PDB-4w61: Crystal structure of beta-ketoacyl thiolase B (BktB) from Ralston...

ID or keywords:

Entry

Database: PDB / ID: 4w61

Title

Crystal structure of beta-ketoacyl thiolase B (BktB) from Ralstonia eutropha

Components

Beta-ketothiolase BktB

Keywords

TRANSFERASE / beta-ketoacyl thiolase / biosynthetic thiolase

Function / homology

Function and homology information

acetyl-CoA C-acyltransferase / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity
Similarity search - Function

Biological species

Cupriavidus necator (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.01 Å

Authors

Fage, C.D. / Keatinge-Clay, A.T.

Funding support

United States, 1items

Citation

Journal: J. Mol. Catal., B Enzym. / Year: 2015
Title: Coenzyme A-free activity, crystal structure, and rational engineering of a promiscuous beta-ketoacyl thiolase fromRalstonia eutropha.
Authors: Fage, C.D. / Meinke, J.L. / Keatinge-Clay, A.T.

History

Deposition	Aug 19, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 9, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Derived calculations / Refinement description Category: pdbx_audit_support / pdbx_struct_oper_list / software Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Apr 18, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3	Dec 25, 2019	Group: Author supporting evidence / Source and taxonomy / Category: entity_src_gen / pdbx_audit_support Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_audit_support.funding_organization
Revision 1.4	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4w61.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb4w61.ent.gz	914.5 KB	Display	PDB format
PDBx/mmJSON format	4w61.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4w61_validation.pdf.gz	585.9 KB	Display	wwPDB validaton report
Full document	4w61_full_validation.pdf.gz	680.7 KB	Display
Data in XML	4w61_validation.xml.gz	239.8 KB	Display
Data in CIF	4w61_validation.cif.gz	304.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w6/4w61 ftp://data.pdbj.org/pub/pdb/validation_reports/w6/4w61	HTTPS FTP

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Related structure data

Related structure data	4dd5S 4w62 PDB Unreleased entry S: Starting model for refinement
Similar structure data	4nzs-1 2wkv-d 2vu2-d 2wku-d 6are-d 1dlu-d 6arl-d 4o99-d 5f38-d 1m1o-d 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) 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

4dd5S

4w62
PDB Unreleased entry

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	#216 - Dec 2017 Biodegradable Plastic similarity (11) #90 - Jun 2007 Fatty Acid Synthase similarity (1)

Deposited unit

A: Beta-ketothiolase BktB

B: Beta-ketothiolase BktB

C: Beta-ketothiolase BktB

D: Beta-ketothiolase BktB

E: Beta-ketothiolase BktB

F: Beta-ketothiolase BktB

G: Beta-ketothiolase BktB

H: Beta-ketothiolase BktB

I: Beta-ketothiolase BktB

J: Beta-ketothiolase BktB

K: Beta-ketothiolase BktB

L: Beta-ketothiolase BktB

M: Beta-ketothiolase BktB

N: Beta-ketothiolase BktB

O: Beta-ketothiolase BktB

P: Beta-ketothiolase BktB

690 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-ketothiolase BktB

B: Beta-ketothiolase BktB

C: Beta-ketothiolase BktB

D: Beta-ketothiolase BktB

defined by author&software
172 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Beta-ketothiolase BktB

F: Beta-ketothiolase BktB

G: Beta-ketothiolase BktB

H: Beta-ketothiolase BktB

defined by author&software
172 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

I: Beta-ketothiolase BktB

J: Beta-ketothiolase BktB

K: Beta-ketothiolase BktB

L: Beta-ketothiolase BktB

defined by author&software
172 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

