PDB-4xc8: Isobutyryl-CoA mutase fused with bound butyryl-CoA, GDP, and Mg a...

ID or keywords:

Entry

Database: PDB / ID: 4xc8

Title

Isobutyryl-CoA mutase fused with bound butyryl-CoA, GDP, and Mg and without cobalamin (apo-IcmF/GDP)

Components

Isobutyryl-CoA mutase fused

Keywords

ISOMERASE / Radical enzyme / complex / G-protein chaperone

Function / homology

Function and homology information

isobutyryl-CoA mutase / pivalyl-CoA mutase activity / isobutyryl-CoA mutase activity / methylmalonyl-CoA mutase activity / acyl-CoA metabolic process / cobalamin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding / magnesium ion binding
Similarity search - Function

Biological species

Ralstonia metallidurans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.25 Å

Authors

Jost, M. / Drennan, C.L.

Funding support

United States, 2items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Visualization of a radical B12 enzyme with its G-protein chaperone.
Authors: Jost, M. / Cracan, V. / Hubbard, P.A. / Banerjee, R. / Drennan, C.L.

History

Deposition	Dec 17, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 11, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 4, 2015	Group: Database references
Revision 1.2	Jan 27, 2016	Group: Non-polymer description
Revision 1.3	Sep 13, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Nov 20, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Sep 27, 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_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4xc8.cif.gz	841.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4xc8.ent.gz	696.3 KB	Display	PDB format
PDBx/mmJSON format	4xc8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4xc8_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	4xc8_full_validation.pdf.gz	1.5 MB	Display
Data in XML	4xc8_validation.xml.gz	71.3 KB	Display
Data in CIF	4xc8_validation.cif.gz	94.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xc/4xc8 ftp://data.pdbj.org/pub/pdb/validation_reports/xc/4xc8	HTTPS FTP

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Related structure data

Related structure data	4xc6C 4xc7SC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5cju-d 5cjt-d 5cjv-d 4xc6-d 5cjw-d 4xc7-d 6wdq-d 1j5o-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: Isobutyryl-CoA mutase fused

B: Isobutyryl-CoA mutase fused

hetero molecules

249 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)	316.510, 316.510, 342.270
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	155
Space group name H-M	H32

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
1	2
2	2
1	3
2	3
1	4
2	4
1	5
2	5

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain A and (resseq 24:36 or resseq 54:66 or resseq 68:107 or resseq 109:112 or resseq 120:207)
2	1	1	chain B and (resseq 24:36 or resseq 54:66 or resseq 68:107 or resseq 109:112 or resseq 120:207)
1	1	2	(chain A and (resseq 209:216 or resseq 221:230 or resseq...
2	1	2	(chain B and (resseq 209:216 or resseq 221:230 or resseq...
1	1	3	chain A and (resseq 442:447 or resseq 449:477 or resseq...
2	1	3	chain B and (resseq 442:447 or resseq 449:477 or resseq...
1	1	4	chain A and (resseq 603:608 or resseq 620:621 or resseq...
2	1	4	chain B and (resseq 603:608 or resseq 620:621 or resseq...
1	1	5	chain A and (resseq 781:782 or resseq 784:808 or resseq...
2	1	5	chain B and (resseq 781:782 or resseq 784:808 or resseq...

NCS ensembles :

ID
1
2
3
4
5

#1: Protein	Isobutyryl-CoA mutase fused Mass: 122927.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: IcmF is misannotated as sbm in the genome of Cupriavidus metallidurans. Source: (gene. exp.) Ralstonia metallidurans (strain CH34 / ATCC 43123 / DSM 2839) (bacteria) Strain: CH34 / ATCC 43123 / DSM 2839 / Gene: IcmF, Rmet_0210 / Plasmid: pET28a Details (production host): gene inserted at NdeI and BamHI sites, N-terminal hexahistidine tag Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1LRY0, isobutyryl-CoA mutase
#2: Chemical	ChemComp-BCO / Butyryl Coenzyme A / S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} butanethioate (non-preferred name) Mass: 837.624 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₅H₄₂N₇O₁₇P₃S
#3: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 6.7 Å³/Da / Density % sol: 82 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: precipitant: 700 - 750 mM sodium potassium tartrate, 100 mM tris pH 8.5 protein in 50 mM NaCl, 20 mM HEPES pH 8, 10 mM butyryl-CoA, mixed with precipitant 1 uL + 1uL crystal soaked with 1 mM ...Details: precipitant: 700 - 750 mM sodium potassium tartrate, 100 mM tris pH 8.5 protein in 50 mM NaCl, 20 mM HEPES pH 8, 10 mM butyryl-CoA, mixed with precipitant 1 uL + 1uL crystal soaked with 1 mM GDP and 1.5 mM MgCl2 for 6 hours

