PDB-2x5h: Crystal structure of the ORF131 L26M L51M double mutant from Sulf...

ID or keywords:

Entry

Database: PDB / ID: 2x5h

Title

Crystal structure of the ORF131 L26M L51M double mutant from Sulfolobus islandicus rudivirus 1

Components

ORF 131

Keywords

VIRAL PROTEIN

Function / homology

Signal recognition particle alu RNA binding heterodimer, srp9/1 - #60 / : / PHA01746-like protein / Signal recognition particle alu RNA binding heterodimer, srp9/1 / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein 131

Function and homology information

Biological species

SULFOLOBUS ISLANDICUS RUDIVIRUS 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Naismith, J.H. / White, M.F.

Citation

Journal: J.Struct.Funct.Genom. / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...

History

Deposition	Feb 8, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 21, 2010	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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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Download

PDBx/mmCIF format	2x5h.cif.gz	168.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2x5h.ent.gz	136.2 KB	Display	PDB format
PDBx/mmJSON format	2x5h.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2x5h_validation.pdf.gz	463 KB	Display	wwPDB validaton report
Full document	2x5h_full_validation.pdf.gz	466.9 KB	Display
Data in XML	2x5h_validation.xml.gz	19.9 KB	Display
Data in CIF	2x5h_validation.cif.gz	28.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x5/2x5h ftp://data.pdbj.org/pub/pdb/validation_reports/x5/2x5h	HTTPS FTP

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Related structure data

Related structure data	2ivyC 2jg5C 2jg6C 2vw8C 2vxzC 2wj9C 2x0oC 2x3dC 2x3eC 2x3fC 2x3gC 2x3lC 2x3mC 2x3nC 2x3oC 2x48C 2x4gC 2x4hC 2x4iC 2x4jC 2x4kC 2x4lC 2x5cC 2x5dC 2x5fC 2x5gSC 2x5pC 2x5qC 2x5rC 2x5tC 2x7bC 2x7iC 2xu2C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2lq8-d 6ere-2 2wpt-d 6dnm-d 4qao-2 4ifi-d 5t20-1 4cso-1 4cso-3 4gao-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) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ORF 131

B: ORF 131

C: ORF 131

D: ORF 131

hetero molecules

44.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ORF 131

D: ORF 131

hetero molecules

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

2

B: ORF 131

C: ORF 131

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

Unit cell

Length a, b, c (Å)	37.940, 46.971, 48.976
Angle α, β, γ (deg.)	90.22, 95.05, 91.78
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
1	2	A
2	2	B
3	2	D
1	3	A
2	3	D
1	4	A
2	4	D
1	5	A
2	5	D
1	6	A
2	6	D