M: Beta-ketothiolase BktB

N: Beta-ketothiolase BktB

O: Beta-ketothiolase BktB

P: Beta-ketothiolase BktB

defined by author&software
172 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	72.050, 105.987, 201.142
Angle α, β, γ (deg.)	89.97, 89.98, 89.93
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	THR	THR	ARG	ARG	A	A	2 - 393	22 - 413
2	1	THR	THR	ARG	ARG	B	B	2 - 393	22 - 413
1	2	THR	THR	ARG	ARG	A	A	2 - 393	22 - 413
2	2	THR	THR	ARG	ARG	C	C	2 - 393	22 - 413
1	3	THR	THR	ARG	ARG	A	A	2 - 393	22 - 413
2	3	THR	THR	ARG	ARG	D	D	2 - 393	22 - 413
1	4	THR	THR	ARG	ARG	A	A	2 - 393	22 - 413
2	4	THR	THR	ARG	ARG	E	E	2 - 393	22 - 413
1	5	THR	THR	ARG	ARG	A	A	2 - 393	22 - 413
2	5	THR	THR	ARG	ARG	F	F	2 - 393	22 - 413
1	6	MET	MET	ARG	ARG	A	A	1 - 393	21 - 413
2	6	MET	MET	ARG	ARG	G	G	1 - 393	21 - 413
1	7	THR	THR	GLU	GLU	A	A	2 - 392	22 - 412
2	7	THR	THR	GLU	GLU	H	H	2 - 392	22 - 412
1	8	MET	MET	ARG	ARG	A	A	1 - 393	21 - 413
2	8	MET	MET	ARG	ARG	I	I	1 - 393	21 - 413
1	9	THR	THR	ARG	ARG	A	A	2 - 393	22 - 413
2	9	THR	THR	ARG	ARG	J	J	2 - 393	22 - 413
1	10	THR	THR	GLU	GLU	A	A	2 - 392	22 - 412
2	10	THR	THR	GLU	GLU	K	K	2 - 392	22 - 412
1	11	THR	THR	ARG	ARG	A	A	2 - 393	22 - 413
2	11	THR	THR	ARG	ARG	L	L	2 - 393	22 - 413
1	12	THR	THR	ARG	ARG	A	A	2 - 393	22 - 413
2	12	THR	THR	ARG	ARG	M	M	2 - 393	22 - 413
1	13	THR	THR	GLU	GLU	A	A	2 - 392	22 - 412
2	13	THR	THR	GLU	GLU	N	N	2 - 392	22 - 412
1	14	THR	THR	ARG	ARG	A	A	2 - 393	22 - 413
2	14	THR	THR	ARG	ARG	O	O	2 - 393	22 - 413
1	15	THR	THR	ARG	ARG	A	A	2 - 393	22 - 413
2	15	THR	THR	ARG	ARG	P	P	2 - 393	22 - 413
1	16	THR	THR	ILE	ILE	B	B	2 - 394	22 - 414
2	16	THR	THR	ILE	ILE	C	C	2 - 394	22 - 414
1	17	THR	THR	GLU	GLU	B	B	2 - 392	22 - 412
2	17	THR	THR	GLU	GLU	D	D	2 - 392	22 - 412
1	18	THR	THR	ILE	ILE	B	B	2 - 394	22 - 414
2	18	THR	THR	ILE	ILE	E	E	2 - 394	22 - 414
1	19	THR	THR	ARG	ARG	B	B	2 - 393	22 - 413
2	19	THR	THR	ARG	ARG	F	F	2 - 393	22 - 413
1	20	THR	THR	ARG	ARG	B	B	2 - 393	22 - 413
2	20	THR	THR	ARG	ARG	G	G	2 - 393	22 - 413
1	21	THR	THR	ILE	ILE	B	B	2 - 394	22 - 414
2	21	THR	THR	ILE	ILE	H	H	2 - 394	22 - 414
1	22	THR	THR	ILE	ILE	B	B	2 - 394	22 - 414
2	22	THR	THR	ILE	ILE	I	I	2 - 394	22 - 414
1	23	THR	THR	ARG	ARG	B	B	2 - 393	22 - 413
2	23	THR	THR	ARG	ARG	J	J	2 - 393	22 - 413
1	24	THR	THR	ILE	ILE	B	B	2 - 394	22 - 414
2	24	THR	THR	ILE	ILE	K	K	2 - 394	22 - 414
1	25	THR	THR	GLU	GLU	B	B	2 - 392	22 - 412
2	25	THR	THR	GLU	GLU	L	L	2 - 392	22 - 412
1	26	THR	THR	ILE	ILE	B	B	2 - 394	22 - 414
2	26	THR	THR	ILE	ILE	M	M	2 - 394	22 - 414
1	27	THR	THR	ARG	ARG	B	B	2 - 393	22 - 413
2	27	THR	THR	ARG	ARG	N	N	2 - 393	22 - 413
1	28	THR	THR	ARG	ARG	B	B	2 - 393	22 - 413