Crystal

Density Matthews: 6.7 Å³/Da / Density % sol: 82 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: precipitant: 700 - 750 mM sodium potassium tartrate, 100 mM tris pH 8.5 protein in 50 mM NaCl, 20 mM HEPES pH 8, 10 mM butyryl-CoA, mixed with precipitant 1 uL + 1uL crystal soaked with 1 mM ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 17, 2014
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 3.25→100 Å / Num. obs: 102338 / % possible obs: 99.3 % / Redundancy: 5.1 % / R_sym value: 0.146 / Net I/σ(I): 11.3
Reflection shell	Resolution: 3.25→3.33 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.9 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: dev_1760)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4XC7

4xc7

Resolution: 3.25→99.159 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.66 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2218	5143	5.03 %	retained from related apo-IcmF set
R_work	0.2054	-	-	-
obs	0.2063	102263	99.26 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.25→99.159 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16093	0	152	0	16245

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	16532
X-RAY DIFFRACTION	f_angle_d	0.582	22435
X-RAY DIFFRACTION	f_dihedral_angle_d	11.235	6005
X-RAY DIFFRACTION	f_chiral_restr	0.021	2511
X-RAY DIFFRACTION	f_plane_restr	0.003	2960

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	1168	X-RAY DIFFRACTION	POSITIONAL
1	2	B	1168	X-RAY DIFFRACTION	POSITIONAL	0.009
2	1	A	1251	X-RAY DIFFRACTION	POSITIONAL
2	2	B	1251	X-RAY DIFFRACTION	POSITIONAL	0.013
3	1	A	978	X-RAY DIFFRACTION	POSITIONAL
3	2	B	978	X-RAY DIFFRACTION	POSITIONAL	0.041
4	1	A	1458	X-RAY DIFFRACTION	POSITIONAL
4	2	B	1458	X-RAY DIFFRACTION	POSITIONAL	0.012
5	1	A	1463	X-RAY DIFFRACTION	POSITIONAL
5	2	B	1463	X-RAY DIFFRACTION	POSITIONAL	0.011

