PDB-2qg3: CRYSTAL STRUCTURE OF A TYW3 METHYLTRANSFERASE-LIKE PROTEIN (AF_20...

ID or keywords:

Entry

Database: PDB / ID: 2qg3

Title

CRYSTAL STRUCTURE OF A TYW3 METHYLTRANSFERASE-LIKE PROTEIN (AF_2059) FROM ARCHAEOGLOBUS FULGIDUS DSM 4304 AT 1.95 A RESOLUTION

Components

UPF0130 protein AF_2059

Keywords

UNKNOWN FUNCTION / TYW3 METHYLTRANSFERASE-LIKE PRROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2

Function / homology

Function and homology information

tRNAPhe 7-[(3-amino-3-carboxypropyl)-4-demethylwyosine37-N4]-methyltransferase / wybutosine biosynthetic process / tRNA methyltransferase activity / tRNA methylation
Similarity search - Function

Biological species

Archaeoglobus fulgidus DSM 4304 (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.95 Å

Authors

Joint Center for Structural Genomics (JCSG)

Citation

Journal: To be published
Title: Crystal structure of uncharacterized protein AF2059 (2648472) from Archaeoglobus fulgidus at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)

History

Deposition	Jun 28, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 17, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4	Jan 25, 2023	Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5	Nov 20, 2024	Group: Data collection / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2qg3.cif.gz	90.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2qg3_validation.pdf.gz	436.2 KB	Display	wwPDB validaton report
Full document	2qg3_full_validation.pdf.gz	438.1 KB	Display
Data in XML	2qg3_validation.xml.gz	15.7 KB	Display
Data in CIF	2qg3_validation.cif.gz	21.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qg/2qg3 ftp://data.pdbj.org/pub/pdb/validation_reports/qg/2qg3	HTTPS FTP

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Related structure data

Similar structure data	5xnc-3 4b2g-1 4e99-d 4rgp-d 5iro-6 5iro-3 5xnf-d 3dpn-1 6qb5-3 1i5z-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: 355678

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: UPF0130 protein AF_2059

B: UPF0130 protein AF_2059

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

1

A: UPF0130 protein AF_2059

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

2

B: UPF0130 protein AF_2059

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

Unit cell

Length a, b, c (Å)	59.334, 59.334, 109.102
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	77
Space group name H-M	P4₂

Components on special symmetry positions

ID	Model	Components
1	1	A-223- HOH

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	MSE	MSE	ASP	ASP	2	A	A	2 - 24	14 - 36
2	1	1	MSE	MSE	ASP	ASP	2	B	B	2 - 24	14 - 36
3	2	1	PHE	PHE	PHE	PHE	6	A	A	25	37
4	2	1	PHE	PHE	PHE	PHE	6	B	B	25	37
5	3	1	ASP	ASP	ASN	ASN	2	A	A	26 - 35	38 - 47
6	3	1	ASP	ASP	ASN	ASN	2	B	B	26 - 35	38 - 47
7	4	1	SER	SER	ASP	ASP	5	A	A	36 - 38	48 - 50
8	4	1	SER	SER	ASP	ASP	5	B	B	36 - 38	48 - 50
1	1	2	ASP	ASP	LEU	LEU	2	A	A	39 - 55	51 - 67
2	1	2	ASP	ASP	LEU	LEU	2	B	B	39 - 55	51 - 67
3	2	2	GLU	GLU	GLU	GLU	6	A	A	56	68
4	2	2	GLU	GLU	GLU	GLU	6	B	B	56	68
1	1	3	LYS	LYS	LYS	LYS	6	A	A	57	69
2	1	3	LYS	LYS	LYS	LYS	6	B	B	57	69
3	2	3	PRO	PRO	GLY	GLY	2	A	A	58 - 68	70 - 80
4	2	3	PRO	PRO	GLY	GLY	2	B	B	58 - 68	70 - 80
5	3	3	ALA	ALA	ARG	ARG	2	A	A	82 - 87	94 - 99
6	3	3	ALA	ALA	ARG	ARG	2	B	B	82 - 87	94 - 99
1	1	4	LYS	LYS	ALA	ALA	2	A	A	88 - 109	100 - 121
2	1	4	LYS	LYS	ALA	ALA	2	B	B	88 - 109	100 - 121
3	2	4	LYS	LYS	LYS	LYS	5	A	A	110	122
4	2	4	LYS	LYS	LYS	LYS	5	B	B	110	122
5	3	4	LEU	LEU	ALA	ALA	2	A	A	111 - 116	123 - 128
6	3	4	LEU	LEU	ALA	ALA	2	B	B	111 - 116	123 - 128
7	4	4	ASN	ASN	ASN	ASN	5	A	A	117	129
8	4	4	ASN	ASN	ASN	ASN	5	B	B	117	129
9	5	4	THR	THR	ARG	ARG	2	A	A	118 - 123	130 - 135
10	5	4	THR	THR	ARG	ARG	2	B	B	118 - 123	130 - 135
11	6	4	SER	SER	SER	SER	5	A	A	124	136
12	6	4	SER	SER	SER	SER	5	B	B	124	136
13	7	4	GLY	GLY	SER	SER	2	A	A	125 - 130	137 - 142
14	7	4	GLY	GLY	SER	SER	2	B	B	125 - 130	137 - 142
15	8	4	ASN	ASN	ASN	ASN	5	A	A	131	143
16	8	4	ASN	ASN	ASN	ASN	5	B	B	131	143
17	9	4	TYR	TYR	ALA	ALA	2	A	A	132 - 137	144 - 149
18	9	4	TYR	TYR	ALA	ALA	2	B	B	132 - 137	144 - 149
19	10	4	GLU	GLU	ASP	ASP	2	A	A	143 - 155	155 - 167
20	10	4	GLU	GLU	ASP	ASP	2	B	B	143 - 155	155 - 167
1	1	5	ASP	ASP	ALA	ALA	2	A	A	156 - 157	168 - 169
2	1	5	ASP	ASP	ALA	ALA	2	B	B	156 - 157	168 - 169
3	2	5	TYR	TYR	TYR	TYR	5	A	A	158	170
4	2	5	TYR	TYR	TYR	TYR	5	B	B	158	170

