PDB-3i2b: The crystal structure of human 6 Pyruvoyl Tetrahydrobiopterin Synthase

ID or keywords:

Entry

Database: PDB / ID: 3i2b

Title

The crystal structure of human 6 Pyruvoyl Tetrahydrobiopterin Synthase

Components

6-pyruvoyl tetrahydrobiopterin synthase

Keywords

LYASE / 6 pyruvoyl tetrahydrobiopterin synthase / PTS / PTP synthase / Structural Genomics / Structural Genomics Consortium / SGC / Disease mutation / Metal-binding / Phenylketonuria / Phosphoprotein / Tetrahydrobiopterin biosynthesis

Function / homology

Function and homology information

6-pyruvoyltetrahydropterin synthase / 6-pyruvoyltetrahydropterin synthase activity / tetrahydrobiopterin biosynthetic process / amino acid metabolic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / central nervous system development / mitochondrion / metal ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Ugochukwu, E. / Cocking, R. / Pilka, E. / Yue, W.W. / Bray, J.E. / Chaikuad, A. / Krojer, T. / Muniz, J. / von Delft, F. / Bountra, C. ...

Citation

Journal: To be Published
Title: The crystal structure of human 6 Pyruvoyl Tetrahydrobiopterin Synthase
Authors: Ugochukwu, E. / Cocking, R. / Pilka, E. / Yue, W.W. / Bray, J.E. / Chaikuad, A. / Krojer, T. / Muniz, J. / Oppermann, U.

History

Deposition	Jun 29, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jul 28, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_conn.ptnr2_label_seq_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 / _struct_ref_seq_dif.details / _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	3i2b.cif.gz	329.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3i2b_validation.pdf.gz	519.7 KB	Display	wwPDB validaton report
Full document	3i2b_full_validation.pdf.gz	527.1 KB	Display
Data in XML	3i2b_validation.xml.gz	56.5 KB	Display
Data in CIF	3i2b_validation.cif.gz	78 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i2/3i2b ftp://data.pdbj.org/pub/pdb/validation_reports/i2/3i2b	HTTPS FTP

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Related structure data

Related structure data	1gtqS S: Starting model for refinement
Similar structure data	1b66-2 1b66-3 6cv6-1 4xxh-d 1v4a-d 6cv6-3 1mvn-1 6cv6-2 6hs8-1 1usu-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

1gtqS

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	#188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (10) #44 - Aug 2003 Calmodulin similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1) #34 - Oct 2002 Dihydrofolate Reductase similarity (1)

Deposited unit

A: 6-pyruvoyl tetrahydrobiopterin synthase

D: 6-pyruvoyl tetrahydrobiopterin synthase

E: 6-pyruvoyl tetrahydrobiopterin synthase

B: 6-pyruvoyl tetrahydrobiopterin synthase

C: 6-pyruvoyl tetrahydrobiopterin synthase

F: 6-pyruvoyl tetrahydrobiopterin synthase

G: 6-pyruvoyl tetrahydrobiopterin synthase

H: 6-pyruvoyl tetrahydrobiopterin synthase

I: 6-pyruvoyl tetrahydrobiopterin synthase

J: 6-pyruvoyl tetrahydrobiopterin synthase

K: 6-pyruvoyl tetrahydrobiopterin synthase

L: 6-pyruvoyl tetrahydrobiopterin synthase

hetero molecules

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

1

A: 6-pyruvoyl tetrahydrobiopterin synthase

D: 6-pyruvoyl tetrahydrobiopterin synthase

E: 6-pyruvoyl tetrahydrobiopterin synthase

hetero molecules

defined by author&software
48.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 6-pyruvoyl tetrahydrobiopterin synthase

C: 6-pyruvoyl tetrahydrobiopterin synthase

F: 6-pyruvoyl tetrahydrobiopterin synthase

hetero molecules

defined by author&software
48.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: 6-pyruvoyl tetrahydrobiopterin synthase

H: 6-pyruvoyl tetrahydrobiopterin synthase

I: 6-pyruvoyl tetrahydrobiopterin synthase

hetero molecules

defined by author&software
48.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

