PDB-8e7p: Staphylococcus aureus ClpP in complex with compound 3421

ID or keywords:

Entry

Database: PDB / ID: 8e7p

Title

Staphylococcus aureus ClpP in complex with compound 3421

Components

ATP-dependent Clp protease proteolytic subunit

Keywords

CYTOSOLIC PROTEIN / ClpP / hydrolase

Function / homology

Function and homology information

endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / cytoplasm
Similarity search - Function

Biological species

Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.68 Å

Authors

Lee, R.E. / Griffith, E.C.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Development of a high throughput and site specific, fluorescent polarization assay to screen for activators of Caseinolytic Protease P leads to the discovery of synthetically tractable new activator class
Authors: Singh, A.C. / Zhao, Y. / Griffith, E.C. / Tangallapally, R. / Jarret, M.W. / Lee, R.E.

History

Deposition	Aug 24, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 5, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 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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Download

PDBx/mmCIF format	8e7p.cif.gz	554.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8e7p.ent.gz	457.1 KB	Display	PDB format
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Validation report

Summary document	8e7p_validation.pdf.gz	4.8 MB	Display	wwPDB validaton report
Full document	8e7p_full_validation.pdf.gz	4.9 MB	Display
Data in XML	8e7p_validation.xml.gz	119 KB	Display
Data in CIF	8e7p_validation.cif.gz	160.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e7/8e7p ftp://data.pdbj.org/pub/pdb/validation_reports/e7/8e7p	HTTPS FTP

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Related structure data

Related structure data	8e71C 8ef8C 3stlS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	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: ATP-dependent Clp protease proteolytic subunit

