PDB-6deb: Crystal Structure of Bifunctional Enzyme FolD-Methylenetetrahydro...

ID or keywords:

Entry

Database: PDB / ID: 6deb

Title

Crystal Structure of Bifunctional Enzyme FolD-Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase in the Complex with Methotrexate from Campylobacter jejuni

Components

Bifunctional protein FolD

Keywords

OXIDOREDUCTASE / MTHFDC / alpha-beta-fold /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

methylenetetrahydrofolate dehydrogenase (NADP+) /

methenyltetrahydrofolate cyclohydrolase /

methenyltetrahydrofolate cyclohydrolase activity /

methylenetetrahydrofolate dehydrogenase (NADP+) activity / methionine biosynthetic process / histidine biosynthetic process / purine nucleotide biosynthetic process / tetrahydrofolate interconversion
Similarity search - Function

Biological species

Campylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Kim, Y. / Makowska-Grzyska, M. / Maltseva, N. / Grimshaw, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of Bifunctional Enzyme FolD-Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase in the Complex with Methotrexate from Campylobacter jejuni
Authors: Kim, Y. / Makowska-Grzyska, M. / Maltseva, N. / Grimshaw, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	May 11, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 23, 2018	Provider: repository / Type: Initial release
Revision 1.1	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Oct 11, 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 / pdbx_struct_conn_angle / struct_conn 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6deb.cif.gz	248.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6deb.ent.gz	197.9 KB	Display	PDB format
PDBx/mmJSON format	6deb.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/de/6deb ftp://data.pdbj.org/pub/pdb/validation_reports/de/6deb	HTTPS FTP

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Related structure data

Related structure data	6de8S S: Starting model for refinement
Similar structure data	3p2o-d 4b4v-d 1dig-d 6ape-2 2gjt-d 4b4u-d 6ecr-d 1a4i-d 1dia-d 2cch-1 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
Related items in Molecule of the Month	#34 - Oct 2002 Dihydrofolate Reductase similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #145 - Jan 2012 Messenger RNA Capping similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #127 - Jul 2010 Crystallins similarity (1) #174 - Jun 2014 GFP-like Proteins similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

Deposited unit

A: Bifunctional protein FolD

B: Bifunctional protein FolD

hetero molecules

63.3 kDa, 2 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)	163.867, 59.086, 72.993
Angle α, β, γ (deg.)	90.00, 100.08, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein , 1 types, 2 molecules AB

#1: Protein	Bifunctional protein FolD / Mass: 30656.723 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter) Strain: ATCC 700819 / NCTC 11168 / Gene: folD, Cj0855 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 magic References: UniProt: Q0PA35, methylenetetrahydrofolate dehydrogenase (NADP+), methenyltetrahydrofolate cyclohydrolase

#1: Protein

Bifunctional protein FolD /

Mass: 30656.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter)
Strain: ATCC 700819 / NCTC 11168 / Gene: folD, Cj0855 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21DE3 magic
References: UniProt: Q0PA35,

methylenetetrahydrofolate dehydrogenase (NADP+),

methenyltetrahydrofolate cyclohydrolase

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Non-polymers , 8 types, 511 molecules

#2: Chemical	ChemComp-GUN / GUANINE / Guanine Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₅N₅O
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#7: Chemical	ChemComp-MTX / METHOTREXATE / Methotrexate Mass: 454.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₂₂N₈O₅ / Comment: chemotherapy*YM
#8: Chemical	ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₂S₂
#9: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.84 Å³/Da / Density % sol: 56.65 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 M potassium chloride, 20 % w/v Polyehtlyene glycol 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 26, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97934 Å / Relative weight: 1
Reflection	Resolution: 1.7→50 Å / Num. obs: 72243 / % possible obs: 95.5 % / Redundancy: 4.2 % / R_merge(I) obs: 0.052 / Net I/σ(I): 14.5
Reflection shell	Resolution: 1.7→1.73 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.263 / Num. unique obs: 2555 / % possible all: 68.3

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Processing

Software

Name	Version	Classification
PHENIX	1.8.1_1161	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6DE8

6de8

Resolution: 1.7→38.137 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.3

	R_factor	Num. reflection	% reflection
R_free	0.188	3639	5.04 %
R_work	0.161	-	-
obs	0.1624	72236	95.25 %

Solvent computation

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

Displacement parameters

B_iso mean: 23.6 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→38.137 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4268	0	127	497	4892

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4639
X-RAY DIFFRACTION	f_angle_d	1.306	6289
X-RAY DIFFRACTION	f_dihedral_angle_d	12.92	1751
X-RAY DIFFRACTION	f_chiral_restr	0.085	750
X-RAY DIFFRACTION	f_plane_restr	0.005	803