J: 6-pyruvoyl tetrahydrobiopterin synthase

K: 6-pyruvoyl tetrahydrobiopterin synthase

L: 6-pyruvoyl tetrahydrobiopterin synthase

hetero molecules

defined by author&software
48.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	73.290, 118.720, 234.980
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	LEU	LEU	GLU	GLU	6	A	A	26 - 35	22 - 31
2	1	1	LEU	LEU	GLU	GLU	6	B	D	26 - 35	22 - 31
3	1	1	LEU	LEU	GLU	GLU	6	C	E	26 - 35	22 - 31
4	1	1	LEU	LEU	GLU	GLU	6	D	B	26 - 35	22 - 31
5	1	1	LEU	LEU	GLU	GLU	6	E	C	26 - 35	22 - 31
6	1	1	LEU	LEU	GLU	GLU	6	F	F	26 - 35	22 - 31
7	1	1	LEU	LEU	GLU	GLU	6	G	G	26 - 35	22 - 31
8	1	1	LEU	LEU	GLU	GLU	6	H	H	26 - 35	22 - 31
9	1	1	LEU	LEU	GLU	GLU	6	I	I	26 - 35	22 - 31
10	1	1	LEU	LEU	GLU	GLU	6	J	J	26 - 35	22 - 31
11	1	1	LEU	LEU	GLU	GLU	6	K	K	26 - 35	22 - 31
12	1	1	LEU	LEU	GLU	GLU	6	L	L	26 - 35	22 - 31
1	2	1	ILE	ILE	LYS	LYS	6	A	A	63 - 77	59 - 73
2	2	1	ILE	ILE	LYS	LYS	6	B	D	63 - 77	59 - 73
3	2	1	ILE	ILE	LYS	LYS	6	C	E	63 - 77	59 - 73
4	2	1	ILE	ILE	LYS	LYS	6	D	B	63 - 77	59 - 73
5	2	1	ILE	ILE	LYS	LYS	6	E	C	63 - 77	59 - 73
6	2	1	ILE	ILE	LYS	LYS	6	F	F	63 - 77	59 - 73
7	2	1	ILE	ILE	LYS	LYS	6	G	G	63 - 77	59 - 73
8	2	1	ILE	ILE	LYS	LYS	6	H	H	63 - 77	59 - 73
9	2	1	ILE	ILE	LYS	LYS	6	I	I	63 - 77	59 - 73
10	2	1	ILE	ILE	LYS	LYS	6	J	J	63 - 77	59 - 73
11	2	1	ILE	ILE	LYS	LYS	6	K	K	63 - 77	59 - 73
12	2	1	ILE	ILE	LYS	LYS	6	L	L	63 - 77	59 - 73
1	3	1	ASN	ASN	VAL	VAL	6	A	A	117 - 126	113 - 122
2	3	1	ASN	ASN	VAL	VAL	6	B	D	117 - 126	113 - 122
3	3	1	ASN	ASN	VAL	VAL	6	C	E	117 - 126	113 - 122
4	3	1	ASN	ASN	VAL	VAL	6	D	B	117 - 126	113 - 122
5	3	1	ASN	ASN	VAL	VAL	6	E	C	117 - 126	113 - 122
6	3	1	ASN	ASN	VAL	VAL	6	F	F	117 - 126	113 - 122
7	3	1	ASN	ASN	VAL	VAL	6	G	G	117 - 126	113 - 122
8	3	1	ASN	ASN	VAL	VAL	6	H	H	117 - 126	113 - 122
9	3	1	ASN	ASN	VAL	VAL	6	I	I	117 - 126	113 - 122
10	3	1	ASN	ASN	VAL	VAL	6	J	J	117 - 126	113 - 122
11	3	1	ASN	ASN	VAL	VAL	6	K	K	117 - 126	113 - 122
12	3	1	ASN	ASN	VAL	VAL	6	L	L	117 - 126	113 - 122
1	1	2	GLN	GLN	ARG	ARG	2	A	A	11 - 25	7 - 21
2	1	2	GLN	GLN	ARG	ARG	2	B	D	11 - 25	7 - 21
3	1	2	GLN	GLN	ARG	ARG	2	C	E	11 - 25	7 - 21