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	LYS	LYS	ALA	ALA	5	A	A	13 - 40	14 - 41
2	1	1	LYS	LYS	ALA	ALA	5	B	B	13 - 40	14 - 41
3	1	1	LYS	LYS	ALA	ALA	5	C	C	13 - 40	14 - 41
1	2	1	TYR	TYR	THR	THR	5	A	A	49 - 52	50 - 53
2	2	1	TYR	TYR	THR	THR	5	B	B	49 - 52	50 - 53
3	2	1	TYR	TYR	THR	THR	5	C	C	49 - 52	50 - 53
1	3	1	ILE	ILE	SER	SER	5	A	A	63 - 84	64 - 85
2	3	1	ILE	ILE	SER	SER	5	B	B	63 - 84	64 - 85
3	3	1	ILE	ILE	SER	SER	5	C	C	63 - 84	64 - 85
1	1	2	VAL	VAL	ARG	ARG	6	A	A	41 - 48	42 - 49
2	1	2	VAL	VAL	ARG	ARG	6	B	B	41 - 48	42 - 49
3	1	2	VAL	VAL	ARG	ARG	6	D	D	41 - 48	42 - 49
1	2	2	ILE	ILE	GLN	GLN	6	A	A	53 - 62	54 - 63
2	2	2	ILE	ILE	GLN	GLN	6	B	B	53 - 62	54 - 63
3	2	2	ILE	ILE	GLN	GLN	6	D	D	53 - 62	54 - 63
1	3	2	ASP	ASP	TYR	TYR	6	A	A	85 - 90	86 - 91
2	3	2	ASP	ASP	TYR	TYR	6	B	B	85 - 90	86 - 91
3	3	2	ASP	ASP	TYR	TYR	6	D	D	85 - 90	86 - 91
1	1	3	GLN	GLN	ARG	ARG	5	A	A	14 - 24	15 - 25
2	1	3	GLN	GLN	ARG	ARG	5	D	D	14 - 24	15 - 25
1	2	3	ASP	ASP	LEU	LEU	5	A	A	69 - 80	70 - 81
2	2	3	ASP	ASP	LEU	LEU	5	D	D	69 - 80	70 - 81
1	1	4	ILE	ILE	PRO	PRO	6	A	A	25 - 42	26 - 43
2	1	4	ILE	ILE	PRO	PRO	6	D	D	25 - 42	26 - 43
1	1	5	LYS	LYS	GLN	GLN	6	A	A	46 - 68	47 - 69
2	1	5	LYS	LYS	GLN	GLN	6	D	D	46 - 68	47 - 69
1	1	6	GLU	GLU	TYR	TYR	6	A	A	81 - 90	82 - 91
2	1	6	GLU	GLU	TYR	TYR	6	D	D	81 - 90	82 - 91

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	ORF 131 / UNCHARACTERIZED PROTEIN 131 / CAG38830 Mass: 11199.035 Da / Num. of mol.: 4 / Fragment: TRUNCATED VERSION, RESIDUES 1-96 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS ISLANDICUS RUDIVIRUS 1 / Variant: XX / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): BL21 / References: UniProt: Q8QL44
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, LEU 26 TO MET ENGINEERED RESIDUE IN CHAIN A, LEU 51 TO MET ...ENGINEERED RESIDUE IN CHAIN A, LEU 26 TO MET ENGINEERED RESIDUE IN CHAIN A, LEU 51 TO MET ENGINEERED RESIDUE IN CHAIN B, LEU 26 TO MET ENGINEERED RESIDUE IN CHAIN B, LEU 51 TO MET ENGINEERED RESIDUE IN CHAIN C, LEU 26 TO MET ENGINEERED RESIDUE IN CHAIN C, LEU 51 TO MET ENGINEERED RESIDUE IN CHAIN D, LEU 26 TO MET ENGINEERED RESIDUE IN CHAIN D, LEU 51 TO MET

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 43 % / Description: NONE
Crystal grow	Details: 2.1 M SODIUM MALONATE AND CRYOPROTECTED WITH 2.4 M MALONATE.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
Detector	Type: ADSC CCD / Detector: CCD / Date: Jul 26, 2004 / Details: MIRRORS
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.939 Å / Relative weight: 1
Reflection	Resolution: 1.8→14 Å / Num. obs: 28543 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / B_iso Wilson estimate: 0 Å² / R_merge(I) obs: 0.04 / Net I/σ(I): 24.8
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.19 / Mean I/σ(I) obs: 6.5 / % possible all: 95

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X5G

2x5g

Resolution: 1.8→14 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.909 / SU B: 6.297 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25715	1521	5.1 %	RANDOM
R_work	0.19996	-	-	-
obs	0.20282	28543	96.68 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 27.173 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.19 Å²	-0.33 Å²	-0.08 Å²
2-	-	0.2 Å²	0.19 Å²
3-	-	-	-0.04 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2998	0	5	380	3383