NCS ensembles :

ID
1
2
3
4
5

#1: Protein	UPF0130 protein AF_2059 Mass: 23804.623 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea) Species: Archaeoglobus fulgidus / Strain: VC-16, DSM 4304, JCM 9628, NBRC 100126 / Gene: 2648472, AF_2059 / Plasmid: pMH1 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: O28220
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 81 / 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: 2

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)	Description
1	2.02	39.01	TWO CRYSTALS WERE USED FOR MAD PHASING. A HIGHER RESOLUTION (1.95 A) PEAK WAVELENGTH DATA SET WAS COMBINED WITH THE THREE-WAVELENGTH MAD DATA COLLECTED FROM A PREVIOUS CRYSTAL TO 2.7 A USING AUTOSHARP.
2

Crystal grow

Temperature (K)	Crystal-ID	Method	pH	Details
293	1	vapor diffusion, sitting drop	4	NANODROP, 0.09M Citric acid, 0.01M Trisodium citrate, 20% MPD, Additive: 0.01 M Phenol, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 4.0
293	2	vapor diffusion, sitting drop	4.1	NANODROP, 0.08M Citric acid, 0.02M Trisodium citrate, 22% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 4.1

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	2

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SSRL	BL9-2	1	0.979105
SYNCHROTRON	SSRL	BL11-1	2	0.885567, 0.979508, 0.979224

Detector

Type	ID	Detector	Date	Details
ADSC QUANTUM 315	1	CCD	Jul 31, 2004	Flat collimating mirror, toroid focusing mirror
ADSC QUANTUM 315	2	CCD	Jul 5, 2004	Flat mirror (vertical focusing)

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Double crystal Si(111)	SINGLE WAVELENGTH	M	x-ray	1
2	Single crystal Si(111) bent (horizontal focusing)	MAD	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.979105	1
2	0.885567	1
3	0.979508	1
4	0.979224	1

Reflection

Resolution: 1.95→28.628 Å / Num. obs: 27454 / % possible obs: 99.8 % / Redundancy: 3.7 % / B_iso Wilson estimate: 24.94 Å² / R_merge(I) obs: 0.088 / R_sym value: 0.088 / Net I/σ(I): 7.5

Reflection shell

Diffraction-ID: 1,2

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.95-2.06	3.8	0.756	1	14992	3997	0.756	99.8
2.06-2.18	3.8	0.538	1.4	14289	3792	0.538	99.8
2.18-2.33	3.8	0.358	2.1	13333	3550	0.358	99.9
2.33-2.52	3.8	0.271	2.8	12407	3292	0.271	99.9
2.52-2.76	3.8	0.173	4.3	11531	3055	0.173	100
2.76-3.08	3.8	0.104	7.2	10408	2756	0.104	99.9
3.08-3.56	3.8	0.065	10.5	9179	2445	0.065	99.9
3.56-4.36	3.7	0.045	14.4	7692	2070	0.045	99.9
4.36-6.17	3.7	0.031	19.9	5868	1604	0.031	99.7
6.17-28.628	3.6	0.022	21.7	3247	893	0.022	98.8

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
MolProbity	3beta29	model building
SHELX		phasing
REFMAC	5.2.0005	refinement
SCALA		data scaling
XSCALE		data scaling
PDB_EXTRACT	3	data extraction
SHARP		phasing
Blu-Ice		data collection
XDS		data reduction
SHELXD		phasing

Refinement

Method to determine structure:

MAD / Resolution: 1.95→28.628 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.926 / SU B: 11.074 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.169
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. THERE ARE SOME UNMODELED DIFFERENCE DENSITY PEAKS ALONG THE CRYSTALLOGRAPHIC TWO- ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.253	1377	5 %	RANDOM
R_work	0.199	-	-	-
obs	0.201	27438	99.77 %	-

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 mean: 25.35 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.41 Å²	0 Å²	0 Å²
2-	-	1.41 Å²	0 Å²
3-	-	-	-2.83 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→28.628 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2876	0	0	81	2957