4	1	2	GLN	GLN	ARG	ARG	2	D	B	11 - 25	7 - 21
5	1	2	GLN	GLN	ARG	ARG	2	E	C	11 - 25	7 - 21
6	1	2	GLN	GLN	ARG	ARG	2	F	F	11 - 25	7 - 21
7	1	2	GLN	GLN	ARG	ARG	2	G	G	11 - 25	7 - 21
8	1	2	GLN	GLN	ARG	ARG	2	H	H	11 - 25	7 - 21
9	1	2	GLN	GLN	ARG	ARG	2	I	I	11 - 25	7 - 21
10	1	2	GLN	GLN	ARG	ARG	2	J	J	11 - 25	7 - 21
11	1	2	GLN	GLN	ARG	ARG	2	K	K	11 - 25	7 - 21
12	1	2	GLN	GLN	ARG	ARG	2	L	L	11 - 25	7 - 21
1	2	2	ASN	ASN	GLU	GLU	2	A	A	36 - 62	32 - 58
2	2	2	ASN	ASN	GLU	GLU	2	B	D	36 - 62	32 - 58
3	2	2	ASN	ASN	GLU	GLU	2	C	E	36 - 62	32 - 58
4	2	2	ASN	ASN	GLU	GLU	2	D	B	36 - 62	32 - 58
5	2	2	ASN	ASN	GLU	GLU	2	E	C	36 - 62	32 - 58
6	2	2	ASN	ASN	GLU	GLU	2	F	F	36 - 62	32 - 58
7	2	2	ASN	ASN	GLU	GLU	2	G	G	36 - 62	32 - 58
8	2	2	ASN	ASN	GLU	GLU	2	H	H	36 - 62	32 - 58
9	2	2	ASN	ASN	GLU	GLU	2	I	I	36 - 62	32 - 58
10	2	2	ASN	ASN	GLU	GLU	2	J	J	36 - 62	32 - 58
11	2	2	ASN	ASN	GLU	GLU	2	K	K	36 - 62	32 - 58
12	2	2	ASN	ASN	GLU	GLU	2	L	L	36 - 62	32 - 58
1	3	2	LYS	LYS	ASP	ASP	2	A	A	78 - 116	74 - 112
2	3	2	LYS	LYS	ASP	ASP	2	B	D	78 - 116	74 - 112
3	3	2	LYS	LYS	ASP	ASP	2	C	E	78 - 116	74 - 112
4	3	2	LYS	LYS	ASP	ASP	2	D	B	78 - 116	74 - 112
5	3	2	LYS	LYS	ASP	ASP	2	E	C	78 - 116	74 - 112
6	3	2	LYS	LYS	ASP	ASP	2	F	F	78 - 116	74 - 112
7	3	2	LYS	LYS	ASP	ASP	2	G	G	78 - 116	74 - 112
8	3	2	LYS	LYS	ASP	ASP	2	H	H	78 - 116	74 - 112
9	3	2	LYS	LYS	ASP	ASP	2	I	I	78 - 116	74 - 112
10	3	2	LYS	LYS	ASP	ASP	2	J	J	78 - 116	74 - 112
11	3	2	LYS	LYS	ASP	ASP	2	K	K	78 - 116	74 - 112
12	3	2	LYS	LYS	ASP	ASP	2	L	L	78 - 116	74 - 112
1	4	2	LEU	LEU	VAL	VAL	2	A	A	127 - 141	123 - 137
2	4	2	LEU	LEU	VAL	VAL	2	B	D	127 - 141	123 - 137
3	4	2	LEU	LEU	VAL	VAL	2	C	E	127 - 141	123 - 137
4	4	2	LEU	LEU	VAL	VAL	2	D	B	127 - 141	123 - 137
5	4	2	LEU	LEU	VAL	VAL	2	E	C	127 - 141	123 - 137
6	4	2	LEU	LEU	VAL	VAL	2	F	F	127 - 141	123 - 137
7	4	2	LEU	LEU	VAL	VAL	2	G	G	127 - 141	123 - 137
8	4	2	LEU	LEU	VAL	VAL	2	H	H	127 - 141	123 - 137
9	4	2	LEU	LEU	VAL	VAL	2	I	I	127 - 141	123 - 137
10	4	2	LEU	LEU	VAL	VAL	2	J	J	127 - 141	123 - 137
11	4	2	LEU	LEU	VAL	VAL	2	K	K	127 - 141	123 - 137
12	4	2	LEU	LEU	VAL	VAL	2	L	L	127 - 141	123 - 137