B: ATP-dependent Clp protease proteolytic subunit

C: ATP-dependent Clp protease proteolytic subunit

D: ATP-dependent Clp protease proteolytic subunit

E: ATP-dependent Clp protease proteolytic subunit

F: ATP-dependent Clp protease proteolytic subunit

G: ATP-dependent Clp protease proteolytic subunit

I: ATP-dependent Clp protease proteolytic subunit

K: ATP-dependent Clp protease proteolytic subunit

L: ATP-dependent Clp protease proteolytic subunit

M: ATP-dependent Clp protease proteolytic subunit

N: ATP-dependent Clp protease proteolytic subunit

S: ATP-dependent Clp protease proteolytic subunit

T: ATP-dependent Clp protease proteolytic subunit

hetero molecules

325 kDa, 14 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)	94.073, 126.143, 145.475
Angle α, β, γ (deg.)	90.000, 93.880, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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	ILE	ILE	PRO	PRO	A	A	4 - 192	4 - 192
2	1	ILE	ILE	PRO	PRO	B	B	4 - 192	4 - 192
1	2	ILE	ILE	PRO	PRO	A	A	4 - 192	4 - 192
2	2	ILE	ILE	PRO	PRO	C	C	4 - 192	4 - 192
1	3	ILE	ILE	PRO	PRO	A	A	4 - 192	4 - 192
2	3	ILE	ILE	PRO	PRO	D	D	4 - 192	4 - 192
1	4	ILE	ILE	PRO	PRO	A	A	4 - 192	4 - 192
2	4	ILE	ILE	PRO	PRO	E	E	4 - 192	4 - 192
1	5	ILE	ILE	PRO	PRO	A	A	4 - 192	4 - 192
2	5	ILE	ILE	PRO	PRO	F	F	4 - 192	4 - 192
1	6	ILE	ILE	VAL	VAL	A	A	4 - 191	4 - 191
2	6	ILE	ILE	VAL	VAL	G	G	4 - 191	4 - 191
1	7	ILE	ILE	VAL	VAL	A	A	4 - 191	4 - 191
2	7	ILE	ILE	VAL	VAL	I	H	4 - 191	4 - 191
1	8	ILE	ILE	PRO	PRO	A	A	4 - 192	4 - 192
2	8	ILE	ILE	PRO	PRO	K	I	4 - 192	4 - 192
1	9	ILE	ILE	PRO	PRO	A	A	4 - 192	4 - 192
2	9	ILE	ILE	PRO	PRO	L	J	4 - 192	4 - 192
1	10	ILE	ILE	PRO	PRO	A	A	4 - 192	4 - 192
2	10	ILE	ILE	PRO	PRO	M	K	4 - 192	4 - 192
1	11	ILE	ILE	PRO	PRO	A	A	4 - 192	4 - 192
2	11	ILE	ILE	PRO	PRO	N	L	4 - 192	4 - 192
1	12	ILE	ILE	PRO	PRO	A	A	4 - 192	4 - 192
2	12	ILE	ILE	PRO	PRO	S	M	4 - 192	4 - 192
1	13	ILE	ILE	PRO	PRO	A	A	4 - 192	4 - 192
2	13	ILE	ILE	PRO	PRO	T	N	4 - 192	4 - 192
1	14	ILE	ILE	PRO	PRO	B	B	4 - 192	4 - 192
2	14	ILE	ILE	PRO	PRO	C	C	4 - 192	4 - 192
1	15	ILE	ILE	PRO	PRO	B	B	4 - 192	4 - 192
