PDB-4djd: Crystal structure of folate-free corrinoid iron-sulfur protein (C...

ID or keywords:

Entry

Database: PDB / ID: 4djd

Title

Crystal structure of folate-free corrinoid iron-sulfur protein (CFeSP) in complex with its methyltransferase (MeTr)

Components

(Corrinoid/iron-sulfur protein ...) x 2
5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase

Keywords

TRANSFERASE/VITAMIN-BINDING PROTEIN / TIM barrel / Rossmann fold / B12-dependent methyltransferase / TRANSFERASE-VITAMIN-BINDING PROTEIN complex

Function / homology

Function and homology information

5-methyltetrahydrofolate-corrinoid/iron-sulfur protein Co-methyltransferase / methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase activity / pteridine-containing compound metabolic process / acetyl-CoA catabolic process / methionine synthase activity / carbon fixation / cobalamin binding / methyltransferase activity / one-carbon metabolic process / 4 iron, 4 sulfur cluster binding ...
Similarity search - Function

Biological species

Moorella thermoacetica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.38 Å

Authors

Kung, Y. / Doukov, T.I. / Blasiak, L.C. / Drennan, C.L.

Citation

Journal: Nature / Year: 2012
Title: Visualizing molecular juggling within a B12-dependent methyltransferase complex.
Authors: Kung, Y. / Ando, N. / Doukov, T.I. / Blasiak, L.C. / Bender, G. / Seravalli, J. / Ragsdale, S.W. / Drennan, C.L.

History

Deposition	Feb 1, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 14, 2012	Provider: repository / Type: Initial release
Revision 1.1	Mar 28, 2012	Group: Database references
Revision 1.2	Apr 25, 2012	Group: Database references
Revision 1.3	Oct 24, 2012	Group: Non-polymer description
Revision 1.4	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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.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_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	4djd.cif.gz	782.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4djd.ent.gz	647.6 KB	Display	PDB format
PDBx/mmJSON format	4djd.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4djd_validation.pdf.gz	1008.2 KB	Display	wwPDB validaton report
Full document	4djd_full_validation.pdf.gz	1 MB	Display
Data in XML	4djd_validation.xml.gz	78.4 KB	Display
Data in CIF	4djd_validation.cif.gz	106.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dj/4djd ftp://data.pdbj.org/pub/pdb/validation_reports/dj/4djd	HTTPS FTP

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Related structure data

Related structure data	4djeC 4djfC C: citing same article (ref.)
Similar structure data	4djf-d 4dje-d 4f93-d 5urk-d 5urj-d 6zl1-d 6s8o-d 3hm2-d 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: 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase

B: 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase

C: Corrinoid/iron-sulfur protein large subunit

D: Corrinoid/iron-sulfur protein small subunit

E: Corrinoid/iron-sulfur protein large subunit

F: Corrinoid/iron-sulfur protein small subunit

hetero molecules

228 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)	125.614, 242.843, 79.665
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

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Protein , 1 types, 2 molecules AB

#1: Protein	5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase Mass: 28638.119 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moorella thermoacetica (bacteria) / Gene: acsE / Production host: Escherichia coli (E. coli) / References: UniProt: Q46389

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Corrinoid/iron-sulfur protein ... , 2 types, 4 molecules CEDF

#2: Protein	Corrinoid/iron-sulfur protein large subunit / C/Fe-SP Mass: 48207.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Moorella thermoacetica (bacteria) / References: UniProt: Q07340
#3: Protein	Corrinoid/iron-sulfur protein small subunit / C/Fe-SP Mass: 35107.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Moorella thermoacetica (bacteria) / References: UniProt: Q07341

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Non-polymers , 5 types, 417 molecules

