894	2619	X-RAY DIFFRACTION	99
3.304-3.4012	0.2809	141	0.2008	2532	X-RAY DIFFRACTION	96
3.4012-3.5109	0.2755	142	0.1793	2647	X-RAY DIFFRACTION	99
3.5109-3.6363	0.2823	151	0.1812	2640	X-RAY DIFFRACTION	99
3.6363-3.7818	0.2316	128	0.1726	2660	X-RAY DIFFRACTION	99
3.7818-3.9538	0.2324	149	0.1564	2646	X-RAY DIFFRACTION	99
3.9538-4.1622	0.2238	152	0.1466	2639	X-RAY DIFFRACTION	99
4.1622-4.4227	0.1901	110	0.1405	2663	X-RAY DIFFRACTION	99
4.4227-4.7638	0.212	129	0.1351	2684	X-RAY DIFFRACTION	98
4.7638-5.2425	0.2038	150	0.1359	2678	X-RAY DIFFRACTION	99
5.2425-5.9994	0.1965	144	0.1532	2719	X-RAY DIFFRACTION	100
5.9994-7.5523	0.2019	150	0.166	2706	X-RAY DIFFRACTION	98
7.5523-43.7335	0.1533	131	0.148	2819	X-RAY DIFFRACTION	97

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	6.2844	2.9371	5.69	5.9399	3.348	8.1429	0.2318	0.3965	-0.461	-0.156	-0.293	0.606	0.6383	-0.1826	0.1432	0.7555	0.1491	-0.0735	0.8694	0.014	0.798	26.0331	7.9116	101.6958
2	7.273	0.1644	-0.1058	5.0262	-1.1826	7.074	-0.1112	-2.2979	0.9744	1.1202	0.1537	0.216	-0.7442	-0.5267	0.0632	0.667	0.1119	-0.0048	1.183	-0.2997	0.6364	30.0096	17.4681	121.6014
3	4.1762	-0.7979	0.2139	3.0369	-1.8742	4.9813	0.2481	-0.7201	0.5131	0.3759	-0.2548	-0.2066	-0.4924	0.4754	0.0399	0.4546	-0.1007	-0.0046	0.6724	-0.1334	0.5639	46.652	18.977	112.3016
4	8.1929	-5.4285	-1.3052	5.7071	1.0308	3.4935	-0.2896	0.61	0.1346	0.0366	-0.1748	-0.1546	-0.0985	-0.0562	0.3774	0.574	-0.0406	-0.1307	0.5202	-0.0671	0.5864	35.8994	18.7558	99.1377
5	6.4662	-0.6617	2.5096	5.1126	-1.3127	3.464	0.0108	0.0009	0.1383	0.0248	0.0312	-0.2167	-0.0561	0.2133	-0.0177	0.4494	0.0038	0.0152	0.5454	-0.0859	0.3888	23.6865	17.0255	101.3655
6	2.3893	-0.7795	-0.2422	2.1658	-1.6613	2.0261	0.1777	0.0342	-1.0428	-0.0166	-0.4811	0.3422	0.4181	0.0448	0.0417	0.9257	-0.1506	-0.3296	0.6094	0.0488	1.0701	9.1478	-32.8632	74.0475
7	1.9178	-0.8342	-0.0718	2.1478	-0.494	2.2002	0.4747	0.3303	-1.0451	-0.292	-0.2217	0.4407	0.5941	-0.6428	-0.3128	0.7966	-0.1743	-0.2767	0.7534	-0.1256	1.0121	-4.323	-24.5613	62.6181
8	2.6476	-1.3896	-3.0157	4.462	-0.2375	4.4986	0.3466	0.1778	-0.0652	-0.227	0.1041	-0.5028	-0.304	-0.0504	-0.2319	0.6828	0.0259	-0.1387	0.6489	-0.0373	0.5739	6.4034	-9.0669	65.3152
9	7.887	-3.4753	-1.9794	2.8376	-0.7592	2.6469	0.204	1.47	-1.5661	-0.3604	-0.5999	0.653	0.2477	-0.1711	0.1977	0.7581	-0.0193	-0.1806	0.9181	-0.2367	0.5918	13.1127	-19.2658	63.1464
10	6.9677	-3.4574	-2.4727	5.4372	-1.8352	5.954	0.0603	1.2427	0.1461	0.1232	-0.036	-0.3898	0.3416	0.2696	-0.0589	0.6911	-0.1206	-0.1491	0.699	-0.1413	0.5786	23.5952	-17.2477	68.167
11	5.0818	-1.3206	0.2703	5.3662	-1.0853	6.9728	0.4188	-0.4306	-0.8328	-0.554	0.2779	0.339	-0.0188	-0.0088	-0.6941	0.697	-0.1449	-0.2587	0.6557	-0.0294	0.6172	12.7031	-21.7987	76.9161
12	5.2502	0.9524	0.3708	3.1382	1.0265	3.6	-0.0727	0.549	0.0495	-0.1733	0.251	-0.0952	-0.1551	0.0656	-0.1876	0.5609	0.0406	-0.0103	0.7611	0.0199	0.4559	8.7454	8.8042	34.2729
13	4.6867	1.1785	0.2422	2.1515	0.2405	2.1662	-0.0531	-0.0098	0.1774	0.206	-0.0444	0.0583	-0.209	-0.283	0.1452	0.555	0.0691	-0.0576	0.5763	0.0484	0.4321	5.4224	11.9356	47.0968
14	3.7373	1.2466	1.5351	4.4635	-2.9133	6.1783	-0.0313	-0.8249	0.9679	0.2081	0.0694	-0.0744	-0.2004	0.5252	0.0718	0.8337	0.0375	-0.1625	0.9788	-0.3618	0.6449	4.9294	20.2652	93.2747
15	6.1942	0.5621	2.4089	2.5987	2.9591	4.9646	-0.0695	-0.8975	0.7333	-0.0621	0.0502	1.2076	-0.2142	-1.4075	0.0059	0.575	0.1541	-0.064	1.0109	-0.1695	0.7109	-13.7368	17.7127	91.1219
16	5.4921	-0.9818	0.3154	3.2208	0.4731	2.5542	-0.1269	0.023	0.0075	-0.3095	0.0322	0.6144	0.2174	-0.8068	0.0276	0.5499	-0.1595	-0.0771	0.944	0.0455	0.5417	-13.6445	7.4304	80.3543