2	15	ILE	ILE	PRO	PRO	D	D	4 - 192	4 - 192
1	16	ILE	ILE	PRO	PRO	B	B	4 - 192	4 - 192
2	16	ILE	ILE	PRO	PRO	E	E	4 - 192	4 - 192
1	17	ILE	ILE	PRO	PRO	B	B	4 - 192	4 - 192
2	17	ILE	ILE	PRO	PRO	F	F	4 - 192	4 - 192
1	18	ILE	ILE	VAL	VAL	B	B	4 - 191	4 - 191
2	18	ILE	ILE	VAL	VAL	G	G	4 - 191	4 - 191
1	19	ILE	ILE	VAL	VAL	B	B	4 - 191	4 - 191
2	19	ILE	ILE	VAL	VAL	I	H	4 - 191	4 - 191
1	20	ILE	ILE	PRO	PRO	B	B	4 - 192	4 - 192
2	20	ILE	ILE	PRO	PRO	K	I	4 - 192	4 - 192
1	21	ILE	ILE	PRO	PRO	B	B	4 - 192	4 - 192
2	21	ILE	ILE	PRO	PRO	L	J	4 - 192	4 - 192
1	22	ILE	ILE	PRO	PRO	B	B	4 - 192	4 - 192
2	22	ILE	ILE	PRO	PRO	M	K	4 - 192	4 - 192
1	23	ILE	ILE	PRO	PRO	B	B	4 - 192	4 - 192
2	23	ILE	ILE	PRO	PRO	N	L	4 - 192	4 - 192
1	24	ILE	ILE	PRO	PRO	B	B	4 - 192	4 - 192
2	24	ILE	ILE	PRO	PRO	S	M	4 - 192	4 - 192
1	25	ILE	ILE	PRO	PRO	B	B	4 - 192	4 - 192
2	25	ILE	ILE	PRO	PRO	T	N	4 - 192	4 - 192
1	26	LEU	LEU	GLU	GLU	C	C	3 - 193	3 - 193
2	26	LEU	LEU	GLU	GLU	D	D	3 - 193	3 - 193
1	27	ILE	ILE	PRO	PRO	C	C	4 - 192	4 - 192
2	27	ILE	ILE	PRO	PRO	E	E	4 - 192	4 - 192
1	28	ILE	ILE	VAL	VAL	C	C	8 - 191	8 - 191
2	28	ILE	ILE	VAL	VAL	F	F	4 - 191	4 - 191
1	29	ILE	ILE	GLU	GLU	C	C	4 - 193	4 - 193
2	29	ILE	ILE	GLU	GLU	G	G	4 - 193	4 - 193
1	30	ILE	ILE	GLU	GLU	C	C	4 - 193	4 - 193
2	30	ILE	ILE	GLU	GLU	I	H	4 - 193	4 - 193
1	31	ILE	ILE	PRO	PRO	C	C	4 - 192	4 - 192
2	31	ILE	ILE	PRO	PRO	K	I	4 - 192	4 - 192
1	32	ILE	ILE	PRO	PRO	C	C	4 - 192	4 - 192
2	32	ILE	ILE	PRO	PRO	L	J	4 - 192	4 - 192
1	33	LEU	LEU	PRO	PRO	C	C	3 - 192	3 - 192
2	33	LEU	LEU	PRO	PRO	M	K	3 - 192	3 - 192
1	34	ILE	ILE	PRO	PRO	C	C	4 - 192	4 - 192
2	34	ILE	ILE	PRO	PRO	N	L	4 - 192	4 - 192
1	35	ILE	ILE	PRO	PRO	C	C	4 - 192	4 - 192
2	35	ILE	ILE	PRO	PRO	S	M	4 - 192	4 - 192
1	36	ILE	ILE	PRO	PRO	C	C	4 - 192	4 - 192
2	36	ILE	ILE	PRO	PRO	T	N	4 - 192	4 - 192
1	37	ILE	ILE	GLU	GLU	D	D	4 - 193	4 - 193
2	37	ILE	ILE	GLU	GLU	E	E	4 - 193	4 - 193
1	38	ARG	ARG	VAL	VAL	D	D	16 - 191	16 - 191
2	38	PRO	PRO	VAL	VAL	F	F	5 - 191	5 - 191
1	39	ILE	ILE	GLU	GLU	D	D	4 - 193	4 - 193
2	39	ILE	ILE	GLU	GLU	G	G	4 - 193	4 - 193
1	40	ILE	ILE	GLU	GLU	D	D	4 - 193	4 - 193
2	40	ILE	ILE	GLU	GLU	I	H	4 - 193	4 - 193