#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₄S₄
#6: Chemical	ChemComp-B12 / COBALAMIN Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆₂H₈₉CoN₁₃O₁₄P
#7: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃H₈O₃
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.71 Å³/Da / Density % sol: 54.67 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM Bis-Tris, 100 mM calcium acetate, 9% PEG 5000 MME, 20% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2009
Radiation	Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.38→50 Å / Num. all: 97575 / Num. obs: 97575 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 2.38→2.47 Å / % possible all: 100

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.2_869)	refinement
HKL-2000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.38→39.833 Å / SU ML: 0.58 / σ(F): 1.34 / Phase error: 23.2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2287	4866	4.99 %	Random
R_work	0.1869	-	-	-
obs	0.1891	97485	98.96 %	-
all	-	97485	-	-

Solvent computation

Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 65.381 Å² / k_sol: 0.367 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.9958 Å²	-0 Å²	0 Å²
2-	-	-14.294 Å²	0 Å²
3-	-	-	10.7664 Å²

Refinement step

Cycle: LAST / Resolution: 2.38→39.833 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15162	0	260	401	15823

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	15709
X-RAY DIFFRACTION	f_angle_d	1.273	21471
X-RAY DIFFRACTION	f_dihedral_angle_d	14.541	5685
X-RAY DIFFRACTION	f_chiral_restr	0.237	2517
X-RAY DIFFRACTION	f_plane_restr	0.007	2795

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 (%)
2.38-2.4071	0.2882	137	0.2342	2397	X-RAY DIFFRACTION	77
2.4071-2.4354	0.2968	149	0.2432	3097	X-RAY DIFFRACTION	100
2.4354-2.4651	0.2979	143	0.2322	3070	X-RAY DIFFRACTION	100
2.4651-2.4963	0.2676	158	0.224	3067	X-RAY DIFFRACTION	100
2.4963-2.5291	0.2879	177	0.2118	3092	X-RAY DIFFRACTION	100
2.5291-2.5638	0.3032	136	0.2149	3128	X-RAY DIFFRACTION	100
2.5638-2.6004	0.2649	163	0.194	3029	X-RAY DIFFRACTION	100
2.6004-2.6392	0.2648	149	0.1907	3119	X-RAY DIFFRACTION	100
2.6392-2.6804	0.2404	152	0.1833	3080	X-RAY DIFFRACTION	100
2.6804-2.7243	0.2401	172	0.1774	3086	X-RAY DIFFRACTION	100
2.7243-2.7713	0.2091	157	0.181	3090	X-RAY DIFFRACTION	100
2.7713-2.8217	0.2529	157	0.1851	3124	X-RAY DIFFRACTION	100
2.8217-2.876	0.2535	164	0.1841	3080	X-RAY DIFFRACTION	100
2.876-2.9346	0.2215	147	0.1826	3123	X-RAY DIFFRACTION	100
2.9346-2.9984	0.2342	174	0.1865	3059	X-RAY DIFFRACTION	100
2.9984-3.0682	0.2414	168	0.1876	3118	X-RAY DIFFRACTION	100
3.0682-3.1448	0.2466	170	0.1854	3051	X-RAY DIFFRACTION	100
3.1448-3.2298	0.2389	170	0.179	3114	X-RAY DIFFRACTION	100
3.2298-3.3248	0.2348	174	0.1779	3094	X-RAY DIFFRACTION	100
3.3248-3.4321	0.2378	158	0.1829	3090	X-RAY DIFFRACTION	100
3.4321-3.5547	0.2099	167	0.1775	3119	X-RAY DIFFRACTION	100
3.5547-3.6969	0.2083	167	0.1756	3093	X-RAY DIFFRACTION	100
3.6969-3.865	0.2033	158	0.1733	3103	X-RAY DIFFRACTION	100
3.865-4.0686	0.2196	171	0.1708	3114	X-RAY DIFFRACTION	99
4.0686-4.3233	0.1851	187	0.1612	3113	X-RAY DIFFRACTION	100
4.3233-4.6566	0.2161	150	0.1624	3173	X-RAY DIFFRACTION	100
4.6566-5.1243	0.1977	165	0.1784	3130	X-RAY DIFFRACTION	100
5.1243-5.8638	0.254	162	0.2215	3175	X-RAY DIFFRACTION	100
5.8638-7.3801	0.2842	158	0.2237	3222	X-RAY DIFFRACTION	99
7.3801-39.8381	0.2126	206	0.1924	3269	X-RAY DIFFRACTION	98