2	28	THR	THR	ARG	ARG	O	O	2 - 393	22 - 413
1	29	THR	THR	ARG	ARG	B	B	2 - 393	22 - 413
2	29	THR	THR	ARG	ARG	P	P	2 - 393	22 - 413
1	30	THR	THR	ARG	ARG	C	C	2 - 393	22 - 413
2	30	THR	THR	ARG	ARG	D	D	2 - 393	22 - 413
1	31	THR	THR	ILE	ILE	C	C	2 - 394	22 - 414
2	31	THR	THR	ILE	ILE	E	E	2 - 394	22 - 414
1	32	THR	THR	GLU	GLU	C	C	2 - 392	22 - 412
2	32	THR	THR	GLU	GLU	F	F	2 - 392	22 - 412
1	33	THR	THR	GLU	GLU	C	C	2 - 392	22 - 412
2	33	THR	THR	GLU	GLU	G	G	2 - 392	22 - 412
1	34	THR	THR	ILE	ILE	C	C	2 - 394	22 - 414
2	34	THR	THR	ILE	ILE	H	H	2 - 394	22 - 414
1	35	THR	THR	ARG	ARG	C	C	2 - 393	22 - 413
2	35	THR	THR	ARG	ARG	I	I	2 - 393	22 - 413
1	36	THR	THR	ARG	ARG	C	C	2 - 393	22 - 413
2	36	THR	THR	ARG	ARG	J	J	2 - 393	22 - 413
1	37	THR	THR	ILE	ILE	C	C	2 - 394	22 - 414
2	37	THR	THR	ILE	ILE	K	K	2 - 394	22 - 414
1	38	THR	THR	ARG	ARG	C	C	2 - 393	22 - 413
2	38	THR	THR	ARG	ARG	L	L	2 - 393	22 - 413
1	39	THR	THR	ILE	ILE	C	C	2 - 394	22 - 414
2	39	THR	THR	ILE	ILE	M	M	2 - 394	22 - 414
1	40	THR	THR	ARG	ARG	C	C	2 - 393	22 - 413
2	40	THR	THR	ARG	ARG	N	N	2 - 393	22 - 413
1	41	THR	THR	GLU	GLU	C	C	2 - 392	22 - 412
2	41	THR	THR	GLU	GLU	O	O	2 - 392	22 - 412
1	42	THR	THR	GLU	GLU	C	C	2 - 392	22 - 412
2	42	THR	THR	GLU	GLU	P	P	2 - 392	22 - 412
1	43	THR	THR	ARG	ARG	D	D	2 - 393	22 - 413
2	43	THR	THR	ARG	ARG	E	E	2 - 393	22 - 413
1	44	THR	THR	ARG	ARG	D	D	2 - 393	22 - 413
2	44	THR	THR	ARG	ARG	F	F	2 - 393	22 - 413
1	45	THR	THR	ARG	ARG	D	D	2 - 393	22 - 413
2	45	THR	THR	ARG	ARG	G	G	2 - 393	22 - 413
1	46	THR	THR	ARG	ARG	D	D	2 - 393	22 - 413
2	46	THR	THR	ARG	ARG	H	H	2 - 393	22 - 413
1	47	THR	THR	ARG	ARG	D	D	2 - 393	22 - 413
2	47	THR	THR	ARG	ARG	I	I	2 - 393	22 - 413
1	48	THR	THR	ARG	ARG	D	D	2 - 393	22 - 413
2	48	THR	THR	ARG	ARG	J	J	2 - 393	22 - 413
1	49	THR	THR	ARG	ARG	D	D	2 - 393	22 - 413
2	49	THR	THR	ARG	ARG	K	K	2 - 393	22 - 413
1	50	THR	THR	ARG	ARG	D	D	2 - 393	22 - 413
2	50	THR	THR	ARG	ARG	L	L	2 - 393	22 - 413
1	51	THR	THR	ARG	ARG	D	D	2 - 393	22 - 413
2	51	THR	THR	ARG	ARG	M	M	2 - 393	22 - 413
1	52	THR	THR	ARG	ARG	D	D	2 - 393	22 - 413
2	52	THR	THR	ARG	ARG	N	N	2 - 393	22 - 413
1	53	THR	THR	ARG	ARG	D	D	2 - 393	22 - 413
2	53	THR	THR	ARG	ARG	O	O	2 - 393	22 - 413
1	54	THR	THR	ARG	ARG	D	D	2 - 393	22 - 413
2	54	THR	THR	ARG	ARG	P	P	2 - 393	22 - 413
1	55	THR	THR	ARG	ARG	E	E	2 - 393	22 - 413
2	55	THR	THR	ARG	ARG	F	F	2 - 393	22 - 413
1	56	THR	THR	ARG	ARG	E	E	2 - 393	22 - 413
2	56	THR	THR	ARG	ARG	G	G	2 - 393	22 - 413
1	57	THR	THR	ILE	ILE	E	E	2 - 394	22 - 414
2	57	THR	THR	ILE	ILE	H	H	2 - 394	22 - 414
1	58	THR	THR	ILE	ILE	E	E	2 - 394	22 - 414
2	58	THR	THR	ILE	ILE	I	I	2 - 394	22 - 414
1	59	THR	THR	ARG	ARG	E	E	2 - 393	22 - 413
