PDB-4iym: Crystal structure of putative methylmalonate-semialdehyde dehydro...

ID or keywords:

Entry

Database: PDB / ID: 4iym

Title

Crystal structure of putative methylmalonate-semialdehyde dehydrogenase from Sinorhizobium meliloti 1021 complexed with NAD, target 011934

Components

Methylmalonate-semialdehyde dehydrogenase

Keywords

OXIDOREDUCTASE / structural genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC

Function / homology

Function and homology information

methylmalonate-semialdehyde dehydrogenase (CoA-acylating) / methylmalonate-semialdehyde dehydrogenase (acylating, NAD) activity / thymine catabolic process / L-valine catabolic process / nucleotide binding
Similarity search - Function

Biological species

Sinorhizobium meliloti (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.2 Å

Authors

Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. ...

Citation

Journal: To be Published
Title: Crystal structure of putative methylmalonate-semialdehyde dehydrogenase from Sinorhizobium meliloti 1021 complexed with NAD, target 011934
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. ...

History

Deposition	Jan 28, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 3, 2013	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2	Dec 6, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iy/4iym ftp://data.pdbj.org/pub/pdb/validation_reports/iy/4iym	HTTPS FTP

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Related structure data

Related structure data	4e4gS S: Starting model for refinement
Similar structure data	4e4g-1 4e4g-2 4zz7-3 5fhz-1 1o9j-d 4zz7-2 5ac2-1 1o04-2 4f3x-d 1nzw-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: NYSGRC-011934

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (7) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (7)

Deposited unit

A: Methylmalonate-semialdehyde dehydrogenase

B: Methylmalonate-semialdehyde dehydrogenase

C: Methylmalonate-semialdehyde dehydrogenase

D: Methylmalonate-semialdehyde dehydrogenase

E: Methylmalonate-semialdehyde dehydrogenase

F: Methylmalonate-semialdehyde dehydrogenase

G: Methylmalonate-semialdehyde dehydrogenase

H: Methylmalonate-semialdehyde dehydrogenase

I: Methylmalonate-semialdehyde dehydrogenase

J: Methylmalonate-semialdehyde dehydrogenase

K: Methylmalonate-semialdehyde dehydrogenase

L: Methylmalonate-semialdehyde dehydrogenase

M: Methylmalonate-semialdehyde dehydrogenase

N: Methylmalonate-semialdehyde dehydrogenase

O: Methylmalonate-semialdehyde dehydrogenase

P: Methylmalonate-semialdehyde dehydrogenase

hetero molecules

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

1

A: Methylmalonate-semialdehyde dehydrogenase

B: Methylmalonate-semialdehyde dehydrogenase

C: Methylmalonate-semialdehyde dehydrogenase

D: Methylmalonate-semialdehyde dehydrogenase

hetero molecules

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

2

E: Methylmalonate-semialdehyde dehydrogenase

F: Methylmalonate-semialdehyde dehydrogenase

G: Methylmalonate-semialdehyde dehydrogenase

H: Methylmalonate-semialdehyde dehydrogenase

hetero molecules

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

3

I: Methylmalonate-semialdehyde dehydrogenase

J: Methylmalonate-semialdehyde dehydrogenase

K: Methylmalonate-semialdehyde dehydrogenase

L: Methylmalonate-semialdehyde dehydrogenase

hetero molecules

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

4

M: Methylmalonate-semialdehyde dehydrogenase

N: Methylmalonate-semialdehyde dehydrogenase

O: Methylmalonate-semialdehyde dehydrogenase

P: Methylmalonate-semialdehyde dehydrogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	159.472, 170.910, 170.466
Angle α, β, γ (deg.)	90.000, 106.330, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

#1: Protein	Methylmalonate-semialdehyde dehydrogenase Mass: 57243.699 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: iolA, mmsA, R00726, SMc00781 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL References: UniProt: Q92RW4, methylmalonate-semialdehyde dehydrogenase (CoA-acylating)
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4622 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.43 Å³/Da / Density % sol: 49.47 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M MgCl2, 0.1M MES, pH 6.5, 30% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 1.075 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2012