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	3078
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2204
X-RAY DIFFRACTION	r_angle_refined_deg	1.149	1.979	4121
X-RAY DIFFRACTION	r_angle_other_deg	0.772	3	5434
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.658	5	381
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.429	25.664	143
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.229	15	663
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.823	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	463
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	3312
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	556
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	599
X-RAY DIFFRACTION	r_nbd_other	0.179	0.2	2281
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	1488
X-RAY DIFFRACTION	r_nbtor_other	0.082	0.2	1760
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	276
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	0.154	0.2	21
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.225	0.2	85
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.159	0.2	41
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	0.902	1.5	2504
X-RAY DIFFRACTION	r_mcbond_other	0.16	1.5	755
X-RAY DIFFRACTION	r_mcangle_it	0.995	2	3018
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.787	3	1384
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.451	4.5	1096
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

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	317	medium positional	0.21	0.5
1	2	B	317	medium positional	0.14	0.5
1	3	C	317	medium positional	0.2	0.5
3	1	A	136	medium positional	0.15	0.5
3	2	D	136	medium positional	0.15	0.5
1	1	A	412	loose positional	0.86	5
1	2	B	412	loose positional	0.71	5
1	3	C	412	loose positional	0.79	5
2	1	A	351	loose positional	0.98	5
2	2	B	351	loose positional	0.99	5
2	3	D	351	loose positional	1.49	5
3	1	A	173	loose positional	0.8	5
3	2	D	173	loose positional	0.8	5
4	1	A	226	loose positional	0.81	5
4	2	D	226	loose positional	0.81	5
5	1	A	317	loose positional	1	5
5	2	D	317	loose positional	1	5
6	1	A	156	loose positional	0.84	5
6	2	D	156	loose positional	0.84	5
1	1	A	317	medium thermal	0.67	2
1	2	B	317	medium thermal	0.65	2
1	3	C	317	medium thermal	0.73	2
3	1	A	136	medium thermal	0.6	2
3	2	D	136	medium thermal	0.6	2
1	1	A	412	loose thermal	1.22	10
1	2	B	412	loose thermal	1.02	10
1	3	C	412	loose thermal	1.37	10
2	1	A	351	loose thermal	2.29	10
2	2	B	351	loose thermal	1.99	10
2	3	D	351	loose thermal	2.16	10
3	1	A	173	loose thermal	1.19	10
3	2	D	173	loose thermal	1.19	10
4	1	A	226	loose thermal	1.16	10
4	2	D	226	loose thermal	1.16	10
5	1	A	317	loose thermal	1.76	10
5	2	D	317	loose thermal	1.76	10
6	1	A	156	loose thermal	2.03	10
6	2	D	156	loose thermal	2.03	10

LS refinement shell

Resolution: 1.8→1.846 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.261	117	-
R_work	0.195	1989	-
obs	-	-	95.29 %

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	0.6706	-0.3702	1.1783	0.743	-0.4057	3.7868	-0.0202	-0.0389	0.0056	0.0754	0.018	0.0116	0.0631	0.0453	0.0022	-0.1991	0.0332	0.022	-0.1811	0.0014	-0.1424	39.565	0.561	6.396
2	0.6372	-0.8156	-0.3248	3.0417	3.4488	4.7706	0.0391	0.0338	0.0083	-0.2488	-0.0338	-0.0028	-0.3085	-0.0005	-0.0053	-0.1483	-0.0024	0.0197	-0.1926	-0.0044	-0.121	18.04	22.338	-8.091
3	1.6615	0.9227	1.9065	2.1024	0.9367	5.862	0.14	-0.1778	-0.2409	0.1817	-0.0699	-0.1304	0.2138	-0.1	-0.0702	-0.1559	0.0315	0.0521	-0.1596	-0.0026	-0.0522	18.055	23.062	7.57
4	0.6663	0.025	-0.3008	1.0166	1.378	5.1278	0.005	-0.0208	-0.0899	-0.062	0.0792	-0.1134	-0.0692	0.101	-0.0842	-0.1633	0.0117	0.0088	-0.1734	0.0148	-0.1143	39.492	0.84	-8.687

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 91
2	X-RAY DIFFRACTION	2	B	0 - 91
3	X-RAY DIFFRACTION	3	C	2 - 94
4	X-RAY DIFFRACTION	4	D	1 - 94

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