2	59	THR	THR	ARG	ARG	J	J	2 - 393	22 - 413
1	60	THR	THR	ILE	ILE	E	E	2 - 394	22 - 414
2	60	THR	THR	ILE	ILE	K	K	2 - 394	22 - 414
1	61	THR	THR	ARG	ARG	E	E	2 - 393	22 - 413
2	61	THR	THR	ARG	ARG	L	L	2 - 393	22 - 413
1	62	THR	THR	ILE	ILE	E	E	2 - 394	22 - 414
2	62	THR	THR	ILE	ILE	M	M	2 - 394	22 - 414
1	63	THR	THR	ARG	ARG	E	E	2 - 393	22 - 413
2	63	THR	THR	ARG	ARG	N	N	2 - 393	22 - 413
1	64	THR	THR	ARG	ARG	E	E	2 - 393	22 - 413
2	64	THR	THR	ARG	ARG	O	O	2 - 393	22 - 413
1	65	THR	THR	ARG	ARG	E	E	2 - 393	22 - 413
2	65	THR	THR	ARG	ARG	P	P	2 - 393	22 - 413
1	66	THR	THR	GLU	GLU	F	F	2 - 392	22 - 412
2	66	THR	THR	GLU	GLU	G	G	2 - 392	22 - 412
1	67	THR	THR	ARG	ARG	F	F	2 - 393	22 - 413
2	67	THR	THR	ARG	ARG	H	H	2 - 393	22 - 413
1	68	THR	THR	GLU	GLU	F	F	2 - 392	22 - 412
2	68	THR	THR	GLU	GLU	I	I	2 - 392	22 - 412
1	69	THR	THR	ARG	ARG	F	F	2 - 393	22 - 413
2	69	THR	THR	ARG	ARG	J	J	2 - 393	22 - 413
1	70	THR	THR	ARG	ARG	F	F	2 - 393	22 - 413
2	70	THR	THR	ARG	ARG	K	K	2 - 393	22 - 413
1	71	THR	THR	ARG	ARG	F	F	2 - 393	22 - 413
2	71	THR	THR	ARG	ARG	L	L	2 - 393	22 - 413
1	72	THR	THR	ARG	ARG	F	F	2 - 393	22 - 413
2	72	THR	THR	ARG	ARG	M	M	2 - 393	22 - 413
1	73	THR	THR	ARG	ARG	F	F	2 - 393	22 - 413
2	73	THR	THR	ARG	ARG	N	N	2 - 393	22 - 413
1	74	THR	THR	ARG	ARG	F	F	2 - 393	22 - 413
2	74	THR	THR	ARG	ARG	O	O	2 - 393	22 - 413
1	75	THR	THR	ARG	ARG	F	F	2 - 393	22 - 413
2	75	THR	THR	ARG	ARG	P	P	2 - 393	22 - 413
1	76	THR	THR	ARG	ARG	G	G	2 - 393	22 - 413
2	76	THR	THR	ARG	ARG	H	H	2 - 393	22 - 413
1	77	MET	MET	GLU	GLU	G	G	1 - 392	21 - 412
2	77	MET	MET	GLU	GLU	I	I	1 - 392	21 - 412
1	78	THR	THR	ARG	ARG	G	G	2 - 393	22 - 413
2	78	THR	THR	ARG	ARG	J	J	2 - 393	22 - 413
1	79	THR	THR	ARG	ARG	G	G	2 - 393	22 - 413
2	79	THR	THR	ARG	ARG	K	K	2 - 393	22 - 413
1	80	THR	THR	ARG	ARG	G	G	2 - 393	22 - 413
2	80	THR	THR	ARG	ARG	L	L	2 - 393	22 - 413
1	81	THR	THR	GLU	GLU	G	G	2 - 392	22 - 412
2	81	THR	THR	GLU	GLU	M	M	2 - 392	22 - 412
1	82	THR	THR	ARG	ARG	G	G	2 - 393	22 - 413
2	82	THR	THR	ARG	ARG	N	N	2 - 393	22 - 413
1	83	THR	THR	GLU	GLU	G	G	2 - 392	22 - 412
2	83	THR	THR	GLU	GLU	O	O	2 - 392	22 - 412
1	84	THR	THR	GLU	GLU	G	G	2 - 392	22 - 412
2	84	THR	THR	GLU	GLU	P	P	2 - 392	22 - 412
1	85	THR	THR	ILE	ILE	H	H	2 - 394	22 - 414
2	85	THR	THR	ILE	ILE	I	I	2 - 394	22 - 414
1	86	THR	THR	ARG	ARG	H	H	2 - 393	22 - 413
2	86	THR	THR	ARG	ARG	J	J	2 - 393	22 - 413
1	87	THR	THR	ILE	ILE	H	H	2 - 394	22 - 414
2	87	THR	THR	ILE	ILE	K	K	2 - 394	22 - 414
1	88	THR	THR	ARG	ARG	H	H	2 - 393	22 - 413
2	88	THR	THR	ARG	ARG	L	L	2 - 393	22 - 413
1	89	THR	THR	ILE	ILE	H	H	2 - 394	22 - 414
2	89	THR	THR	ILE	ILE	M	M	2 - 394	22 - 414
1	90	THR	THR	ARG	ARG	H	H	2 - 393	22 - 413