1	41	ILE	ILE	PRO	PRO	D	D	4 - 192	4 - 192
2	41	ILE	ILE	PRO	PRO	K	I	4 - 192	4 - 192
1	42	ILE	ILE	GLU	GLU	D	D	4 - 193	4 - 193
2	42	ILE	ILE	GLU	GLU	L	J	4 - 193	4 - 193
1	43	LEU	LEU	PRO	PRO	D	D	3 - 192	3 - 192
2	43	LEU	LEU	PRO	PRO	M	K	3 - 192	3 - 192
1	44	ILE	ILE	PRO	PRO	D	D	4 - 192	4 - 192
2	44	ILE	ILE	PRO	PRO	N	L	4 - 192	4 - 192
1	45	ILE	ILE	PRO	PRO	D	D	4 - 192	4 - 192
2	45	ILE	ILE	PRO	PRO	S	M	4 - 192	4 - 192
1	46	ILE	ILE	PRO	PRO	D	D	4 - 192	4 - 192
2	46	ILE	ILE	PRO	PRO	T	N	4 - 192	4 - 192
1	47	ILE	ILE	VAL	VAL	E	E	8 - 191	8 - 191
2	47	ILE	ILE	VAL	VAL	F	F	4 - 191	4 - 191
1	48	ILE	ILE	GLU	GLU	E	E	4 - 193	4 - 193
2	48	ILE	ILE	GLU	GLU	G	G	4 - 193	4 - 193
1	49	ILE	ILE	GLU	GLU	E	E	4 - 193	4 - 193
2	49	ILE	ILE	GLU	GLU	I	H	4 - 193	4 - 193
1	50	ILE	ILE	PRO	PRO	E	E	4 - 192	4 - 192
2	50	ILE	ILE	PRO	PRO	K	I	4 - 192	4 - 192
1	51	ILE	ILE	GLU	GLU	E	E	4 - 193	4 - 193
2	51	ILE	ILE	GLU	GLU	L	J	4 - 193	4 - 193
1	52	ILE	ILE	VAL	VAL	E	E	4 - 191	4 - 191
2	52	ILE	ILE	VAL	VAL	M	K	4 - 191	4 - 191
1	53	ILE	ILE	PRO	PRO	E	E	4 - 192	4 - 192
2	53	ILE	ILE	PRO	PRO	N	L	4 - 192	4 - 192
1	54	ILE	ILE	PRO	PRO	E	E	4 - 192	4 - 192
2	54	ILE	ILE	PRO	PRO	S	M	4 - 192	4 - 192
1	55	ILE	ILE	PRO	PRO	E	E	4 - 192	4 - 192
2	55	ILE	ILE	PRO	PRO	T	N	4 - 192	4 - 192
1	56	ILE	ILE	PRO	PRO	F	F	4 - 192	4 - 192
2	56	ILE	ILE	PRO	PRO	G	G	4 - 192	4 - 192
1	57	ILE	ILE	PRO	PRO	F	F	4 - 192	4 - 192
2	57	ILE	ILE	PRO	PRO	I	H	4 - 192	4 - 192
1	58	ILE	ILE	PRO	PRO	F	F	4 - 192	4 - 192
2	58	ILE	ILE	PRO	PRO	K	I	4 - 192	4 - 192
1	59	ILE	ILE	VAL	VAL	F	F	4 - 191	4 - 191
2	59	ILE	ILE	VAL	VAL	L	J	8 - 191	8 - 191
1	60	PRO	PRO	VAL	VAL	F	F	5 - 191	5 - 191
2	60	ARG	ARG	VAL	VAL	M	K	16 - 191	16 - 191
1	61	ILE	ILE	PRO	PRO	F	F	4 - 192	4 - 192
2	61	ILE	ILE	PRO	PRO	N	L	4 - 192	4 - 192
1	62	ILE	ILE	PRO	PRO	F	F	4 - 192	4 - 192
2	62	ILE	ILE	PRO	PRO	S	M	4 - 192	4 - 192
1	63	ILE	ILE	PRO	PRO	F	F	4 - 192	4 - 192
2	63	ILE	ILE	PRO	PRO	T	N	4 - 192	4 - 192
1	64	ILE	ILE	GLU	GLU	G	G	4 - 193	4 - 193
2	64	ILE	ILE	GLU	GLU	I	H	4 - 193	4 - 193
1	65	ILE	ILE	VAL	VAL	G	G	4 - 191	4 - 191
2	65	ILE	ILE	VAL	VAL	K	I	4 - 191	4 - 191
1	66	ILE	ILE	GLU	GLU	G	G	4 - 193	4 - 193
