PDB-5ntd: Structure of Leucyl aminopeptidase from Trypanosoma brucei in com...

ID or keywords:

Entry

Database: PDB / ID: 5ntd

Title

Structure of Leucyl aminopeptidase from Trypanosoma brucei in complex with Bestatin

Components

leucyl aminopeptidase

Keywords

HYDROLASE / M17 leucyl aminopeptidase / aminopeptidase / tryanosoma brucei bestatin

Function / homology

Function and homology information

metalloaminopeptidase activity / aminopeptidase activity / peptidase activity / manganese ion binding / proteolysis / cytoplasm
Similarity search - Function

Biological species

Trypanosoma brucei brucei (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Timm, J. / Wilson, K.

Citation

Journal: mSphere / Year: 2018
Title: Structural Characterization of Acidic M17 Leucine Aminopeptidases from the TriTryps and Evaluation of Their Role in Nutrient Starvation inTrypanosoma brucei.
Authors: Timm, J. / Valente, M. / Garcia-Caballero, D. / Wilson, K.S. / Gonzalez-Pacanowska, D.

History

Deposition	Apr 27, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 2, 2017	Provider: repository / Type: Initial release
Revision 1.1	Aug 30, 2017	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2	Feb 21, 2018	Group: Database references / Category: citation / Item: _citation.title
Revision 1.3	Mar 28, 2018	Group: Data collection / Database references / Category: citation / Item: _citation.title / _citation.year
Revision 1.4	Jan 17, 2024	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 / struct_ncs_dom_lim 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_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_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	5ntd.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb5ntd.ent.gz	968.8 KB	Display	PDB format
PDBx/mmJSON format	5ntd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ntd_validation.pdf.gz	3.6 MB	Display	wwPDB validaton report
Full document	5ntd_full_validation.pdf.gz	3.7 MB	Display
Data in XML	5ntd_validation.xml.gz	231 KB	Display
Data in CIF	5ntd_validation.cif.gz	325.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nt/5ntd ftp://data.pdbj.org/pub/pdb/validation_reports/nt/5ntd	HTTPS FTP

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Related structure data

Related structure data	5nskSC 5nsmC 5nsqC 5ntfC 5ntgC 5nthC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5nsm-2 5nsm-3 5nsm-1 5nsk-d 5nsq-d 4efd-d 5ntf-1 5lhj-1 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

5nskSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #49 - Jan 2004 Carbonic Anhydrase similarity (1) #59 - Nov 2004 Photosystem II similarity (1)

Deposited unit

A: leucyl aminopeptidase

B: leucyl aminopeptidase

D: leucyl aminopeptidase

C: leucyl aminopeptidase

E: leucyl aminopeptidase

F: leucyl aminopeptidase

G: leucyl aminopeptidase

H: leucyl aminopeptidase

I: leucyl aminopeptidase

J: leucyl aminopeptidase

K: leucyl aminopeptidase

L: leucyl aminopeptidase

hetero molecules

673 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

J: leucyl aminopeptidase

K: leucyl aminopeptidase

L: leucyl aminopeptidase

hetero molecules

G: leucyl aminopeptidase

H: leucyl aminopeptidase

I: leucyl aminopeptidase

hetero molecules

defined by author
Evidence: light scattering
336 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: leucyl aminopeptidase

B: leucyl aminopeptidase

D: leucyl aminopeptidase

C: leucyl aminopeptidase

E: leucyl aminopeptidase

F: leucyl aminopeptidase

hetero molecules

defined by author&software
336 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: leucyl aminopeptidase