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 (%)
3.25-3.2869	0.4284	165	0.4007	3221	X-RAY DIFFRACTION	99
3.2869-3.3256	0.3445	174	0.3612	3234	X-RAY DIFFRACTION	99
3.3256-3.3661	0.3521	178	0.3264	3197	X-RAY DIFFRACTION	99
3.3661-3.4088	0.276	180	0.3024	3178	X-RAY DIFFRACTION	99
3.4088-3.4536	0.2871	150	0.2857	3183	X-RAY DIFFRACTION	98
3.4536-3.5009	0.3327	155	0.282	3200	X-RAY DIFFRACTION	98
3.5009-3.5509	0.2805	169	0.2726	3206	X-RAY DIFFRACTION	100
3.5509-3.6039	0.2695	166	0.2605	3267	X-RAY DIFFRACTION	100
3.6039-3.6603	0.2653	166	0.2549	3256	X-RAY DIFFRACTION	100
3.6603-3.7203	0.2726	183	0.2459	3224	X-RAY DIFFRACTION	100
3.7203-3.7844	0.2346	164	0.2463	3253	X-RAY DIFFRACTION	100
3.7844-3.8532	0.2572	170	0.2278	3253	X-RAY DIFFRACTION	100
3.8532-3.9274	0.2387	178	0.2276	3211	X-RAY DIFFRACTION	100
3.9274-4.0075	0.2244	161	0.2167	3275	X-RAY DIFFRACTION	100
4.0075-4.0947	0.2226	166	0.2107	3226	X-RAY DIFFRACTION	100
4.0947-4.1899	0.1873	174	0.1983	3216	X-RAY DIFFRACTION	100
4.1899-4.2947	0.2256	207	0.1825	3214	X-RAY DIFFRACTION	99
4.2947-4.4108	0.1957	161	0.1815	3227	X-RAY DIFFRACTION	99
4.4108-4.5406	0.1877	167	0.1673	3171	X-RAY DIFFRACTION	98
4.5406-4.6872	0.1829	180	0.1705	3234	X-RAY DIFFRACTION	99
4.6872-4.8547	0.2051	168	0.172	3251	X-RAY DIFFRACTION	100
4.8547-5.0491	0.1832	172	0.178	3260	X-RAY DIFFRACTION	100
5.0491-5.2788	0.2002	172	0.186	3262	X-RAY DIFFRACTION	100
5.2788-5.5571	0.2676	159	0.2001	3275	X-RAY DIFFRACTION	100
5.5571-5.9053	0.2312	185	0.2102	3245	X-RAY DIFFRACTION	100
5.9053-6.3611	0.2285	172	0.2191	3271	X-RAY DIFFRACTION	99
6.3611-7.0011	0.1973	187	0.1825	3159	X-RAY DIFFRACTION	97
7.0011-8.0138	0.2003	169	0.1722	3298	X-RAY DIFFRACTION	100
8.0138-10.095	0.1634	184	0.1418	3315	X-RAY DIFFRACTION	100
10.095-99.2053	0.1911	161	0.1833	3338	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	4.0712	1.297	-0.6592	0.375	-0.3491	1.1725	0.1597	-0.3351	0.3375	0.3323	-0.1026	0.0832	-0.1589	-0.0429	-0.0513	0.8717	-0.0369	0.0786	0.9938	-0.0595	0.9486	-189.8844	-83.1038	13.9383
2	1.2174	0.2107	0.4458	1.8733	-0.5871	2.6179	0.0676	-0.2878	-0.1238	0.0203	-0.091	0.0941	0.3307	-0.4488	0.0187	0.7623	-0.2044	-0.0678	0.9675	0.059	0.4277	-281.1163	-108.883	-39.2958
3	0.7358	-1.6717	1.5551	0.0828	-0.1782	1.1449	-0.1902	0.5445	0.1019	-0.1973	-0.0097	-0.2517	0.0785	0.4687	-0.0597	0.4984	-0.2735	-0.1447	0.9587	0.3035	0.9335	-208.4315	-94.5244	-21.3805
4	1.5553	0.1562	0.0873	0.8462	-0.2287	1.1729	0.0575	-0.2411	0.0976	0.2267	-0.2174	-0.133	-0.3354	-0.0666	0.1407	0.8269	-0.1359	-0.1597	0.7824	0.0693	0.47	-252.1789	-80.836	-29.7982

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 22:435 OR RESID 1102:1102 ) )	A	22 - 435
2	X-RAY DIFFRACTION	1	( CHAIN A AND ( RESID 22:435 OR RESID 1102:1102 ) )	A	1102
3	X-RAY DIFFRACTION	2	( CHAIN B AND ( RESID 22:435 OR RESID 1102:1102 ) )	B	22 - 435
4	X-RAY DIFFRACTION	2	( CHAIN B AND ( RESID 22:435 OR RESID 1102:1102 ) )	B	1102
5	X-RAY DIFFRACTION	3	( CHAIN A AND ( RESID 436:1093 OR RESID 1101:1101 ) )	A	436 - 1093
6	X-RAY DIFFRACTION	3	( CHAIN A AND ( RESID 436:1093 OR RESID 1101:1101 ) )	A	1101
7	X-RAY DIFFRACTION	4	( CHAIN B AND ( RESID 436:1093 OR RESID 1101:1101 ) )	B	436 - 1093
8	X-RAY DIFFRACTION	4	( CHAIN B AND ( RESID 436:1093 OR RESID 1101:1101 ) )	B	1101

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