2	90	THR	THR	ARG	ARG	N	N	2 - 393	22 - 413
1	91	THR	THR	ARG	ARG	H	H	2 - 393	22 - 413
2	91	THR	THR	ARG	ARG	O	O	2 - 393	22 - 413
1	92	THR	THR	ARG	ARG	H	H	2 - 393	22 - 413
2	92	THR	THR	ARG	ARG	P	P	2 - 393	22 - 413
1	93	THR	THR	GLU	GLU	I	I	2 - 392	22 - 412
2	93	THR	THR	GLU	GLU	J	J	2 - 392	22 - 412
1	94	THR	THR	ILE	ILE	I	I	2 - 394	22 - 414
2	94	THR	THR	ILE	ILE	K	K	2 - 394	22 - 414
1	95	THR	THR	ARG	ARG	I	I	2 - 393	22 - 413
2	95	THR	THR	ARG	ARG	L	L	2 - 393	22 - 413
1	96	THR	THR	ILE	ILE	I	I	2 - 394	22 - 414
2	96	THR	THR	ILE	ILE	M	M	2 - 394	22 - 414
1	97	THR	THR	ARG	ARG	I	I	2 - 393	22 - 413
2	97	THR	THR	ARG	ARG	N	N	2 - 393	22 - 413
1	98	THR	THR	GLU	GLU	I	I	2 - 392	22 - 412
2	98	THR	THR	GLU	GLU	O	O	2 - 392	22 - 412
1	99	THR	THR	GLU	GLU	I	I	2 - 392	22 - 412
2	99	THR	THR	GLU	GLU	P	P	2 - 392	22 - 412
1	100	THR	THR	ARG	ARG	J	J	2 - 393	22 - 413
2	100	THR	THR	ARG	ARG	K	K	2 - 393	22 - 413
1	101	THR	THR	ARG	ARG	J	J	2 - 393	22 - 413
2	101	THR	THR	ARG	ARG	L	L	2 - 393	22 - 413
1	102	THR	THR	GLU	GLU	J	J	2 - 392	22 - 412
2	102	THR	THR	GLU	GLU	M	M	2 - 392	22 - 412
1	103	THR	THR	ARG	ARG	J	J	2 - 393	22 - 413
2	103	THR	THR	ARG	ARG	N	N	2 - 393	22 - 413
1	104	THR	THR	ARG	ARG	J	J	2 - 393	22 - 413
2	104	THR	THR	ARG	ARG	O	O	2 - 393	22 - 413
1	105	THR	THR	ARG	ARG	J	J	2 - 393	22 - 413
2	105	THR	THR	ARG	ARG	P	P	2 - 393	22 - 413
1	106	THR	THR	ARG	ARG	K	K	2 - 393	22 - 413
2	106	THR	THR	ARG	ARG	L	L	2 - 393	22 - 413
1	107	THR	THR	ILE	ILE	K	K	2 - 394	22 - 414
2	107	THR	THR	ILE	ILE	M	M	2 - 394	22 - 414
1	108	THR	THR	ARG	ARG	K	K	2 - 393	22 - 413
2	108	THR	THR	ARG	ARG	N	N	2 - 393	22 - 413
1	109	THR	THR	ARG	ARG	K	K	2 - 393	22 - 413
2	109	THR	THR	ARG	ARG	O	O	2 - 393	22 - 413
1	110	THR	THR	ARG	ARG	K	K	2 - 393	22 - 413
2	110	THR	THR	ARG	ARG	P	P	2 - 393	22 - 413
1	111	THR	THR	ARG	ARG	L	L	2 - 393	22 - 413
2	111	THR	THR	ARG	ARG	M	M	2 - 393	22 - 413
1	112	THR	THR	ARG	ARG	L	L	2 - 393	22 - 413
2	112	THR	THR	ARG	ARG	N	N	2 - 393	22 - 413
1	113	THR	THR	ARG	ARG	L	L	2 - 393	22 - 413
2	113	THR	THR	ARG	ARG	O	O	2 - 393	22 - 413
1	114	THR	THR	ARG	ARG	L	L	2 - 393	22 - 413
2	114	THR	THR	ARG	ARG	P	P	2 - 393	22 - 413
1	115	THR	THR	ARG	ARG	M	M	2 - 393	22 - 413
2	115	THR	THR	ARG	ARG	N	N	2 - 393	22 - 413
1	116	THR	THR	ARG	ARG	M	M	2 - 393	22 - 413
2	116	THR	THR	ARG	ARG	O	O	2 - 393	22 - 413
1	117	THR	THR	ARG	ARG	M	M	2 - 393	22 - 413
2	117	THR	THR	ARG	ARG	P	P	2 - 393	22 - 413
1	118	THR	THR	ARG	ARG	N	N	2 - 393	22 - 413
2	118	THR	THR	ARG	ARG	O	O	2 - 393	22 - 413
1	119	THR	THR	ARG	ARG	N	N	2 - 393	22 - 413
2	119	THR	THR	ARG	ARG	P	P	2 - 393	22 - 413
1	120	THR	THR	ARG	ARG	O	O	2 - 393	22 - 413
2	120	THR	THR	ARG	ARG	P	P	2 - 393	22 - 413