H: leucyl aminopeptidase

I: leucyl aminopeptidase

hetero molecules

J: leucyl aminopeptidase

K: leucyl aminopeptidase

L: leucyl aminopeptidase

hetero molecules

defined by author&software
336 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.260, 143.450, 268.030
Angle α, β, γ (deg.)	90.00, 95.54, 90.00
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	THR	THR	LEU	LEU	A	A	3 - 521	3 - 521
2	1	THR	THR	LEU	LEU	B	B	3 - 521	3 - 521
1	2	THR	THR	LEU	LEU	A	A	3 - 521	3 - 521
2	2	THR	THR	LEU	LEU	D	C	3 - 521	3 - 521
1	3	LEU	LEU	LYS	LYS	A	A	4 - 520	4 - 520
2	3	LEU	LEU	LYS	LYS	C	D	4 - 520	4 - 520
1	4	THR	THR	LEU	LEU	A	A	3 - 521	3 - 521
2	4	THR	THR	LEU	LEU	E	E	3 - 521	3 - 521
1	5	THR	THR	LEU	LEU	A	A	3 - 521	3 - 521
2	5	THR	THR	LEU	LEU	F	F	3 - 521	3 - 521
1	6	LEU	LEU	LYS	LYS	A	A	4 - 520	4 - 520
2	6	LEU	LEU	LYS	LYS	G	G	4 - 520	4 - 520
1	7	THR	THR	LEU	LEU	A	A	3 - 521	3 - 521
2	7	THR	THR	LEU	LEU	H	H	3 - 521	3 - 521
1	8	THR	THR	LEU	LEU	A	A	3 - 521	3 - 521
2	8	THR	THR	LEU	LEU	I	I	3 - 521	3 - 521
1	9	THR	THR	LEU	LEU	A	A	3 - 521	3 - 521
2	9	THR	THR	LEU	LEU	J	J	3 - 521	3 - 521
1	10	THR	THR	LEU	LEU	A	A	3 - 521	3 - 521
2	10	THR	THR	LEU	LEU	K	K	3 - 521	3 - 521
1	11	THR	THR	LEU	LEU	A	A	3 - 521	3 - 521
2	11	THR	THR	LEU	LEU	L	L	3 - 521	3 - 521
1	12	THR	THR	LEU	LEU	B	B	3 - 521	3 - 521
2	12	THR	THR	LEU	LEU	D	C	3 - 521	3 - 521
1	13	LEU	LEU	LYS	LYS	B	B	4 - 520	4 - 520
2	13	LEU	LEU	LYS	LYS	C	D	4 - 520	4 - 520
1	14	THR	THR	LEU	LEU	B	B	3 - 521	3 - 521
2	14	THR	THR	LEU	LEU	E	E	3 - 521	3 - 521
1	15	THR	THR	LEU	LEU	B	B	3 - 521	3 - 521
2	15	THR	THR	LEU	LEU	F	F	3 - 521	3 - 521
1	16	LEU	LEU	LYS	LYS	B	B	4 - 520	4 - 520
2	16	LEU	LEU	LYS	LYS	G	G	4 - 520	4 - 520
1	17	THR	THR	LEU	LEU	B	B	3 - 521	3 - 521
2	17	THR	THR	LEU	LEU	H	H	3 - 521	3 - 521
1	18	THR	THR	LEU	LEU	B	B	3 - 521	3 - 521
2	18	THR	THR	LEU	LEU	I	I	3 - 521	3 - 521
1	19	THR	THR	LEU	LEU	B	B	3 - 521	3 - 521
2	19	THR	THR	LEU	LEU	J	J	3 - 521	3 - 521
1	20	THR	THR	LEU	LEU	B	B	3 - 521	3 - 521
2	20	THR	THR	LEU	LEU	K	K	3 - 521	3 - 521
1	21	THR	THR	LEU	LEU	B	B	3 - 521	3 - 521
2	21	THR	THR	LEU	LEU	L	L	3 - 521	3 - 521
1	22	LEU	LEU	LYS	LYS	D	C	4 - 520	4 - 520
2	22	LEU	LEU	LYS	LYS	C	D	4 - 520	4 - 520
1	23	THR	THR	LEU	LEU	D	C	3 - 521	3 - 521
2	23	THR	THR	LEU	LEU	E	E	3 - 521	3 - 521
1	24	THR	THR	LEU	LEU	D	C	3 - 521	3 - 521
2	24	THR	THR	LEU	LEU	F	F	3 - 521	3 - 521
1	25	THR	THR	LYS	LYS	D	C	3 - 520	3 - 520
2	25	THR	THR	LYS	LYS	G	G	3 - 520	3 - 520
1	26	THR	THR	LEU	LEU	D	C	3 - 521	3 - 521
2	26	THR	THR	LEU	LEU	H	H	3 - 521	3 - 521
1	27	THR	THR	LEU	LEU	D	C	3 - 521	3 - 521
2	27	THR	THR	LEU	LEU	I	I	3 - 521	3 - 521
1	28	THR	THR	LEU	LEU	D	C	3 - 521	3 - 521
2	28	THR	THR	LEU	LEU	J	J	3 - 521	3 - 521
1	29	THR	THR	LEU	LEU	D	C	3 - 521	3 - 521
2	29	THR	THR	LEU	LEU	K	K	3 - 521	3 - 521
1	30	THR	THR	LEU	LEU	D	C	3 - 521	3 - 521
2	30	THR	THR	LEU	LEU	L	L	3 - 521	3 - 521
1	31	LEU	LEU	LYS	LYS	C	D	4 - 520	4 - 520
2	31	LEU	LEU	LYS	LYS	E	E	4 - 520	4 - 520