2	66	ILE	ILE	GLU	GLU	L	J	4 - 193	4 - 193
1	67	ILE	ILE	PRO	PRO	G	G	4 - 192	4 - 192
2	67	ILE	ILE	PRO	PRO	M	K	4 - 192	4 - 192
1	68	ILE	ILE	PRO	PRO	G	G	4 - 192	4 - 192
2	68	ILE	ILE	PRO	PRO	N	L	4 - 192	4 - 192
1	69	ILE	ILE	PRO	PRO	G	G	4 - 192	4 - 192
2	69	ILE	ILE	PRO	PRO	S	M	4 - 192	4 - 192
1	70	ILE	ILE	PRO	PRO	G	G	4 - 192	4 - 192
2	70	ILE	ILE	PRO	PRO	T	N	4 - 192	4 - 192
1	71	ILE	ILE	VAL	VAL	I	H	4 - 191	4 - 191
2	71	ILE	ILE	VAL	VAL	K	I	4 - 191	4 - 191
1	72	ILE	ILE	GLU	GLU	I	H	4 - 193	4 - 193
2	72	ILE	ILE	GLU	GLU	L	J	4 - 193	4 - 193
1	73	ILE	ILE	PRO	PRO	I	H	4 - 192	4 - 192
2	73	ILE	ILE	PRO	PRO	M	K	4 - 192	4 - 192
1	74	ILE	ILE	PRO	PRO	I	H	4 - 192	4 - 192
2	74	ILE	ILE	PRO	PRO	N	L	4 - 192	4 - 192
1	75	ILE	ILE	PRO	PRO	I	H	4 - 192	4 - 192
2	75	ILE	ILE	PRO	PRO	S	M	4 - 192	4 - 192
1	76	ILE	ILE	PRO	PRO	I	H	4 - 192	4 - 192
2	76	ILE	ILE	PRO	PRO	T	N	4 - 192	4 - 192
1	77	ILE	ILE	PRO	PRO	K	I	4 - 192	4 - 192
2	77	ILE	ILE	PRO	PRO	L	J	4 - 192	4 - 192
1	78	ILE	ILE	PRO	PRO	K	I	4 - 192	4 - 192
2	78	ILE	ILE	PRO	PRO	M	K	4 - 192	4 - 192
1	79	ILE	ILE	PRO	PRO	K	I	4 - 192	4 - 192
2	79	ILE	ILE	PRO	PRO	N	L	4 - 192	4 - 192
1	80	ILE	ILE	PRO	PRO	K	I	4 - 192	4 - 192
2	80	ILE	ILE	PRO	PRO	S	M	4 - 192	4 - 192
1	81	ILE	ILE	PRO	PRO	K	I	4 - 192	4 - 192
2	81	ILE	ILE	PRO	PRO	T	N	4 - 192	4 - 192
1	82	ILE	ILE	VAL	VAL	L	J	4 - 191	4 - 191
2	82	ILE	ILE	VAL	VAL	M	K	4 - 191	4 - 191
1	83	ILE	ILE	PRO	PRO	L	J	4 - 192	4 - 192
2	83	ILE	ILE	PRO	PRO	N	L	4 - 192	4 - 192
1	84	ILE	ILE	PRO	PRO	L	J	4 - 192	4 - 192
2	84	ILE	ILE	PRO	PRO	S	M	4 - 192	4 - 192
1	85	ILE	ILE	PRO	PRO	L	J	4 - 192	4 - 192
2	85	ILE	ILE	PRO	PRO	T	N	4 - 192	4 - 192
1	86	ILE	ILE	PRO	PRO	M	K	4 - 192	4 - 192
2	86	ILE	ILE	PRO	PRO	N	L	4 - 192	4 - 192
1	87	ILE	ILE	PRO	PRO	M	K	4 - 192	4 - 192
2	87	ILE	ILE	PRO	PRO	S	M	4 - 192	4 - 192
1	88	ILE	ILE	PRO	PRO	M	K	4 - 192	4 - 192
2	88	ILE	ILE	PRO	PRO	T	N	4 - 192	4 - 192
1	89	ILE	ILE	PRO	PRO	N	L	4 - 192	4 - 192
2	89	ILE	ILE	PRO	PRO	S	M	4 - 192	4 - 192
1	90	ILE	ILE	PRO	PRO	N	L	4 - 192	4 - 192
2	90	ILE	ILE	PRO	PRO	T	N	4 - 192	4 - 192
1	91	ILE	ILE	PRO	PRO	S	M	4 - 192	4 - 192
2	91	ILE	ILE	PRO	PRO	T	N	4 - 192	4 - 192