NCS ensembles :

ID
1
2

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Protein , 1 types, 12 molecules ADEBCFGHIJKL

#1: Protein	6-pyruvoyl tetrahydrobiopterin synthase / PTS / PTP synthase / PTPS Mass: 16062.356 Da / Num. of mol.: 12 / Fragment: UNP residues 7-145 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTS / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 References: UniProt: Q03393, 6-pyruvoyltetrahydropterin synthase

#1: Protein

6-pyruvoyl tetrahydrobiopterin synthase / PTS / PTP synthase / PTPS

Mass: 16062.356 Da / Num. of mol.: 12 / Fragment: UNP residues 7-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: PTS / Plasmid: pNIC28-Bsa4 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2
References: UniProt: Q03393, 6-pyruvoyltetrahydropterin synthase

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Non-polymers , 5 types, 279 molecules

#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ni
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.65 Å³/Da / Density % sol: 53.62 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG 3350, 0.20M Mg(form)2, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9788 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 5, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9788 Å / Relative weight: 1
Reflection	Resolution: 2.3→42.94 Å / Num. obs: 91910 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / R_merge(I) obs: 0.095 / R_sym value: 0.095 / Net I/σ(I): 11
Reflection shell	Resolution: 2.3→2.42 Å / Redundancy: 5 % / R_merge(I) obs: 0.792 / Mean I/σ(I) obs: 2.1 / Num. unique all: 66735 / R_sym value: 0.792 / % possible all: 100

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Processing

Software

Name	Version	Classification
MAR345		data collection
PHASER		phasing
REFMAC	5.5.0089	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GTQ

1gtq

Resolution: 2.3→42.94 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.924 / SU B: 13.551 / SU ML: 0.157 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.297 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24566	4603	5 %	RANDOM
R_work	0.20646	-	-	-
all	0.20841	87233	-	-
obs	0.20841	87233	99.92 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 13.883 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.47 Å²	0 Å²	0 Å²
2-	-	-1.29 Å²	0 Å²
3-	-	-	0.82 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→42.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12814	0	25	263	13102