1	32	LEU	LEU	LYS	LYS	C	D	4 - 520	4 - 520
2	32	LEU	LEU	LYS	LYS	F	F	4 - 520	4 - 520
1	33	LEU	LEU	LYS	LYS	C	D	4 - 520	4 - 520
2	33	LEU	LEU	LYS	LYS	G	G	4 - 520	4 - 520
1	34	LEU	LEU	LYS	LYS	C	D	4 - 520	4 - 520
2	34	LEU	LEU	LYS	LYS	H	H	4 - 520	4 - 520
1	35	LEU	LEU	LYS	LYS	C	D	4 - 520	4 - 520
2	35	LEU	LEU	LYS	LYS	I	I	4 - 520	4 - 520
1	36	LEU	LEU	LYS	LYS	C	D	4 - 520	4 - 520
2	36	LEU	LEU	LYS	LYS	J	J	4 - 520	4 - 520
1	37	LEU	LEU	LYS	LYS	C	D	4 - 520	4 - 520
2	37	LEU	LEU	LYS	LYS	K	K	4 - 520	4 - 520
1	38	LEU	LEU	LYS	LYS	C	D	4 - 520	4 - 520
2	38	LEU	LEU	LYS	LYS	L	L	4 - 520	4 - 520
1	39	THR	THR	LEU	LEU	E	E	3 - 521	3 - 521
2	39	THR	THR	LEU	LEU	F	F	3 - 521	3 - 521
1	40	LEU	LEU	LYS	LYS	E	E	4 - 520	4 - 520
2	40	LEU	LEU	LYS	LYS	G	G	4 - 520	4 - 520
1	41	THR	THR	LEU	LEU	E	E	3 - 521	3 - 521
2	41	THR	THR	LEU	LEU	H	H	3 - 521	3 - 521
1	42	THR	THR	LEU	LEU	E	E	3 - 521	3 - 521
2	42	THR	THR	LEU	LEU	I	I	3 - 521	3 - 521
1	43	THR	THR	LEU	LEU	E	E	3 - 521	3 - 521
2	43	THR	THR	LEU	LEU	J	J	3 - 521	3 - 521
1	44	THR	THR	LEU	LEU	E	E	3 - 521	3 - 521
2	44	THR	THR	LEU	LEU	K	K	3 - 521	3 - 521
1	45	THR	THR	LEU	LEU	E	E	3 - 521	3 - 521
2	45	THR	THR	LEU	LEU	L	L	3 - 521	3 - 521
1	46	THR	THR	LYS	LYS	F	F	3 - 520	3 - 520
2	46	THR	THR	LYS	LYS	G	G	3 - 520	3 - 520
1	47	THR	THR	LEU	LEU	F	F	3 - 521	3 - 521
2	47	THR	THR	LEU	LEU	H	H	3 - 521	3 - 521
1	48	THR	THR	LEU	LEU	F	F	3 - 521	3 - 521
2	48	THR	THR	LEU	LEU	I	I	3 - 521	3 - 521
1	49	THR	THR	LEU	LEU	F	F	3 - 521	3 - 521
2	49	THR	THR	LEU	LEU	J	J	3 - 521	3 - 521
1	50	THR	THR	LEU	LEU	F	F	3 - 521	3 - 521
2	50	THR	THR	LEU	LEU	K	K	3 - 521	3 - 521
1	51	THR	THR	LEU	LEU	F	F	3 - 521	3 - 521
2	51	THR	THR	LEU	LEU	L	L	3 - 521	3 - 521
1	52	THR	THR	LYS	LYS	G	G	3 - 520	3 - 520
2	52	THR	THR	LYS	LYS	H	H	3 - 520	3 - 520
1	53	THR	THR	LYS	LYS	G	G	3 - 520	3 - 520
2	53	THR	THR	LYS	LYS	I	I	3 - 520	3 - 520
1	54	LEU	LEU	LYS	LYS	G	G	4 - 520	4 - 520
2	54	LEU	LEU	LYS	LYS	J	J	4 - 520	4 - 520
1	55	LEU	LEU	LYS	LYS	G	G	4 - 520	4 - 520
2	55	LEU	LEU	LYS	LYS	K	K	4 - 520	4 - 520
1	56	THR	THR	LYS	LYS	G	G	3 - 520	3 - 520
2	56	THR	THR	LYS	LYS	L	L	3 - 520	3 - 520
1	57	THR	THR	LEU	LEU	H	H	3 - 521	3 - 521
2	57	THR	THR	LEU	LEU	I	I	3 - 521	3 - 521
1	58	THR	THR	LEU	LEU	H	H	3 - 521	3 - 521
2	58	THR	THR	LEU	LEU	J	J	3 - 521	3 - 521
1	59	THR	THR	LEU	LEU	H	H	3 - 521	3 - 521
2	59	THR	THR	LEU	LEU	K	K	3 - 521	3 - 521
1	60	THR	THR	LEU	LEU	H	H	3 - 521	3 - 521
2	60	THR	THR	LEU	LEU	L	L	3 - 521	3 - 521
1	61	THR	THR	LEU	LEU	I	I	3 - 521	3 - 521
2	61	THR	THR	LEU	LEU	J	J	3 - 521	3 - 521
1	62	THR	THR	LEU	LEU	I	I	3 - 521	3 - 521
2	62	THR	THR	LEU	LEU	K	K	3 - 521	3 - 521
1	63	THR	THR	LEU	LEU	I	I	3 - 521	3 - 521
2	63	THR	THR	LEU	LEU	L	L	3 - 521	3 - 521
1	64	THR	THR	LEU	LEU	J	J	3 - 521	3 - 521
2	64	THR	THR	LEU	LEU	K	K	3 - 521	3 - 521
1	65	THR	THR	LEU	LEU	J	J	3 - 521	3 - 521
2	65	THR	THR	LEU	LEU	L	L	3 - 521	3 - 521
1	66	THR	THR	LEU	LEU	K	K	3 - 521	3 - 521
2	66	THR	THR	LEU	LEU	L	L	3 - 521	3 - 521