Radiation

Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.075 Å / Relative weight: 1

Reflection

Resolution: 2.2→50 Å / Num. obs: 440045 / % possible obs: 99.8 % / Redundancy: 3.8 % / R_merge(I) obs: 0.131 / Χ²: 1.165 / Net I/σ(I): 5.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.2-2.24	3.7	0.64	21797	0.837	1	99.3
2.24-2.28	3.7	0.571	21876	0.851	1	99.3
2.28-2.32	3.7	0.526	21802	0.848	1	99.4
2.32-2.37	3.7	0.482	21917	0.868	1	99.5
2.37-2.42	3.7	0.429	21832	0.878	1	99.5
2.42-2.48	3.7	0.381	21962	0.886	1	99.6
2.48-2.54	3.7	0.333	21951	0.91	1	99.7
2.54-2.61	3.7	0.302	21890	0.928	1	99.8
2.61-2.69	3.7	0.264	22009	0.972	1	99.9
2.69-2.77	3.7	0.234	21988	0.978	1	99.9
2.77-2.87	3.8	0.205	22072	1.008	1	100
2.87-2.99	3.8	0.178	21981	1.056	1	100
2.99-3.12	3.8	0.144	22037	1.12	1	100
3.12-3.29	3.8	0.123	22046	1.186	1	100
3.29-3.49	3.8	0.102	22074	1.385	1	100
3.49-3.76	3.8	0.091	22057	1.669	1	100
3.76-4.14	3.8	0.081	22041	1.903	1	100
4.14-4.74	3.8	0.067	22165	1.844	1	100
4.74-5.97	3.8	0.063	22160	1.482	1	100
5.97-50	3.8	0.051	22388	1.515	1	99.9

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	6.88 Å	46.75 Å
Translation	6.88 Å	46.75 Å

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHASER	2.5.1	phasing
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
CBASS		data collection
HKL-3000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4E4G

4e4g

Resolution: 2.2→19.99 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.945 / WR_factor R_free: 0.1829 / WR_factor R_work: 0.1443 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8582 / SU B: 9.7 / SU ML: 0.124 / SU R Cruickshank DPI: 0.2358 / SU R_free: 0.1847 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2094	22028	5 %	RANDOM
R_work	0.1651	-	-	-
obs	0.1673	439434	99.48 %	-

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: 138.45 Å² / B_iso mean: 26.892 Å² / B_iso min: 7.53 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0 Å²	-0.01 Å²
2-	-	0.01 Å²	-0 Å²
3-	-	-	-0 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→19.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	58959	0	710	4622	64291

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	61228
X-RAY DIFFRACTION	r_angle_refined_deg	1.309	1.99	83136
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.832	5	7873
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.714	23.943	2579
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.586	15	8990
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.498	15	413
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	9136
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	46741

Refine LS restraints NCS

Ens-ID	Dom-ID	Number	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	718	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.31	19.37
1	1	715	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.34	19.37
1	1	715	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.29	19.37
1	1	718	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.25	19.37
1	1	715	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.36	19.37
1	1	715	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.34	19.37
1	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.32	19.37
1	1	717	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.32	19.37
1	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.31	19.37
1	1	717	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.26	19.37
1	1	718	X-RAY DIFFRACTION	TIGHT THERMAL	1.99	38.73
2	1	717	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.31	19.37
2	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.32	19.37
2	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.26	19.37
2	1	717	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.24	19.37
2	1	717	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.31	19.37
2	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.3	19.37
2	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.27	19.37
2	1	717	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.25	19.37
2	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.35	19.37
2	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.32	19.37
2	1	715	X-RAY DIFFRACTION	TIGHT THERMAL	2.42	38.73
3	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.23	19.37
3	1	716	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.3	19.37
3	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.31	19.37
3	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.22	19.37
3	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.26	19.37
3	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.28	19.37
3	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.32	19.37
3	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.28	19.37
3	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.25	19.37
3	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.29	19.37
3	1	718	X-RAY DIFFRACTION	TIGHT THERMAL	2.6	38.73
4	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.32	19.37
4	1	716	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.31	19.37
4	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.28	19.37
4	1	716	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.33	19.37
4	1	719	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.34	19.37
4	1	719	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.3	19.37
4	1	716	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.25	19.37
4	1	716	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.29	19.37
4	1	719	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.31	19.37
4	1	719	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.29	19.37
4	1	715	X-RAY DIFFRACTION	TIGHT THERMAL	2.3	38.73
5	1	716	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.27	19.37
5	1	716	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.3	19.37
5	1	719	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.32	19.37
5	1	716	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.32	19.37
5	1	716	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.28	19.37
5	1	715	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.31	19.37
5	1	715	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.33	19.37
5	1	718	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.32	19.37
5	1	718	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.26	19.37
5	1	715	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.29	19.37
5	1	718	X-RAY DIFFRACTION	TIGHT THERMAL	2.25	38.73
6	1	715	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.33	19.37
6	1	718	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.32	19.37
6	1	718	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.28	19.37
6	1	715	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.3	19.37
6	1	717	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.32	19.37
6	1	718	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.34	19.37
6	1	717	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.3	19.37
6	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.3	19.37
6	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.28	19.37
6	1	717	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.22	19.37
6	1	718	X-RAY DIFFRACTION	TIGHT THERMAL	2.44	38.73
7	1	717	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.31	19.37
7	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.3	19.37
7	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.29	19.37
7	1	717	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.24	19.37
7	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.36	19.37
7	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.33	19.37
7	1	713	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.25	19.37
7	1	713	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.26	19.37
7	1	716	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.31	19.37
7	1	716	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.23	19.37
7	1	715	X-RAY DIFFRACTION	TIGHT THERMAL	2.72	38.73
8	1	713	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.23	19.37
8	1	713	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.28	19.37
8	1	716	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.32	19.37
8	1	713	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.26	19.37
8	1	713	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.26	19.37
8	1	717	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.27	19.37
8	1	713	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.3	19.37
8	1	713	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.27	19.37
8	1	717	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.2	19.37
8	1	717	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.29	19.37
8	1	715	X-RAY DIFFRACTION	TIGHT THERMAL	2.83	38.73
9	1	713	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.31	19.37
9	1	713	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.32	19.37
9	1	717	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.23	19.37
9	1	713	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.24	19.37
9	1	713	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.24	19.37
9	1	717	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.26	19.37
9	1	717	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.15	19.37
9	1	713	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.27	19.37
9	1	713	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.3	19.37
9	1	717	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.27	19.37
9	1	718	X-RAY DIFFRACTION	TIGHT THERMAL	2.69	38.73
10	1	716	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.27	19.37
10	1	713	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.31	19.37
10	1	713	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.25	19.37
10	1	716	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.18	19.37
10	1	713	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.33	19.37
10	1	713	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.31	19.37
10	1	716	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.28	19.37
10	1	716	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.24	19.37
10	1	719	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.28	19.37
10	1	716	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.28	19.37
10	1	718	X-RAY DIFFRACTION	TIGHT THERMAL	2.69	38.73
11	1	716	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.27	19.37
11	1	720	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.29	19.37
11	1	716	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.33	19.37
11	1	716	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.33	19.37
11	1	720	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.24	19.37
11	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.27	19.37
11	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.31	19.37
11	1	718	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.29	19.37
11	1	713	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.34	19.37
11	1	713	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.32	19.37
11	1	715	X-RAY DIFFRACTION	TIGHT THERMAL	2.71	38.73
12	1	714	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.31	19.37
12	1	715	X-RAY DIFFRACTION	TIGHT THERMAL	2.57	38.73
13	1	718	X-RAY DIFFRACTION	TIGHT THERMAL	2.77	38.73
14	1	715	X-RAY DIFFRACTION	TIGHT THERMAL	2.68	38.73
15	1	715	X-RAY DIFFRACTION	TIGHT THERMAL	2.67	38.73
16	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	2.04	38.73
17	1	717	X-RAY DIFFRACTION	TIGHT THERMAL	2.3	38.73
18	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	2.23	38.73
19	1	717	X-RAY DIFFRACTION	TIGHT THERMAL	1.96	38.73
20	1	717	X-RAY DIFFRACTION	TIGHT THERMAL	2.13	38.73
21	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	2.33	38.73
22	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	2.43	38.73
23	1	717	X-RAY DIFFRACTION	TIGHT THERMAL	2.21	38.73
24	1	717	X-RAY DIFFRACTION	TIGHT THERMAL	2.51	38.73
25	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	2.26	38.73
26	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	2.2	38.73
27	1	717	X-RAY DIFFRACTION	TIGHT THERMAL	2.11	38.73
28	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	2.53	38.73
29	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	2.34	38.73
30	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	2.11	38.73
31	1	716	X-RAY DIFFRACTION	TIGHT THERMAL	2.06	38.73
32	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	1.85	38.73
33	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	1.6	38.73
34	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	2.19	38.73
35	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	1.94	38.73
36	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	1.9	38.73
37	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	2.17	38.73
38	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	2.33	38.73
39	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	1.89	38.73
40	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	1.93	38.73
41	1	716	X-RAY DIFFRACTION	TIGHT THERMAL	2.17	38.73
42	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	2.08	38.73
43	1	716	X-RAY DIFFRACTION	TIGHT THERMAL	2.38	38.73
44	1	719	X-RAY DIFFRACTION	TIGHT THERMAL	2.09	38.73
45	1	719	X-RAY DIFFRACTION	TIGHT THERMAL	2.1	38.73
46	1	716	X-RAY DIFFRACTION	TIGHT THERMAL	2	38.73
47	1	716	X-RAY DIFFRACTION	TIGHT THERMAL	2.11	38.73
48	1	719	X-RAY DIFFRACTION	TIGHT THERMAL	1.97	38.73
49	1	719	X-RAY DIFFRACTION	TIGHT THERMAL	2.44	38.73
50	1	716	X-RAY DIFFRACTION	TIGHT THERMAL	2.05	38.73
51	1	716	X-RAY DIFFRACTION	TIGHT THERMAL	2.15	38.73
52	1	719	X-RAY DIFFRACTION	TIGHT THERMAL	2.23	38.73
53	1	716	X-RAY DIFFRACTION	TIGHT THERMAL	2.47	38.73
54	1	716	X-RAY DIFFRACTION	TIGHT THERMAL	2.28	38.73
55	1	715	X-RAY DIFFRACTION	TIGHT THERMAL	1.92	38.73
56	1	715	X-RAY DIFFRACTION	TIGHT THERMAL	1.94	38.73
57	1	718	X-RAY DIFFRACTION	TIGHT THERMAL	2.62	38.73
58	1	718	X-RAY DIFFRACTION	TIGHT THERMAL	1.97	38.73
59	1	715	X-RAY DIFFRACTION	TIGHT THERMAL	2.26	38.73
60	1	715	X-RAY DIFFRACTION	TIGHT THERMAL	2.12	38.73
61	1	718	X-RAY DIFFRACTION	TIGHT THERMAL	2.42	38.73
62	1	718	X-RAY DIFFRACTION	TIGHT THERMAL	2.19	38.73
63	1	715	X-RAY DIFFRACTION	TIGHT THERMAL	2.3	38.73
64	1	717	X-RAY DIFFRACTION	TIGHT THERMAL	2.31	38.73
65	1	718	X-RAY DIFFRACTION	TIGHT THERMAL	2.08	38.73
66	1	717	X-RAY DIFFRACTION	TIGHT THERMAL	1.72	38.73
67	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	2.4	38.73
68	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	1.75	38.73
69	1	717	X-RAY DIFFRACTION	TIGHT THERMAL	1.75	38.73
70	1	717	X-RAY DIFFRACTION	TIGHT THERMAL	2.01	38.73
71	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	2.25	38.73
72	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	1.98	38.73
73	1	717	X-RAY DIFFRACTION	TIGHT THERMAL	1.92	38.73
74	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	2.02	38.73
75	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	2.01	38.73
76	1	713	X-RAY DIFFRACTION	TIGHT THERMAL	2.31	38.73
77	1	713	X-RAY DIFFRACTION	TIGHT THERMAL	1.76	38.73
78	1	716	X-RAY DIFFRACTION	TIGHT THERMAL	1.72	38.73
79	1	716	X-RAY DIFFRACTION	TIGHT THERMAL	1.79	38.73
80	1	713	X-RAY DIFFRACTION	TIGHT THERMAL	2.31	38.73
81	1	713	X-RAY DIFFRACTION	TIGHT THERMAL	1.94	38.73
82	1	716	X-RAY DIFFRACTION	TIGHT THERMAL	1.89	38.73
83	1	713	X-RAY DIFFRACTION	TIGHT THERMAL	1.97	38.73
84	1	713	X-RAY DIFFRACTION	TIGHT THERMAL	2	38.73
85	1	717	X-RAY DIFFRACTION	TIGHT THERMAL	2.26	38.73
86	1	713	X-RAY DIFFRACTION	TIGHT THERMAL	2.24	38.73
87	1	713	X-RAY DIFFRACTION	TIGHT THERMAL	2.68	38.73
88	1	717	X-RAY DIFFRACTION	TIGHT THERMAL	2.03	38.73
89	1	717	X-RAY DIFFRACTION	TIGHT THERMAL	2.18	38.73
90	1	713	X-RAY DIFFRACTION	TIGHT THERMAL	2.25	38.73
91	1	713	X-RAY DIFFRACTION	TIGHT THERMAL	2.78	38.73
92	1	717	X-RAY DIFFRACTION	TIGHT THERMAL	2.37	38.73
93	1	713	X-RAY DIFFRACTION	TIGHT THERMAL	1.52	38.73
94	1	713	X-RAY DIFFRACTION	TIGHT THERMAL	1.91	38.73
95	1	717	X-RAY DIFFRACTION	TIGHT THERMAL	2.32	38.73
96	1	717	X-RAY DIFFRACTION	TIGHT THERMAL	1.77	38.73
97	1	713	X-RAY DIFFRACTION	TIGHT THERMAL	1.95	38.73
98	1	713	X-RAY DIFFRACTION	TIGHT THERMAL	2.03	38.73
99	1	717	X-RAY DIFFRACTION	TIGHT THERMAL	1.96	38.73
100	1	716	X-RAY DIFFRACTION	TIGHT THERMAL	2.18	38.73
101	1	713	X-RAY DIFFRACTION	TIGHT THERMAL	2.3	38.73
102	1	713	X-RAY DIFFRACTION	TIGHT THERMAL	1.93	38.73
103	1	716	X-RAY DIFFRACTION	TIGHT THERMAL	1.65	38.73
104	1	713	X-RAY DIFFRACTION	TIGHT THERMAL	2.04	38.73
105	1	713	X-RAY DIFFRACTION	TIGHT THERMAL	2.02	38.73
106	1	716	X-RAY DIFFRACTION	TIGHT THERMAL	2.66	38.73
107	1	716	X-RAY DIFFRACTION	TIGHT THERMAL	2.26	38.73
108	1	719	X-RAY DIFFRACTION	TIGHT THERMAL	2.37	38.73
109	1	716	X-RAY DIFFRACTION	TIGHT THERMAL	1.57	38.73
110	1	716	X-RAY DIFFRACTION	TIGHT THERMAL	2.33	38.73
111	1	720	X-RAY DIFFRACTION	TIGHT THERMAL	2.12	38.73
112	1	716	X-RAY DIFFRACTION	TIGHT THERMAL	2.18	38.73
113	1	716	X-RAY DIFFRACTION	TIGHT THERMAL	2.73	38.73
114	1	720	X-RAY DIFFRACTION	TIGHT THERMAL	2.13	38.73
115	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	2.02	38.73
116	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	2.32	38.73
117	1	718	X-RAY DIFFRACTION	TIGHT THERMAL	2.16	38.73
118	1	713	X-RAY DIFFRACTION	TIGHT THERMAL	2.34	38.73
119	1	713	X-RAY DIFFRACTION	TIGHT THERMAL	2.22	38.73
120	1	714	X-RAY DIFFRACTION	TIGHT THERMAL	2.41	38.73

LS refinement shell

Resolution: 2.202→2.258 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.27	1614	-
R_work	0.223	29655	-
all	-	31269	-
obs	-	-	97.05 %

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	0.2652	-0.0062	0.0532	0.4329	0.057	0.1373	-0.011	0.0027	-0.0771	0.0401	0.0176	-0.0575	0.0526	0.0253	-0.0065	0.0619	0.0232	0.0207	0.0269	0.0053	0.0397	84.6466	-11.5512	-3.4663
2	0.2412	0.0631	0.0139	0.3963	0.0998	0.3401	-0.035	-0.0527	0.0529	0.008	0.0259	-0.0931	-0.0569	0.0807	0.0091	0.0388	-0.0111	-0.002	0.0455	-0.0167	0.0593	88.6761	25.4375	1.9793
3	0.2643	-0.0291	-0.0222	0.4106	0.0242	1.0082	-0.0534	0.0454	-0.016	-0.0562	-0.0159	0.1215	0.0333	-0.123	0.0693	0.0232	-0.018	-0.0101	0.06	-0.0224	0.0444	46.3367	7.7964	-16.4437
4	0.4009	0.0462	-0.1006	0.4769	0.1841	0.91	-0.0487	-0.1718	0.0653	0.1476	-0.0621	0.127	0.0217	-0.0555	0.1108	0.0815	-0.0093	0.0355	0.1497	-0.0464	0.055	49.8192	13.2773	20.8211
5	0.1617	0.0665	0.0125	0.4701	0.0097	0.2192	-0.0201	-0.0303	-0.0232	-0.0356	-0.0286	0.0732	0.0284	-0.0197	0.0486	0.0333	-0.0042	0.0208	0.0119	0.003	0.0775	17.9102	-8.8268	-78.4596
6	0.2505	0.0676	-0.0078	0.4538	-0.1038	0.2159	-0.0065	0.0173	0.0938	-0.0424	-0.0013	0.1346	-0.0675	-0.044	0.0077	0.0669	0.0203	-0.0172	0.0142	0.0081	0.1231	16.3716	28.3732	-83.849
7	0.3061	0.1329	-0.098	0.4533	-0.0607	0.8921	-0.0163	-0.0944	-0.0895	0.0518	-0.0774	-0.1267	0.0057	0.131	0.0937	0.0164	-0.0082	-0.0242	0.0565	0.0668	0.0964	57.4588	7.8956	-65.9721
8	0.4208	0.0251	-0.167	0.3903	0.0083	0.756	-0.0462	0.1193	0.0071	-0.1247	-0.0129	-0.0857	-0.0591	-0.0032	0.0591	0.087	-0.0013	0.0304	0.0548	0.0349	0.0602	54.0635	13.6727	-103.0307
9	0.2693	0.0879	0.104	0.6541	0.1014	0.1912	-0.0334	0.0013	-0.1147	-0.0441	0.0466	0.1863	0.0078	-0.0248	-0.0132	0.0437	-0.0372	-0.0141	0.0366	0.0212	0.2058	97.4967	-30.5879	-78.8546
10	0.3449	-0.0711	0.081	0.4831	-0.0776	0.231	-0.0499	0.0363	0.0501	-0.0851	0.0566	0.1822	-0.0239	-0.0789	-0.0067	0.0431	-0.0176	-0.0552	0.0503	0.0437	0.1651	96.1877	6.6527	-83.7031
11	0.2748	0.118	0.0793	0.3434	0.0861	0.331	-0.0278	-0.0133	-0.0824	-0.0271	0.0478	-0.0247	0.0117	0.0617	-0.02	0.0199	-0.0113	0.0144	0.0402	-0.004	0.0308	136.9166	-13.9693	-65.6928
12	0.457	0.0081	-0.0309	0.5181	-0.0581	0.4231	-0.0776	0.22	-0.0022	-0.2438	0.053	-0.0498	-0.0388	0.0936	0.0247	0.1631	-0.0978	0.0331	0.155	-0.0099	0.0123	134.0634	-7.8314	-102.6934
13	0.466	-0.2562	-0.0583	0.7644	0.1066	0.123	-0.1521	-0.0982	-0.0873	0.1337	0.1747	-0.1695	0.0805	0.1032	-0.0226	0.1204	0.1184	0.0056	0.1372	-0.0235	0.113	165.8828	-29.9728	-2.741
14	0.3995	0.0859	-0.0015	0.6018	0.1668	0.3828	-0.0844	-0.0552	0.1008	0.0827	0.1515	-0.2272	0.0237	0.2219	-0.0671	0.0382	0.0433	-0.062	0.1692	-0.0896	0.1479	167.4785	7.4533	1.5247
15	0.3428	-0.1855	0.1277	0.3336	0.0071	0.6604	-0.0329	0.0122	-0.0914	0.0447	0.0542	0.0598	0.0969	-0.049	-0.0213	0.0411	0.0026	0.0209	0.0424	0.0075	0.0314	126.3408	-13.3676	-15.5338
16	0.2095	0.0509	-0.0136	0.3646	0.0026	0.5526	-0.0848	-0.1161	0.0242	0.2062	0.0767	0.0365	0.0823	-0.0456	0.008	0.2122	0.1168	0.0339	0.1272	0.0062	0.028	130.027	-6.4505	21.3854