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 (%)
1.6993-1.7217	0.1765	93	0.1658	1711	X-RAY DIFFRACTION	63
1.7217-1.7453	0.2284	87	0.1708	2028	X-RAY DIFFRACTION	72
1.7453-1.7702	0.2281	111	0.1714	2154	X-RAY DIFFRACTION	79
1.7702-1.7966	0.2	127	0.1688	2364	X-RAY DIFFRACTION	86
1.7966-1.8247	0.1929	137	0.1681	2700	X-RAY DIFFRACTION	97
1.8247-1.8546	0.1837	151	0.1553	2711	X-RAY DIFFRACTION	98
1.8546-1.8866	0.2155	164	0.1564	2691	X-RAY DIFFRACTION	99
1.8866-1.9209	0.2421	128	0.155	2728	X-RAY DIFFRACTION	98
1.9209-1.9578	0.1698	145	0.1608	2729	X-RAY DIFFRACTION	99
1.9578-1.9978	0.1957	160	0.165	2712	X-RAY DIFFRACTION	99
1.9978-2.0412	0.1953	141	0.1576	2748	X-RAY DIFFRACTION	99
2.0412-2.0887	0.1976	156	0.1591	2703	X-RAY DIFFRACTION	100
2.0887-2.141	0.1876	132	0.1614	2720	X-RAY DIFFRACTION	99
2.141-2.1988	0.1782	154	0.1545	2734	X-RAY DIFFRACTION	99
2.1988-2.2635	0.1759	146	0.1517	2766	X-RAY DIFFRACTION	100
2.2635-2.3366	0.2034	148	0.1594	2738	X-RAY DIFFRACTION	100
2.3366-2.4201	0.2026	150	0.1591	2774	X-RAY DIFFRACTION	100
2.4201-2.517	0.1791	145	0.1593	2755	X-RAY DIFFRACTION	100
2.517-2.6315	0.2307	149	0.1676	2753	X-RAY DIFFRACTION	100
2.6315-2.7702	0.1878	165	0.1715	2757	X-RAY DIFFRACTION	100
2.7702-2.9437	0.1972	148	0.1712	2783	X-RAY DIFFRACTION	100
2.9437-3.1709	0.2162	134	0.1733	2775	X-RAY DIFFRACTION	100
3.1709-3.4898	0.1832	143	0.168	2802	X-RAY DIFFRACTION	99
3.4898-3.9943	0.1806	138	0.154	2728	X-RAY DIFFRACTION	98
3.9943-5.0305	0.1454	160	0.1392	2720	X-RAY DIFFRACTION	97
5.0305-38.1462	0.1823	127	0.1695	2813	X-RAY DIFFRACTION	96

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	1.1299	2.3779	-0.8362	7.9004	-1.1003	0.8462	0.0884	-0.0428	0.0919	0.3319	-0.0494	0.3391	-0.0933	-0.1162	-0.0639	0.1325	-0.0007	-0.0008	0.2058	-0.0041	0.0975	-39.6951	-2.3744	19.5773
2	6.7726	1.2475	-0.4473	3.3777	1.0719	2.918	0.2984	-0.6975	0.6061	0.2778	-0.1533	-0.2068	-0.2282	0.0779	-0.0949	0.1718	-0.0425	-0.0159	0.1841	-0.0311	0.1614	-22.5874	-7.5159	22.5799
3	3.1456	-0.5079	-0.5411	1.4002	0.2612	3.0546	0.0197	-0.0717	0.1468	0.0275	-0.018	-0.2131	-0.0696	0.2609	0.0041	0.1429	-0.0116	-0.0135	0.1177	0.0102	0.1414	-16.1484	-13.2048	13.0243
4	2.6425	-2.8977	-2.3952	3.61	2.4886	2.022	0.0172	0.1668	-0.1495	-0.0525	-0.1537	0.2133	0.0036	-0.1598	0.1834	0.1263	-0.0072	-0.0078	0.1249	-0.0051	0.1062	-31.4403	-2.6085	3.1984
5	1.7011	-0.1794	-0.8754	2.4932	0.4672	1.966	0.1319	-0.2202	0.2616	0.1275	0.024	-0.2207	-0.2192	0.2099	-0.0901	0.1464	-0.0285	0.0172	0.1381	-0.0239	0.1371	-26.864	15.2695	7.086
6	6.2625	3.1724	2.0253	5.0725	5.532	7.5934	0.2106	0.0251	-0.526	0.1418	-0.2441	-0.0246	0.3354	-0.2734	-0.0304	0.0884	0.0083	0.0138	0.2289	0.018	0.1006	-32.8942	-10.3426	13.1205
7	4.8644	-5.3448	0.6002	5.9587	-1.8994	1.6281	0.2517	0.3174	0.174	-0.4919	-0.2049	-0.4923	-0.0592	0.0854	0.0098	0.1404	-0.008	0.0398	0.1863	0.0004	0.1475	-6.698	-1.9816	-28.0207
8	3.5815	0.7366	-0.5924	1.2349	-0.1217	1.4899	-0.0193	0.2765	0.0045	-0.0374	0.0385	0.0301	-0.0053	-0.1237	-0.0195	0.1458	0.0166	-0.0039	0.1243	-0.0136	0.1165	-24.4357	-16.0319	-23.0669
9	0.8706	1.1804	-2.1088	2.734	-3.3548	5.0169	0.0672	-0.1306	-0.0628	0.0547	-0.2282	-0.1814	-0.0266	0.3356	0.2287	0.1311	0.0123	-0.0157	0.1407	0.0051	0.1349	-15.1957	-2.1702	-11.5415
10	1.7737	-0.3789	-0.4979	0.6371	-0.2506	1.9418	0.1407	0.1325	0.2233	-0.0907	-0.0374	-0.0317	-0.1972	-0.0613	-0.0775	0.1518	0.0131	0.0338	0.0899	0.0174	0.1279	-25.204	12.3901	-17.5375
11	1.3903	-1.4645	-0.1266	7.8497	-0.7968	0.5847	0.0861	0.0982	0.1053	-0.0158	-0.0795	-0.2164	-0.1048	0.0231	0.0096	0.129	-0.0102	0.0327	0.1754	0.0049	0.0757	-15.4264	2.319	-23.9524

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 27 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 28 through 58 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 59 through 121 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 122 through 151 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 152 through 261 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 262 through 282 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid -1 through 27 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 28 through 121 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 122 through 150 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 151 through 243 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 244 through 282 )

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