NCS ensembles :

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Protein , 1 types, 12 molecules ABDCEFGHIJKL

#1: Protein	leucyl aminopeptidase Mass: 55418.141 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: Tb11.02.4440 / Production host: Escherichia coli (E. coli) / References: UniProt: Q385B0

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Non-polymers , 6 types, 2860 molecules

#2: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	... ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mn
#5: Chemical	ChemComp-BES / 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID / BESTATIN Mass: 308.373 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₆H₂₄N₂O₄ / Comment: protease inhibitor*YM
#6: Chemical	ChemComp-BCT / BICARBONATE ION Mass: 61.017 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CHO₃ / Comment: pH buffer*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2798 / 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: 2.51 Å³/Da / Density % sol: 51 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES pH 7.0, 40 % (v/v) MPD, 5 mM MnCl2, 5 mM bestatin

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 29, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 2.3→80.33 Å / Num. obs: 290030 / % possible obs: 99.7 % / Redundancy: 3.9 % / R_merge(I) obs: 0.091 / Net I/σ(I): 9.1
Reflection shell	Resolution: 2.3→2.34 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.523 / Mean I/σ(I) obs: 2.1 / Num. unique all: 14130

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
MOSFLM		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5NSK

5nsk

Resolution: 2.3→80.33 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.937 / SU B: 8.322 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.211 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21375	14322	4.9 %	RANDOM
R_work	0.18871	-	-	-
obs	0.18995	275670	99.71 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 33.041 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.59 Å²	-0 Å²	-1.71 Å²
2-	-	-0.65 Å²	0 Å²
3-	-	-	-1.58 Å²

Refinement step

Cycle: 1 / Resolution: 2.3→80.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	45572	0	436	2798	48806