NCS ensembles :

#1: Protein	ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp Mass: 22607.686 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325 / PS 47 / Gene: clpP, SAOUHSC_00790 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G036, endopeptidase Clp
#2: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#3: Chemical	ChemComp-UTC / (5R,6S,9aS)-N-benzyl-6-[(4-hydroxyphenyl)methyl]-8-[(naphthalen-1-yl)methyl]-4,7-dioxohexahydro-2H-pyrazino[1,2-a]pyrimidine-1(6H)-carboxamide Mass: 548.632 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₃₃H₃₂N₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1994 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.79 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion / pH: 4.5 / Details: 0.1 M NaOAc pH 4.5, 18-35% MPD, 0.02M CaCl2

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 22, 2016

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.68→50 Å / Num. obs: 380426 / % possible obs: 99.9 % / Redundancy: 3.9 % / R_merge(I) obs: 0.08 / R_pim(I) all: 0.046 / R_rim(I) all: 0.092 / Χ²: 1.181 / Net I/σ(I): 8.4 / Num. measured all: 1473470

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.68-1.71	3.7	0.494	18996	0.771	0.297	0.577	0.643	99.9
1.71-1.74	3.7	0.437	18951	0.809	0.262	0.51	0.693	100
1.74-1.77	3.7	0.373	18985	0.852	0.224	0.436	0.747	100
1.77-1.81	3.8	0.328	18964	0.883	0.196	0.383	0.812	100
1.81-1.85	3.8	0.284	18974	0.909	0.17	0.331	0.896	100
1.85-1.89	3.8	0.244	18944	0.928	0.146	0.285	0.972	99.9
1.89-1.94	3.8	0.216	18990	0.939	0.129	0.252	1.032	99.9
1.94-1.99	3.9	0.187	18967	0.957	0.11	0.217	1.132	99.8
1.99-2.05	3.9	0.164	18917	0.961	0.096	0.191	1.186	99.9
2.05-2.12	3.9	0.148	19038	0.969	0.086	0.171	1.252	100
2.12-2.19	3.9	0.134	18985	0.973	0.078	0.156	1.381	100
2.19-2.28	4	0.123	19019	0.975	0.072	0.143	1.414	100
2.28-2.38	4	0.112	18988	0.979	0.065	0.13	1.412	100
2.38-2.51	4	0.104	19012	0.982	0.06	0.121	1.413	100
2.51-2.67	4	0.097	19068	0.983	0.056	0.113	1.465	100
2.67-2.87	4	0.096	19049	0.984	0.055	0.111	1.647	100
2.87-3.16	4	0.083	19079	0.988	0.048	0.096	1.605	100
3.16-3.62	4	0.068	19092	0.991	0.039	0.079	1.437	100
3.62-4.56	4	0.056	19117	0.994	0.032	0.065	1.243	100
4.56-50	3.9	0.05	19291	0.995	0.029	0.058	1.031	99.5

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	4.66 Å	49.85 Å
Translation	4.66 Å	49.85 Å

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
HKL-2000		data scaling
PHASER	2.8.3	phasing
PDB_EXTRACT	3.27	data extraction
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3STL

3stl

Resolution: 1.68→49.9 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.959 / WR_factor R_free: 0.1911 / WR_factor R_work: 0.1746 / FOM work R set: 0.8792 / SU B: 1.696 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0825 / SU R_free: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1816	18992	5 %	RANDOM
R_work	0.166	-	-	-
obs	0.1668	361397	99.65 %	-

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 max: 100.55 Å² / B_iso mean: 24.798 Å² / B_iso min: 12.41 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.06 Å²	0 Å²	-0.34 Å²
2-	-	-0.31 Å²	-0 Å²
3-	-	-	-0.69 Å²

Refinement step

Cycle: final / Resolution: 1.68→49.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19413	0	653	1994	22060
B_iso mean	-	-	39.61	36.64	-
Num. residues	-	-	-	-	2537

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	21078
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	20471
X-RAY DIFFRACTION	r_angle_refined_deg	1.749	1.678	28615
X-RAY DIFFRACTION	r_angle_other_deg	1.53	1.615	47065
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.952	5	2649
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.044	23.337	1031
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.677	15	3696
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.837	15	123
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	2892
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	24112
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4680