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	2941
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2742
X-RAY DIFFRACTION	r_angle_refined_deg	1.495	1.965	3996
X-RAY DIFFRACTION	r_angle_other_deg	0.825	3	6317
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.561	5	388
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.5	25	114
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.935	15	491
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.398	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	468
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3310
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	573
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	581
X-RAY DIFFRACTION	r_nbd_other	0.162	0.2	2596
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	1478
X-RAY DIFFRACTION	r_nbtor_other	0.09	0.2	1825
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.125	0.2	79
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.104	0.2	30
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.184	0.2	89
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.156	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	2.309	3	1948
X-RAY DIFFRACTION	r_mcbond_other	0.553	3	786
X-RAY DIFFRACTION	r_mcangle_it	3.498	5	3036
X-RAY DIFFRACTION	r_scbond_it	5.868	8	1147
X-RAY DIFFRACTION	r_scangle_it	8.115	11	957

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	196	TIGHT POSITIONAL	0.04	0.05
1	291	MEDIUM POSITIONAL	0.18	0.5
1	44	LOOSE POSITIONAL	1.56	5
1	196	TIGHT THERMAL	0.16	0.5
1	291	MEDIUM THERMAL	0.87	2
1	44	LOOSE THERMAL	1.37	10
2	101	TIGHT POSITIONAL	0.06	0.05
2	142	MEDIUM POSITIONAL	0.16	0.5
2	15	LOOSE POSITIONAL	0.46	5
2	101	TIGHT THERMAL	0.29	0.5
2	142	MEDIUM THERMAL	0.92	2
2	15	LOOSE THERMAL	4.25	10
3	99	TIGHT POSITIONAL	0.05	0.05
3	123	MEDIUM POSITIONAL	0.22	0.5
3	12	LOOSE POSITIONAL	0.73	5
3	99	TIGHT THERMAL	0.21	0.5
3	123	MEDIUM THERMAL	0.63	2
3	12	LOOSE THERMAL	1.35	10
4	349	TIGHT POSITIONAL	0.05	0.05
4	551	MEDIUM POSITIONAL	0.19	0.5
4	25	LOOSE POSITIONAL	0.65	5
4	349	TIGHT THERMAL	0.24	0.5
4	551	MEDIUM THERMAL	0.95	2
4	25	LOOSE THERMAL	2.67	10
5	12	TIGHT POSITIONAL	0.03	0.05
5	13	MEDIUM POSITIONAL	0.27	0.5
5	14	LOOSE POSITIONAL	0.16	5
5	12	TIGHT THERMAL	0.19	0.5
5	13	MEDIUM THERMAL	1.26	2
5	14	LOOSE THERMAL	3.08	10

LS refinement shell

Resolution: 1.95→2.001 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.308	92	-
R_work	0.264	1939	-
obs	-	2031	99.75 %

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	1.6633	1.0833	-0.7374	2.088	-0.2977	2.3794	0.0284	-0.1512	0.0378	0.1285	-0.0967	-0.2534	-0.2783	0.9003	0.0683	0.2345	-0.2457	-0.0995	0.354	0.0724	0.1578	17.1281	9.3085	77.7968
2	0.4611	-0.1423	0.3925	0.8925	0.1288	3.6651	0.0957	0.045	0.0513	0.1935	-0.2987	-0.1477	-0.2469	0.4562	0.203	0.0433	-0.1013	-0.0191	0.1535	0.0914	0.1063	8.4693	3.3454	64.6847
3	1.0638	0.4377	0.8532	0.9993	1.1338	1.4322	0.0538	0.0415	0.1832	0.1557	-0.3239	0.0784	-0.1001	0.0167	0.2701	0.2079	-0.0869	-0.0098	0.1182	0.077	0.1139	5.1102	12.2788	61.9469
4	1.246	-0.4182	-0.6283	2.2302	-0.9425	4.2901	-0.0059	0.0261	-0.115	-0.2339	-0.0197	0.0626	0.6375	-0.3507	0.0256	0.0778	-0.0725	-0.0097	-0.0444	0.0027	0.0428	22.7424	11.1077	26.1199
5	0.5454	-0.0205	0.441	0.1917	0.4437	5.4389	0.0186	-0.0294	-0.0033	-0.053	0.0662	-0.0682	0.4642	0.0729	-0.0848	-0.038	-0.0095	-0.0054	-0.0598	-0.0133	0.0733	28.0216	20.4435	39.7287
6	0.1201	0.0465	0.5937	0.5438	0.6023	4.559	0.0113	-0.0515	0.0147	0.0131	-0.015	0.0431	0.0454	-0.5125	0.0037	-0.0851	-0.0247	0.0038	0.0959	0.0025	0.0437	21.0241	23.7007	46.5829

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	2 - 49	14 - 61
2	X-RAY DIFFRACTION	2	A	A	50 - 137	62 - 149
3	X-RAY DIFFRACTION	3	A	A	138 - 196	150 - 208
4	X-RAY DIFFRACTION	4	B	B	1 - 49	13 - 61
5	X-RAY DIFFRACTION	5	B	B	50 - 137	62 - 149
6	X-RAY DIFFRACTION	6	B	B	138 - 189	150 - 201

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