17	4.2005	0.2907	3.4936	1.8693	0.3165	6.2209	-0.0924	-0.1772	-0.0929	-0.0865	0.3033	-0.113	0.3126	-0.3818	-0.1848	0.5073	-0.0064	0.0105	0.5607	-0.0305	0.5289	6.7467	9.8235	90.4613
18	3.9161	-4.2688	0.5701	4.6625	-0.7727	5.1429	-0.7231	0.6948	-0.632	0.6971	0.0009	0.4476	-0.4135	0.1268	0.5314	1.4326	-0.2274	-0.1397	1.822	-0.0692	2.0963	16.0614	13.2003	64.814
19	4.6956	-0.3841	-0.506	6.0766	1.2262	6.7039	-0.3712	0.7489	1.1566	-0.5533	0.1506	-0.6085	-0.9014	1.11	0.1531	0.7279	-0.3287	-0.2311	0.7895	0.2756	0.8631	46.9154	26.3848	54.5869
20	6.3068	1.4077	-0.2133	5.6572	-1.9118	5.4708	-0.4208	-0.3096	0.5191	-0.0679	-0.065	-0.3996	-0.465	0.7143	0.4409	0.4895	0.008	-0.1049	0.6589	-0.0289	0.5025	51.982	16.3549	69.6218
21	4.5706	2.1526	3.6882	3.1118	2.7807	7.707	-0.136	-0.1602	-0.1175	0.1271	0.2854	-0.375	-0.043	0.2951	-0.1371	0.5595	0.0428	-0.1219	0.6056	0.1725	0.6988	34.8145	13.2133	56.6651
22	5.1635	1.6903	0.1226	5.8552	0.4632	7.7479	0.2574	0.4183	-0.1351	-0.2026	-0.2186	0.2735	0.4069	0.2421	-0.1294	0.539	0.1317	0.058	0.6017	-0.0624	0.5797	46.4751	-23.7302	81.0863
23	3.408	-1.0774	0.3112	3.9805	-0.1652	1.3928	0.0889	-0.207	-0.0211	0.1952	-0.1792	-0.3156	0.1502	0.4375	0.0615	0.495	0.0346	-0.0182	0.6776	0.0651	0.4174	51.2143	-9.7776	91.5456
24	7.2733	2.8541	-0.4802	4.3098	1.0995	1.1021	0.3022	-0.6243	-0.4381	-0.0202	-0.1174	0.1919	0.2131	0.0809	-0.2197	0.6068	0.1062	-0.1589	0.6723	0.0275	0.4507	31.9739	-17.3085	83.5164

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 32 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 33 through 79 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 80 through 185 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 186 through 224 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 225 through 292 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 20 through 49 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 50 through 173 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 174 through 199 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 200 through 225 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 226 through 265 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 266 through 292 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 4 through 107 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 108 through 292 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 2 through 49 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 50 through 93 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 94 through 173 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 174 through 292 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid -1 through 15 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 16 through 78 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 79 through 199 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 200 through 292 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 7 through 79 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 80 through 214 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 215 through 292 )

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Protein , 1 types, 6 molecules ABCDEF

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Non-polymers , 6 types, 71 molecules

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Experimental details

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Sample preparation

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Data collection

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About Yorodumi

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Yorodumi