NCS ensembles :

#1: Protein	Beta-ketothiolase BktB / Acetyl-CoA acetyltransferase / Acetyl-CoA acyltransferase Mass: 43124.113 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) (bacteria) Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / Gene: bktB, H16_A1445 / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q0KBP1, acetyl-CoA C-acyltransferase, acetyl-CoA C-acetyltransferase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 673 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Beta-ketothiolase BktB / Acetyl-CoA acetyltransferase / Acetyl-CoA acyltransferase

Mass: 43124.113 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) (bacteria)
Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / Gene: bktB, H16_A1445 / Plasmid: pET28b(+) / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0KBP1, acetyl-CoA C-acyltransferase, acetyl-CoA C-acetyltransferase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 673 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.53 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 22% PEG 4000, 100 mM HEPES 7.0, 12% glycerol

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.2 / Wavelength: 0.9795 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2012

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Redundancy: 1.7 % / Number: 644834 / R_merge(I) obs: 0.056 / Χ²: 1.22 / D res high: 2 Å / D res low: 50 Å / Num. obs: 369679 / % possible obs: 94

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	ID	R_merge(I) obs	Chi squared	Redundancy
5.43	50	1	0.03	0.418	1.8
4.31	5.43	1	0.036	0.652	1.7
3.76	4.31	1	0.042	0.838	1.8
3.42	3.76	1	0.048	1.004	1.8
3.17	3.42	1	0.053	1.058	1.8
2.99	3.17	1	0.057	1.052	1.8
2.84	2.99	1	0.066	1.131	1.8
2.71	2.84	1	0.074	1.199	1.7
2.61	2.71	1	0.087	1.269	1.8
2.52	2.61	1	0.104	1.269	1.7
2.44	2.52	1	0.13	1.465	1.7
2.37	2.44	1	0.141	1.403	1.7
2.31	2.37	1	0.167	1.428	1.7
2.25	2.31	1	0.202	1.613	1.7
2.2	2.25	1	0.225	1.493	1.7
2.15	2.2	1	0.259	1.495	1.7
2.11	2.15	1	0.282	1.499	1.7
2.07	2.11	1	0.31	1.457	1.7
2.03	2.07	1	0.361	1.462	1.7
2	2.03	1	0.444	1.455	1.7

Reflection

Resolution: 2→50 Å / Num. obs: 394877 / % possible obs: 94 % / Redundancy: 1.7 % / R_merge(I) obs: 0.056 / Χ²: 1.222 / Net I/av σ(I): 10.402 / Net I/σ(I): 13.4 / Num. measured all: 644834

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
2-2.03	1.7	0.444	18535	1.455	93.7
2.03-2.07	1.7	0.361	18313	1.462	93.8
2.07-2.11	1.7	0.31	18499	1.457	93.8
2.11-2.15	1.7	0.282	18480	1.499	93.6
2.15-2.2	1.7	0.259	18293	1.495	93.7
2.2-2.25	1.7	0.225	18377	1.493	93.5
2.25-2.31	1.7	0.202	18277	1.613	92.9
2.31-2.37	1.7	0.167	18315	1.428	93.2
2.37-2.44	1.7	0.141	18420	1.403	93.6
2.44-2.52	1.7	0.13	18208	1.465	93
2.52-2.61	1.7	0.104	18357	1.269	93.4
2.61-2.71	1.8	0.087	18423	1.269	93.5
2.71-2.84	1.7	0.074	18372	1.199	93.5
2.84-2.99	1.8	0.066	18387	1.131	93.7
2.99-3.17	1.8	0.057	18525	1.052	94
3.17-3.42	1.8	0.053	18686	1.058	95.1
3.42-3.76	1.8	0.048	18917	1.004	96
3.76-4.31	1.8	0.042	18771	0.838	96
4.31-5.43	1.7	0.036	18608	0.652	94.5
5.43-50	1.8	0.03	18916	0.418	96.3

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0107	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PDB_EXTRACT	3.15	data extraction
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4DD5