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	13125
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	8381
X-RAY DIFFRACTION	r_angle_refined_deg	1.483	1.943	17861
X-RAY DIFFRACTION	r_angle_other_deg	0.984	3	20562
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.426	5	1649
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.196	25.025	605
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.583	15	2123
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.976	15	46
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	2023
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	14781
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	2537
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	3.535	5	8246
X-RAY DIFFRACTION	r_mcbond_other	1.789	5	3319
X-RAY DIFFRACTION	r_mcangle_it	4.529	7	13334
X-RAY DIFFRACTION	r_scbond_it	7.135	9	4879
X-RAY DIFFRACTION	r_scangle_it	7.906	11	4522
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	361	LOOSE POSITIONAL	0.54	5
1	B	361	LOOSE POSITIONAL	0.51	5
1	C	361	LOOSE POSITIONAL	0.68	5
1	D	361	LOOSE POSITIONAL	0.4	5
1	E	361	LOOSE POSITIONAL	0.46	5
1	F	361	LOOSE POSITIONAL	0.53	5
1	G	361	LOOSE POSITIONAL	0.49	5
1	H	361	LOOSE POSITIONAL	0.55	5
1	I	361	LOOSE POSITIONAL	0.57	5
1	J	361	LOOSE POSITIONAL	0.56	5
1	K	361	LOOSE POSITIONAL	0.57	5
1	L	361	LOOSE POSITIONAL	0.5	5
1	A	361	LOOSE THERMAL	5.05	10
1	B	361	LOOSE THERMAL	4.8	10
1	C	361	LOOSE THERMAL	4.69	10
1	D	361	LOOSE THERMAL	4.35	10
1	E	361	LOOSE THERMAL	4.78	10
1	F	361	LOOSE THERMAL	4.42	10
1	G	361	LOOSE THERMAL	4.37	10
1	H	361	LOOSE THERMAL	4.88	10
1	I	361	LOOSE THERMAL	4.64	10
1	J	361	LOOSE THERMAL	5.37	10
1	K	361	LOOSE THERMAL	5.78	10
1	L	361	LOOSE THERMAL	4.38	10
2	A	563	TIGHT POSITIONAL	0.06	0.05
2	B	563	TIGHT POSITIONAL	0.05	0.05
2	C	563	TIGHT POSITIONAL	0.04	0.05
2	D	563	TIGHT POSITIONAL	0.04	0.05
2	E	563	TIGHT POSITIONAL	0.04	0.05
2	F	563	TIGHT POSITIONAL	0.04	0.05
2	G	563	TIGHT POSITIONAL	0.05	0.05
2	H	563	TIGHT POSITIONAL	0.04	0.05
2	I	563	TIGHT POSITIONAL	0.04	0.05
2	J	563	TIGHT POSITIONAL	0.04	0.05
2	K	563	TIGHT POSITIONAL	0.04	0.05
2	L	563	TIGHT POSITIONAL	0.04	0.05
2	A	618	MEDIUM POSITIONAL	0.06	0.5
2	B	618	MEDIUM POSITIONAL	0.05	0.5
2	C	618	MEDIUM POSITIONAL	0.05	0.5
2	D	618	MEDIUM POSITIONAL	0.05	0.5
2	E	618	MEDIUM POSITIONAL	0.05	0.5
2	F	618	MEDIUM POSITIONAL	0.04	0.5
2	G	618	MEDIUM POSITIONAL	0.05	0.5
2	H	618	MEDIUM POSITIONAL	0.04	0.5
2	I	618	MEDIUM POSITIONAL	0.04	0.5
2	J	618	MEDIUM POSITIONAL	0.05	0.5
2	K	618	MEDIUM POSITIONAL	0.04	0.5
2	L	618	MEDIUM POSITIONAL	0.04	0.5
2	A	563	TIGHT THERMAL	0.22	0.5
2	B	563	TIGHT THERMAL	0.23	0.5
2	C	563	TIGHT THERMAL	0.23	0.5
2	D	563	TIGHT THERMAL	0.22	0.5
2	E	563	TIGHT THERMAL	0.19	0.5
2	F	563	TIGHT THERMAL	0.19	0.5
2	G	563	TIGHT THERMAL	0.21	0.5
2	H	563	TIGHT THERMAL	0.18	0.5
2	I	563	TIGHT THERMAL	0.2	0.5
2	J	563	TIGHT THERMAL	0.22	0.5
2	K	563	TIGHT THERMAL	0.18	0.5
2	L	563	TIGHT THERMAL	0.19	0.5
2	A	618	MEDIUM THERMAL	0.19	2
2	B	618	MEDIUM THERMAL	0.22	2
2	C	618	MEDIUM THERMAL	0.19	2
2	D	618	MEDIUM THERMAL	0.21	2
2	E	618	MEDIUM THERMAL	0.17	2
2	F	618	MEDIUM THERMAL	0.17	2
2	G	618	MEDIUM THERMAL	0.16	2
2	H	618	MEDIUM THERMAL	0.15	2
2	I	618	MEDIUM THERMAL	0.16	2
2	J	618	MEDIUM THERMAL	0.19	2
2	K	618	MEDIUM THERMAL	0.17	2
2	L	618	MEDIUM THERMAL	0.16	2

LS refinement shell

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

	R_factor	Num. reflection	% reflection
R_free	0.411	347	-
R_work	0.345	6367	-
obs	-	-	100 %