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	0.5912	0.4948	-0.3882	2.5231	0.5435	0.7959	0.023	-0.0545	-0.0418	-0.0574	-0.0733	0.2439	-0.048	0.0166	-0.0076	0.2865	-0.0196	-0.0371	0.278	-0.0245	0.3265	24.2901	59.1504	10.4243
2	0.2086	-0.0033	0.1368	0.0096	0.0283	0.1894	0.1538	-0.1376	-0.076	0.1282	0.0339	0.1311	-0.0301	-0.1156	0.2262	0.7784	-0.1653	0.5485	0.4987	-0.0197	1.0434	3.1818	59.0579	37.7256
3	1.2523	0.4658	-0.7834	1.1108	-0.2751	0.8433	0.0794	0.0412	0.2109	0.1123	0.0438	0.2913	-0.0849	-0.0788	0.0171	0.1839	0.0133	0.0276	0.2357	0.0329	0.2405	26.0248	97.8911	29.3721
4	0.07	0.0092	-0.0203	0.0006	-0.0214	0.0686	0.3223	0.4884	0.3201	-0.1593	-0.3266	0.0497	-0.3292	0.17	0.0013	1.2812	0.2142	-0.213	0.878	0.2942	0.7958	16.1198	103.5713	-2.9809
5	0.0139	-0	-0.0207	0.009	0.0155	0.0515	-0.229	0.1436	0.0111	0.2355	-0.2768	-0.0964	-0.1777	0.1611	-0.0003	0.7441	-0.0672	0.1892	0.7229	-0.1736	1.429	-7.8562	66.4661	17.4983
6	1.1205	-0.0491	-0.6542	0.8121	0.1378	0.5752	0.0026	-0.1225	0.0159	0.0628	0.0579	-0.1597	-0.0136	0.0355	0	0.2201	0.0258	-0.054	0.2202	-0.0207	0.1671	3.2902	23.6206	8.1402
7	0.054	-0.0107	-0.0227	0.0442	0.0014	0.1027	0.1589	0.0012	0.0103	-0.0806	-0.1514	0.3194	0.1961	0.3359	-0	1.016	0.1202	-0.3347	0.9651	0.0449	1.4863	29.6175	17.2775	28.0174

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 1:301 ) OR ( CHAIN B AND RESID 1:301 )	A	1 - 301
2	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 1:301 ) OR ( CHAIN B AND RESID 1:301 )	B	1 - 301
3	X-RAY DIFFRACTION	2	( CHAIN C AND RESID 2:58 )	C	2 - 58
4	X-RAY DIFFRACTION	3	( CHAIN C AND RESID 59:315 ) OR ( CHAIN D AND RESID 1:323 )	C	59 - 315
5	X-RAY DIFFRACTION	3	( CHAIN C AND RESID 59:315 ) OR ( CHAIN D AND RESID 1:323 )	D	1 - 323
6	X-RAY DIFFRACTION	4	( CHAIN C AND RESID 316:442 )	C	316 - 442
7	X-RAY DIFFRACTION	5	( CHAIN E AND RESID 2:58 )	E	2 - 58
8	X-RAY DIFFRACTION	6	( CHAIN E AND RESID 59:315 ) OR ( CHAIN F AND RESID 1:323 )	E	59 - 315
9	X-RAY DIFFRACTION	6	( CHAIN E AND RESID 59:315 ) OR ( CHAIN F AND RESID 1:323 )	F	1 - 323
10	X-RAY DIFFRACTION	7	( CHAIN E AND RESID 316:442 )	E	316 - 442

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