4dd5

Resolution: 2.01→41.79 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.943 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20831	18732	5.1 %	RANDOM
R_work	0.1761	-	-	-
obs	0.17774	350785	92.92 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 39.135 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.1 Å²	-4.49 Å²	-4.98 Å²
2-	-	-7.33 Å²	4.65 Å²
3-	-	-	3.23 Å²

Refinement step

Cycle: LAST / Resolution: 2.01→41.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	45347	0	0	673	46020

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.019	46017
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	45376
X-RAY DIFFRACTION	r_angle_refined_deg	0.686	1.961	62394
X-RAY DIFFRACTION	r_angle_other_deg	3.594	3	103747
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.751	5	6214
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.92	23.555	1831
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.543	15	7373
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.409	15	390
X-RAY DIFFRACTION	r_chiral_restr	0.053	0.2	7335
X-RAY DIFFRACTION	r_gen_planes_refined	0.015	0.021	53374
X-RAY DIFFRACTION	r_gen_planes_other	0.028	0.02	10032
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	6.438	3.586	24937
X-RAY DIFFRACTION	r_mcbond_other	6.438	3.586	24936
X-RAY DIFFRACTION	r_mcangle_it	7.936	5.367	31124
X-RAY DIFFRACTION	r_mcangle_other	7.936	5.367	31125
X-RAY DIFFRACTION	r_scbond_it	7.329	4.126	21080
X-RAY DIFFRACTION	r_scbond_other	7.328	4.126	21081
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	9.761	5.989	31271
X-RAY DIFFRACTION	r_long_range_B_refined	11.498	29.014	49931
X-RAY DIFFRACTION	r_long_range_B_other	11.5	29.014	49880
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	46998	0.09
1	2	B	46998	0.09
2	1	A	46288	0.1
2	2	C	46288	0.1
3	1	A	47156	0.09
3	2	D	47156	0.09
4	1	A	46306	0.09
4	2	E	46306	0.09
5	1	A	46158	0.1
5	2	F	46158	0.1
6	1	A	46704	0.1
6	2	G	46704	0.1
7	1	A	46560	0.1
7	2	H	46560	0.1
8	1	A	46560	0.1
8	2	I	46560	0.1
9	1	A	46746	0.1
9	2	J	46746	0.1
10	1	A	46966	0.09
10	2	K	46966	0.09
11	1	A	46452	0.1
11	2	L	46452	0.1
12	1	A	46748	0.1
12	2	M	46748	0.1
13	1	A	46538	0.1
13	2	N	46538	0.1
14	1	A	47090	0.08
14	2	O	47090	0.08
15	1	A	46310	0.1
15	2	P	46310	0.1
16	1	B	47046	0.09
16	2	C	47046	0.09
17	1	B	47124	0.09
17	2	D	47124	0.09
18	1	B	46656	0.09
18	2	E	46656	0.09
19	1	B	46814	0.09
19	2	F	46814	0.09
20	1	B	47226	0.08
20	2	G	47226	0.08
21	1	B	47318	0.09
21	2	H	47318	0.09
22	1	B	47156	0.09
22	2	I	47156	0.09
23	1	B	46708	0.1
23	2	J	46708	0.1
24	1	B	47284	0.09
24	2	K	47284	0.09
25	1	B	46974	0.08
25	2	L	46974	0.08
26	1	B	47500	0.08
26	2	M	47500	0.08
27	1	B	46894	0.1
27	2	N	46894	0.1
28	1	B	47238	0.08
28	2	O	47238	0.08
29	1	B	46780	0.09
29	2	P	46780	0.09
30	1	C	47018	0.08
30	2	D	47018	0.08
31	1	C	46234	0.1
31	2	E	46234	0.1
32	1	C	46628	0.09
32	2	F	46628	0.09
33	1	C	46744	0.08
33	2	G	46744	0.08
34	1	C	46654	0.09
34	2	H	46654	0.09
35	1	C	46984	0.08
35	2	I	46984	0.08
36	1	C	46434	0.1
36	2	J	46434	0.1
37	1	C	46762	0.09
37	2	K	46762	0.09
38	1	C	47040	0.09
38	2	L	47040	0.09
39	1	C	47348	0.09
39	2	M	47348	0.09
40	1	C	46656	0.1