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.019	47108
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.02	44060
X-RAY DIFFRACTION	r_angle_refined_deg	1.475	1.974	64128
X-RAY DIFFRACTION	r_angle_other_deg	2.348	3	101121
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.888	5	6233
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.752	24.322	1828
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.499	15	6770
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.75	15	219
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	7550
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	54396
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	10283
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	1.588	3.257	24920
X-RAY DIFFRACTION	r_mcbond_other	1.588	3.256	24919
X-RAY DIFFRACTION	r_mcangle_it	2.491	4.883	31133
X-RAY DIFFRACTION	r_mcangle_other	2.491	4.883	31134
X-RAY DIFFRACTION	r_scbond_it	2.161	3.439	22188
X-RAY DIFFRACTION	r_scbond_other	2.14	3.439	22153
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.284	5.098	32952
X-RAY DIFFRACTION	r_long_range_B_refined	4.971	26.654	54205
X-RAY DIFFRACTION	r_long_range_B_other	4.971	26.655	54206
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	60940	0.06
1	2	B	60940	0.06
2	1	A	61772	0.06
2	2	D	61772	0.06
3	1	A	61336	0.06
3	2	C	61336	0.06
4	1	A	61384	0.06
4	2	E	61384	0.06
5	1	A	61942	0.05
5	2	F	61942	0.05
6	1	A	61116	0.05
6	2	G	61116	0.05
7	1	A	60892	0.06
7	2	H	60892	0.06
8	1	A	61106	0.06
8	2	I	61106	0.06
9	1	A	62090	0.06
9	2	J	62090	0.06
10	1	A	61024	0.06
10	2	K	61024	0.06
11	1	A	61460	0.05
11	2	L	61460	0.05
12	1	B	61192	0.05
12	2	D	61192	0.05
13	1	B	60878	0.05
13	2	C	60878	0.05
14	1	B	61852	0.04
14	2	E	61852	0.04
15	1	B	61478	0.05
15	2	F	61478	0.05
16	1	B	60966	0.05
16	2	G	60966	0.05
17	1	B	61232	0.04
17	2	H	61232	0.04
18	1	B	61162	0.04
18	2	I	61162	0.04
19	1	B	61650	0.05
19	2	J	61650	0.05
20	1	B	61500	0.05
20	2	K	61500	0.05
21	1	B	61222	0.05
21	2	L	61222	0.05
22	1	D	61678	0.04
22	2	C	61678	0.04
23	1	D	61602	0.05
23	2	E	61602	0.05
24	1	D	62236	0.04
24	2	F	62236	0.04
25	1	D	61472	0.04
25	2	G	61472	0.04
26	1	D	61274	0.04
26	2	H	61274	0.04
27	1	D	61570	0.04
27	2	I	61570	0.04
28	1	D	62268	0.04
28	2	J	62268	0.04
29	1	D	61244	0.05
29	2	K	61244	0.05
30	1	D	61762	0.04
30	2	L	61762	0.04
31	1	C	61354	0.05
31	2	E	61354	0.05
32	1	C	62072	0.05
32	2	F	62072	0.05
33	1	C	61724	0.03
33	2	G	61724	0.03
34	1	C	61294	0.05
34	2	H	61294	0.05
35	1	C	61144	0.05
35	2	I	61144	0.05
36	1	C	61980	0.05
36	2	J	61980	0.05
37	1	C	61004	0.06
37	2	K	61004	0.06
38	1	C	61392	0.04
38	2	L	61392	0.04
39	1	E	61836	0.05
39	2	F	61836	0.05
40	1	E	61566	0.05
40	2	G	61566	0.05
41	1	E	61554	0.05
41	2	H	61554	0.05
42	1	E	61270	0.05
42	2	I	61270	0.05
43	1	E	62036	0.05
43	2	J	62036	0.05
44	1	E	61904	0.05
44	2	K	61904	0.05
45	1	E	61132	0.05
45	2	L	61132	0.05
46	1	F	61656	0.05
46	2	G	61656	0.05
47	1	F	61752	0.05
47	2	H	61752	0.05
48	1	F	61694	0.04
48	2	I	61694	0.04
49	1	F	62492	0.05
49	2	J	62492	0.05
50	1	F	61558	0.05
50	2	K	61558	0.05
51	1	F	62176	0.04
51	2	L	62176	0.04
52	1	G	60990	0.05
52	2	H	60990	0.05
53	1	G	61256	0.04
53	2	I	61256	0.04
54	1	G	61862	0.04
54	2	J	61862	0.04
55	1	G	60960	0.05
55	2	K	60960	0.05
56	1	G	61140	0.04
56	2	L	61140	0.04
57	1	H	60846	0.04
57	2	I	60846	0.04
58	1	H	61490	0.05
58	2	J	61490	0.05
59	1	H	61468	0.05
59	2	K	61468	0.05
60	1	H	61178	0.04
60	2	L	61178	0.04
61	1	I	61772	0.04
61	2	J	61772	0.04
62	1	I	61046	0.05
62	2	K	61046	0.05
63	1	I	61282	0.03
63	2	L	61282	0.03
64	1	J	61714	0.05
64	2	K	61714	0.05
65	1	J	61988	0.04
65	2	L	61988	0.04
66	1	K	61172	0.05
66	2	L	61172	0.05

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.31	1081	-
R_work	0.29	20181	-
obs	-	-	98.91 %

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