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	4.3838	-2.9784	2.7901	4.4364	-2.0961	3.3848	0.4163	0.2685	-0.317	-0.4105	-0.1869	-0.0079	0.5068	0.3572	-0.2294	0.2194	0.0697	-0.042	0.116	-0.0266	0.047	17.4701	-20.4045	-31.3584
2	5.0154	1.6103	-0.9186	2.8506	-0.994	2.8087	-0.0212	-0.0415	0.326	-0.018	-0.0218	0.173	-0.3736	-0.0786	0.043	0.1304	0.0258	-0.0372	0.0533	0.0095	0.0412	6.2926	4.9667	-27.4741
3	1.5955	0.6151	1.1973	6.3161	3.1903	5.11	-0.0616	0.3447	0.0992	-0.1356	0.1104	-0.8197	-0.1467	0.7405	-0.0488	0.0747	-0.0568	0.0368	0.3339	0.154	0.2368	34.3129	1.4343	-26.3196
4	4.0097	-3.0532	1.8271	3.6278	-1.2829	1.9264	-0.0436	-0.1666	0.0533	0.2988	0.0826	0.0699	-0.101	-0.0783	-0.039	0.1173	-0.0004	-0.0124	0.0303	0.0066	0.1233	-20.4074	6.9101	-55.2438
5	3.6009	1.9439	-1.2151	5.4349	-2.1774	3.8049	0.0256	0.186	-0.0046	0.1183	-0.0495	-0.4191	0.1833	0.2714	0.0239	0.0836	0.0834	-0.0775	0.12	-0.0446	0.1081	-3.2696	-14.4607	-60.9695
6	1.7279	-1.0339	-0.5633	4.9243	2.9438	5.8853	0.1884	0.3992	0.3788	-0.5714	-0.2011	-0.4194	-0.3575	0.3431	0.0127	0.1414	0.0256	0.0089	0.2842	0.218	0.2384	-7.1044	7.238	-79.4132
7	2.4829	0.0144	2.394	5.4942	2.0665	5.6224	0.1896	-0.1039	-0.2955	0.3168	0.1287	-0.0674	0.3244	0.2166	-0.3183	0.1519	0.0216	-0.052	0.1731	0.0983	0.1053	26.4862	-23.2465	-4.9323
8	8.0902	1.3146	-1.9683	2.369	-0.6806	3.4243	-0.1333	-0.3388	0.6079	0.5412	0.0451	-0.2265	-0.3338	0.1839	0.0882	0.327	0.0067	-0.1467	0.1653	-0.0188	0.1222	25.229	4.205	0.7361
9	4.0005	-2.3769	2.0104	6.1371	-2.7696	3.6261	0.0271	-0.5769	-0.1074	0.4132	0.0787	0.3019	-0.0537	-0.4598	-0.1057	0.1522	-0.0418	0.0868	0.2883	0.0349	0.0629	1.9013	-9.8696	-3.4859
10	6.2309	2.601	0.7046	4.2054	0.4237	1.7519	0.048	0.0046	-0.2024	-0.1806	-0.0188	-0.6444	0.2	0.0279	-0.0292	0.1251	0.0066	-0.0126	0.0202	0.0396	0.2038	28.6015	34.8037	-52.4666
11	1.7716	0.7355	-0.0775	4.465	-2.6846	6.0585	0.1707	-0.1651	-0.0691	0.3251	-0.2215	-0.8078	-0.269	0.3155	0.0507	0.0822	-0.0692	-0.1168	0.1031	-0.0004	0.4395	39.3423	59.0291	-42.6602
12	1.8086	-1.4753	-0.7302	5.5918	2.2563	2.7155	0.1315	-0.4084	-0.1625	0.6649	-0.2645	-0.1248	0.1726	-0.202	0.133	0.3281	-0.2283	-0.1475	0.2991	0.0531	0.1286	21.177	44.0091	-27.448

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	9 - 144
2	X-RAY DIFFRACTION	2	D	7 - 144
3	X-RAY DIFFRACTION	3	E	7 - 144
4	X-RAY DIFFRACTION	4	B	7 - 144
5	X-RAY DIFFRACTION	5	C	8 - 144
6	X-RAY DIFFRACTION	6	F	7 - 144
7	X-RAY DIFFRACTION	7	G	9 - 144
8	X-RAY DIFFRACTION	8	H	8 - 144
9	X-RAY DIFFRACTION	9	I	7 - 144
10	X-RAY DIFFRACTION	10	J	8 - 144
11	X-RAY DIFFRACTION	11	K	7 - 144
12	X-RAY DIFFRACTION	12	L	7 - 144

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