40	2	N	46656	0.1
41	1	C	46922	0.08
41	2	O	46922	0.08
42	1	C	46932	0.08
42	2	P	46932	0.08
43	1	D	46578	0.09
43	2	E	46578	0.09
44	1	D	46692	0.09
44	2	F	46692	0.09
45	1	D	47110	0.08
45	2	G	47110	0.08
46	1	D	47176	0.09
46	2	H	47176	0.09
47	1	D	46880	0.09
47	2	I	46880	0.09
48	1	D	47316	0.08
48	2	J	47316	0.08
49	1	D	47406	0.08
49	2	K	47406	0.08
50	1	D	46774	0.09
50	2	L	46774	0.09
51	1	D	47118	0.09
51	2	M	47118	0.09
52	1	D	47360	0.09
52	2	N	47360	0.09
53	1	D	47658	0.07
53	2	O	47658	0.07
54	1	D	46670	0.09
54	2	P	46670	0.09
55	1	E	46007	0.1
55	2	F	46007	0.1
56	1	E	46570	0.09
56	2	G	46570	0.09
57	1	E	46674	0.09
57	2	H	46674	0.09
58	1	E	46236	0.1
58	2	I	46236	0.1
59	1	E	46412	0.09
59	2	J	46412	0.09
60	1	E	46560	0.09
60	2	K	46560	0.09
61	1	E	46016	0.09
61	2	L	46016	0.09
62	1	E	46849	0.09
62	2	M	46849	0.09
63	1	E	46524	0.09
63	2	N	46524	0.09
64	1	E	47010	0.08
64	2	O	47010	0.08
65	1	E	46114	0.1
65	2	P	46114	0.1
66	1	F	46566	0.08
66	2	G	46566	0.08
67	1	F	46380	0.1
67	2	H	46380	0.1
68	1	F	46744	0.09
68	2	I	46744	0.09
69	1	F	46340	0.1
69	2	J	46340	0.1
70	1	F	46452	0.1
70	2	K	46452	0.1
71	1	F	46672	0.09
71	2	L	46672	0.09
72	1	F	46878	0.09
72	2	M	46878	0.09
73	1	F	46472	0.1
73	2	N	46472	0.1
74	1	F	46852	0.09
74	2	O	46852	0.09
75	1	F	46708	0.09
75	2	P	46708	0.09
76	1	G	46964	0.09
76	2	H	46964	0.09
77	1	G	46886	0.08
77	2	I	46886	0.08
78	1	G	46962	0.09
78	2	J	46962	0.09
79	1	G	47100	0.08
79	2	K	47100	0.08
80	1	G	47000	0.08
80	2	L	47000	0.08
81	1	G	47348	0.08
81	2	M	47348	0.08
82	1	G	46938	0.09
82	2	N	46938	0.09
83	1	G	47152	0.08
83	2	O	47152	0.08
84	1	G	46912	0.08
84	2	P	46912	0.08
85	1	H	46960	0.09
85	2	I	46960	0.09
86	1	H	46764	0.1
86	2	J	46764	0.1
87	1	H	47456	0.08
87	2	K	47456	0.08
88	1	H	46672	0.09
88	2	L	46672	0.09
89	1	H	47130	0.09
89	2	M	47130	0.09
90	1	H	47124	0.1
90	2	N	47124	0.1
91	1	H	47316	0.08
91	2	O	47316	0.08
92	1	H	46652	0.09
92	2	P	46652	0.09
93	1	I	46288	0.1
93	2	J	46288	0.1
94	1	I	47092	0.09
94	2	K	47092	0.09
95	1	I	46852	0.09
95	2	L	46852	0.09
96	1	I	47074	0.09
96	2	M	47074	0.09
97	1	I	46508	0.1
97	2	N	46508	0.1
98	1	I	47002	0.08
98	2	O	47002	0.08
99	1	I	46734	0.08
99	2	P	46734	0.08
100	1	J	47306	0.09
100	2	K	47306	0.09
101	1	J	46544	0.1
101	2	L	46544	0.1
102	1	J	46902	0.09
102	2	M	46902	0.09
103	1	J	46938	0.09
103	2	N	46938	0.09
104	1	J	47224	0.08
104	2	O	47224	0.08
105	1	J	46670	0.1
105	2	P	46670	0.1
106	1	K	46928	0.09
106	2	L	46928	0.09
107	1	K	47304	0.09
107	2	M	47304	0.09
108	1	K	46982	0.1
108	2	N	46982	0.1
109	1	K	47392	0.08
109	2	O	47392	0.08
110	1	K	46800	0.09
110	2	P	46800	0.09
111	1	L	47468	0.08
111	2	M	47468	0.08
112	1	L	46510	0.1
112	2	N	46510	0.1
113	1	L	46900	0.09
113	2	O	46900	0.09
114	1	L	46948	0.09
114	2	P	46948	0.09
115	1	M	47206	0.09
115	2	N	47206	0.09
116	1	M	47454	0.09
116	2	O	47454	0.09
117	1	M	47468	0.08
117	2	P	47468	0.08
118	1	N	47408	0.08
118	2	O	47408	0.08
119	1	N	46670	0.09
119	2	P	46670	0.09
120	1	O	46976	0.08
120	2	P	46976	0.08

LS refinement shell

Resolution: 2.007→2.059 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.283	1174	-
R_work	0.233	21982	-
obs	-	-	78.67 %

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi