PDB-5yhi: Crystal structure of YiiM from Escherichia coli

ID or keywords:

Entry

Database: PDB / ID: 5yhi

Title

Crystal structure of YiiM from Escherichia coli

Components

Protein YiiM

Keywords

OXIDOREDUCTASE / enzyme / MOSC

Function / homology

Function and homology information

toxin catabolic process / oxidoreductase activity, acting on other nitrogenous compounds as donors / molybdenum ion binding / response to toxic substance / pyridoxal phosphate binding / oxidoreductase activity / protein homodimerization activity / cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.85 Å

Authors

Namgung, B. / Kim, J.H. / Song, W.S. / Yoon, S.I.

Citation

Journal: Sci Rep / Year: 2018
Title: Crystal structure of the hydroxylaminopurine resistance protein, YiiM, and its putative molybdenum cofactor-binding catalytic site.
Authors: Namgung, B. / Kim, J.H. / Song, W.S. / Yoon, S.I.

History

Deposition	Sep 28, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 7, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5yhi.cif.gz	174.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5yhi.ent.gz	138.7 KB	Display	PDB format
PDBx/mmJSON format	5yhi.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5yhi_validation.pdf.gz	1008.4 KB	Display	wwPDB validaton report
Full document	5yhi_full_validation.pdf.gz	1010.1 KB	Display
Data in XML	5yhi_validation.xml.gz	15.4 KB	Display
Data in CIF	5yhi_validation.cif.gz	20.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yh/5yhi ftp://data.pdbj.org/pub/pdb/validation_reports/yh/5yhi	HTTPS FTP

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Related structure data

Related structure data	5yhhC 1o65S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	7mc5-d 2ih4-2 1x7i-d 4on0-1 2np6-2 1li7-1 3axs-d 2q6w-2 2ih2-2 2jg3-1 Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (1)

Deposited unit

A: Protein YiiM

B: Protein YiiM

hetero molecules

52.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	56.162, 84.837, 107.630
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	TYR	TYR	TYR	TYR	5	A	A	3 - 8	9 - 14
2	1	1	TYR	TYR	TYR	TYR	5	B	B	3 - 8	9 - 14
1	1	2	ILE	ILE	GLY	GLY	5	A	A	26 - 41	32 - 47
2	1	2	ILE	ILE	GLY	GLY	5	B	B	26 - 41	32 - 47
1	1	3	ASP	ASP	PRO	PRO	3	A	A	42 - 61	48 - 67
2	1	3	ASP	ASP	PRO	PRO	3	B	B	42 - 61	48 - 67
1	1	4	ARG	ARG	GLY	GLY	3	A	A	62 - 85	68 - 91
2	1	4	ARG	ARG	GLY	GLY	3	B	B	62 - 85	68 - 91
1	2	4	ARG	ARG	GLY	GLY	3	A	A	117 - 143	123 - 149
2	2	4	ARG	ARG	GLY	GLY	3	B	B	117 - 143	123 - 149
1	1	5	GLU	GLU	PRO	PRO	3	A	A	86 - 116	92 - 122
2	1	5	GLU	GLU	PRO	PRO	3	B	B	86 - 116	92 - 122
1	1	6	TRP	TRP	VAL	VAL	3	A	A	144 - 166	150 - 172
2	1	6	TRP	TRP	VAL	VAL	3	B	B	144 - 166	150 - 172
1	1	7	SER	SER	ARG	ARG	3	A	A	167 - 220	173 - 226
2	1	7	SER	SER	ARG	ARG	3	B	B	167 - 220	173 - 226
1	1	8	PO4	PO4	PO4	PO4	1	A	C	301
2	1	8	PO4	PO4	PO4	PO4	1	B	D	301

NCS ensembles :

ID
1
2
3
4
5
6
7
8

#1: Protein	Protein YiiM Mass: 25930.303 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: yiiM, b3910, JW5559 / Production host: Escherichia coli (E. coli) / Strain (production host): TP1000 / References: UniProt: P32157
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.24 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 1.1M ammonium dihydrogen phosphate, 0.08M CHES, pH 9.5, 20% glycerol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.98 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 24, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.85→30 Å / Num. obs: 12483 / % possible obs: 99.7 % / Redundancy: 6.3 % / R_merge(I) obs: 0.122 / Net I/σ(I): 14.7
Reflection shell	Resolution: 2.85→2.9 Å / R_merge(I) obs: 0.43 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 590

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1O65

1o65

Resolution: 2.85→30 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.909 / SU B: 33.578 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R Free: 0.366 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24227	599	4.8 %	RANDOM
R_work	0.20147	-	-	-
obs	0.20345	11838	99.54 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å

Displacement parameters

B_iso mean: 51.648 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.46 Å²	0 Å²	0 Å²
2-	-	2.45 Å²	0 Å²
3-	-	-	-0.99 Å²

Refinement step

Cycle: 1 / Resolution: 2.85→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3193	0	10	0	3203

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	3285
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2220
X-RAY DIFFRACTION	r_angle_refined_deg	1.283	1.949	4461
X-RAY DIFFRACTION	r_angle_other_deg	0.88	3	5362
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.364	5	397
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.656	23.462	156
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.237	15	517
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.675	15	23
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	470
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	3664
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	699
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	0.35	1.5	2002
X-RAY DIFFRACTION	r_mcbond_other	0.086	1.5	818
X-RAY DIFFRACTION	r_mcangle_it	0.708	2	3200
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.244	3	1283
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.988	4.5	1261
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Number	Type	Rms dev position (Å)	Weight position
1	35	MEDIUM POSITIONAL	0.1	0.5
1	51	LOOSE POSITIONAL	0.19	5
1	35	MEDIUM THERMAL	0.46	2
1	51	LOOSE THERMAL	0.35	10
2	93	MEDIUM POSITIONAL	0.15	0.5
2	99	LOOSE POSITIONAL	0.42	5
2	93	MEDIUM THERMAL	0.2	2
2	99	LOOSE THERMAL	0.34	10
3	63	TIGHT POSITIONAL	0.03	0.05
3	69	LOOSE POSITIONAL	0.04	5
3	63	TIGHT THERMAL	0.06	0.5
3	69	LOOSE THERMAL	0.07	10
4	300	TIGHT POSITIONAL	0.03	0.05
4	402	LOOSE POSITIONAL	0.04	5
4	300	TIGHT THERMAL	0.06	0.5
4	402	LOOSE THERMAL	0.08	10
5	182	TIGHT POSITIONAL	0.03	0.05
5	220	LOOSE POSITIONAL	0.04	5
5	182	TIGHT THERMAL	0.06	0.5
5	220	LOOSE THERMAL	0.09	10
6	135	TIGHT POSITIONAL	0.03	0.05
6	148	LOOSE POSITIONAL	0.04	5
6	135	TIGHT THERMAL	0.07	0.5
6	148	LOOSE THERMAL	0.08	10
7	321	TIGHT POSITIONAL	0.04	0.05
7	412	LOOSE POSITIONAL	0.05	5
7	321	TIGHT THERMAL	0.08	0.5
7	412	LOOSE THERMAL	0.09	10
8	5	TIGHT POSITIONAL	0.02	0.05
8	5	TIGHT THERMAL	0.13	0.5

LS refinement shell

Resolution: 2.852→2.926 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.368	39	-
R_work	0.27	827	-
obs	-	-	96.12 %

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	2.5567	-1.0161	-1.6448	2.8771	0.4819	3.8946	-0.2336	-0.0412	-0.3032	0.1983	0.0709	0.3668	0.639	-0.0753	0.1627	0.285	0.0214	-0.069	0.7169	0.0149	0.1592	56.421	-0.645	221.389
2	3.2284	-0.9027	-2.1811	1.7897	1.9895	5.7916	0.1645	0.4697	0.0404	-0.3268	-0.1261	0.1014	-0.1941	-0.3833	-0.0385	0.2411	0.0419	-0.0624	0.7357	0.0047	0.1077	59.248	17.713	187.236
3	4.2031	-0.1081	-2.4871	3.5717	-0.3466	4.0255	0.207	-0.0196	0.3131	-0.1063	-0.0023	0.0093	-0.0514	0.0163	-0.2047	0.1275	0.025	-0.0355	0.6337	-0.0237	0.0458	53.583	18.656	216.888
4	3.9565	-3.109	1.0185	4.102	-1.8713	5.2433	-0.1084	-0.0674	-0.2077	-0.0454	0.1061	-0.1775	0.326	0.3692	0.0023	0.1878	0.0986	0.015	0.8257	-0.0752	0.0906	72.554	6.636	197.765

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 166
2	X-RAY DIFFRACTION	2	B	0 - 166
3	X-RAY DIFFRACTION	3	A	167 - 224
4	X-RAY DIFFRACTION	4	B	167 - 223

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