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	5877	0.05
1	2	B	5877	0.05
2	1	A	5817	0.06
2	2	C	5817	0.06
3	1	A	5811	0.07
3	2	D	5811	0.07
4	1	A	5821	0.07
4	2	E	5821	0.07
5	1	A	5775	0.06
5	2	F	5775	0.06
6	1	A	5792	0.06
6	2	G	5792	0.06
7	1	A	5815	0.06
7	2	I	5815	0.06
8	1	A	5849	0.06
8	2	K	5849	0.06
9	1	A	5858	0.05
9	2	L	5858	0.05
10	1	A	5850	0.06
10	2	M	5850	0.06
11	1	A	5835	0.07
11	2	N	5835	0.07
12	1	A	5842	0.05
12	2	S	5842	0.05
13	1	A	5810	0.06
13	2	T	5810	0.06
14	1	B	5840	0.05
14	2	C	5840	0.05
15	1	B	5840	0.06
15	2	D	5840	0.06
16	1	B	5856	0.06
16	2	E	5856	0.06
17	1	B	5798	0.06
17	2	F	5798	0.06
18	1	B	5844	0.04
18	2	G	5844	0.04
19	1	B	5875	0.04
19	2	I	5875	0.04
20	1	B	5877	0.05
20	2	K	5877	0.05
21	1	B	5879	0.05
21	2	L	5879	0.05
22	1	B	5872	0.06
22	2	M	5872	0.06
23	1	B	5855	0.06
23	2	N	5855	0.06
24	1	B	5892	0.04
24	2	S	5892	0.04
25	1	B	5835	0.05
25	2	T	5835	0.05
26	1	C	5816	0.08
26	2	D	5816	0.08
27	1	C	5820	0.07
27	2	E	5820	0.07
28	1	C	5688	0.07
28	2	F	5688	0.07
29	1	C	5842	0.05
29	2	G	5842	0.05
30	1	C	5823	0.06
30	2	I	5823	0.06
31	1	C	5825	0.07
31	2	K	5825	0.07
32	1	C	5865	0.06
32	2	L	5865	0.06
33	1	C	5878	0.06
33	2	M	5878	0.06
34	1	C	5780	0.07
34	2	N	5780	0.07
35	1	C	5798	0.06
35	2	S	5798	0.06
36	1	C	5786	0.06
36	2	T	5786	0.06
37	1	D	5780	0.07
37	2	E	5780	0.07
38	1	D	5626	0.06
38	2	F	5626	0.06
39	1	D	5741	0.07
39	2	G	5741	0.07
40	1	D	5804	0.06
40	2	I	5804	0.06
41	1	D	5732	0.08
41	2	K	5732	0.08
42	1	D	5826	0.07
42	2	L	5826	0.07
43	1	D	5832	0.06
43	2	M	5832	0.06
44	1	D	5772	0.07
44	2	N	5772	0.07
45	1	D	5778	0.07
45	2	S	5778	0.07
46	1	D	5722	0.06
46	2	T	5722	0.06
47	1	E	5635	0.06
47	2	F	5635	0.06
48	1	E	5767	0.07
48	2	G	5767	0.07
49	1	E	5819	0.05
49	2	I	5819	0.05
50	1	E	5784	0.07
50	2	K	5784	0.07
51	1	E	5853	0.07
51	2	L	5853	0.07
52	1	E	5820	0.05
52	2	M	5820	0.05
53	1	E	5771	0.06
53	2	N	5771	0.06
54	1	E	5763	0.07
54	2	S	5763	0.07
55	1	E	5756	0.06
55	2	T	5756	0.06
56	1	F	5825	0.06
56	2	G	5825	0.06
57	1	F	5848	0.04
57	2	I	5848	0.04
58	1	F	5846	0.06
58	2	K	5846	0.06
59	1	F	5772	0.07
59	2	L	5772	0.07
60	1	F	5766	0.05
60	2	M	5766	0.05
61	1	F	5872	0.05
61	2	N	5872	0.05
62	1	F	5869	0.05
62	2	S	5869	0.05
63	1	F	5837	0.05
63	2	T	5837	0.05
64	1	G	5966	0.06
64	2	I	5966	0.06
65	1	G	5887	0.06
65	2	K	5887	0.06
66	1	G	5958	0.06
66	2	L	5958	0.06
67	1	G	5940	0.06
67	2	M	5940	0.06
68	1	G	5909	0.06
68	2	N	5909	0.06
69	1	G	5937	0.05
69	2	S	5937	0.05
70	1	G	5907	0.06
70	2	T	5907	0.06
71	1	I	5787	0.06
71	2	K	5787	0.06
72	1	I	5836	0.06
72	2	L	5836	0.06
73	1	I	5834	0.05
73	2	M	5834	0.05
74	1	I	5816	0.05
74	2	N	5816	0.05
75	1	I	5825	0.05
75	2	S	5825	0.05
76	1	I	5800	0.04
76	2	T	5800	0.04
77	1	K	5806	0.06
77	2	L	5806	0.06
78	1	K	5791	0.08
78	2	M	5791	0.08
79	1	K	5791	0.07
79	2	N	5791	0.07
80	1	K	5788	0.05
80	2	S	5788	0.05
81	1	K	5768	0.07
81	2	T	5768	0.07
82	1	L	5921	0.06
82	2	M	5921	0.06
83	1	L	5852	0.07
83	2	N	5852	0.07
84	1	L	5886	0.06
84	2	S	5886	0.06
85	1	L	5862	0.06
85	2	T	5862	0.06
86	1	M	5858	0.06
86	2	N	5858	0.06
87	1	M	5869	0.07
87	2	S	5869	0.07
88	1	M	5867	0.05
88	2	T	5867	0.05
89	1	N	5822	0.06
89	2	S	5822	0.06
90	1	N	5775	0.06
90	2	T	5775	0.06
91	1	S	5769	0.06
91	2	T	5769	0.06

LS refinement shell

Resolution: 1.684→1.727 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.25	1295	-
R_work	0.24	25758	-
all	-	27053	-
obs	-	-	96.19 %

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