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-1 - 486
2	X-RAY DIFFRACTION	1	A	501
3	X-RAY DIFFRACTION	2	B	-1 - 486
4	X-RAY DIFFRACTION	2	B	500
5	X-RAY DIFFRACTION	3	C	-4 - 486
6	X-RAY DIFFRACTION	3	C	500
7	X-RAY DIFFRACTION	4	D	-1 - 486
8	X-RAY DIFFRACTION	4	D	500
9	X-RAY DIFFRACTION	5	E	-2 - 487
10	X-RAY DIFFRACTION	5	E	500
11	X-RAY DIFFRACTION	6	F	-1 - 486
12	X-RAY DIFFRACTION	6	F	501
13	X-RAY DIFFRACTION	7	G	-1 - 486
14	X-RAY DIFFRACTION	7	G	501
15	X-RAY DIFFRACTION	8	H	-1 - 487
16	X-RAY DIFFRACTION	8	H	500
17	X-RAY DIFFRACTION	9	I	-1 - 487
18	X-RAY DIFFRACTION	9	I	501
19	X-RAY DIFFRACTION	10	J	-1 - 486
20	X-RAY DIFFRACTION	10	J	500
21	X-RAY DIFFRACTION	11	K	-1 - 486
22	X-RAY DIFFRACTION	11	K	500
23	X-RAY DIFFRACTION	12	L	-1 - 487
24	X-RAY DIFFRACTION	12	L	500
25	X-RAY DIFFRACTION	13	M	-1 - 487
26	X-RAY DIFFRACTION	13	M	500
27	X-RAY DIFFRACTION	14	N	-1 - 486
28	X-RAY DIFFRACTION	14	N	500
29	X-RAY DIFFRACTION	15	O	-2 - 486
30	X-RAY DIFFRACTION	15	O	501
31	X-RAY DIFFRACTION	16	P	-1 - 487
32	X-RAY DIFFRACTION	16	P	500

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