PDB-5cz3: Crystal Structure of Myxoma Virus M64

ID or keywords:

Entry

Database: PDB / ID: 5cz3

Title

Crystal Structure of Myxoma Virus M64

Components

M64R

Keywords

VIRAL PROTEIN / host-range / poxvirus / myxoma / beta-sandwich

Function / homology

Poxvirus C7/F8A / Poxvirus C7/F8A protein / viral process / BETA-MERCAPTOETHANOL / Probable host range protein 2-3

Function and homology information

Biological species

Myxoma virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Krumm, B.E. / Meng, X. / Li, Y. / Xiang, Y. / Deng, J.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI079217	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI113539	United States

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural basis for antagonizing a host restriction factor by C7 family of poxvirus host-range proteins.
Authors: Meng, X. / Krumm, B. / Li, Y. / Deng, J. / Xiang, Y.

History

Deposition	Jul 31, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 18, 2015	Provider: repository / Type: Initial release
Revision 1.1	Dec 2, 2015	Group: Database references
Revision 1.2	Dec 16, 2015	Group: Database references
Revision 1.3	Sep 13, 2017	Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Sep 27, 2023	Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5cz3.cif.gz	142.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5cz3.ent.gz	112.8 KB	Display	PDB format
PDBx/mmJSON format	5cz3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5cz3_validation.pdf.gz	436.3 KB	Display	wwPDB validaton report
Full document	5cz3_full_validation.pdf.gz	436.5 KB	Display
Data in XML	5cz3_validation.xml.gz	12.9 KB	Display
Data in CIF	5cz3_validation.cif.gz	16.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cz/5cz3 ftp://data.pdbj.org/pub/pdb/validation_reports/cz/5cz3	HTTPS FTP

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Related structure data

Related structure data	5cywSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5yis-2 3f59-3 5iox-d 3knx-2 1wko-1 4i1k-1 1dj8-3 5y7w-1 4a83-d 3zxb-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 - 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	#234 - Jun 2019 MDM2 and Cancer similarity (1) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (1) #9 - Sep 2000 Lysozyme similarity (1)

Deposited unit

A: M64R

B: M64R

hetero molecules

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

1

A: M64R

hetero molecules

defined by author
24.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: M64R

hetero molecules

defined by author
24.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	51.782, 70.846, 115.432
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	M64R / Probable host range protein 2-3 Mass: 23993.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myxoma virus / Gene: m064R / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Q8N4
#2: Chemical	ChemComp-BME / BETA-MERCAPTOETHANOL Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆OS
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.21 Å³/Da / Density % sol: 44.25 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 28% w/v PEG MME, 0.1 M Bis-Tris, pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2008
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97921 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. obs: 15289 / % possible obs: 100 % / Redundancy: 9.3 % / B_iso Wilson estimate: 49.96 Å² / R_sym value: 0.127 / Net I/σ(I): 22.6
Reflection shell	Resolution: 2.5→2.54 Å / Redundancy: 8.2 % / R_merge(I) obs: 0.82 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 5CYW

5cyw

Resolution: 2.5→44.747 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.73 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.232	780	5.14 %
R_work	0.2066	-	-
obs	0.2079	15168	99.27 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.5→44.747 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2479	0	8	52	2539

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	2546
X-RAY DIFFRACTION	f_angle_d	0.699	3455
X-RAY DIFFRACTION	f_dihedral_angle_d	11.794	931
X-RAY DIFFRACTION	f_chiral_restr	0.029	391
X-RAY DIFFRACTION	f_plane_restr	0.002	429

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.5001-2.6567	0.306	127	0.2973	2314	X-RAY DIFFRACTION	98
2.6567-2.8618	0.3181	146	0.2871	2318	X-RAY DIFFRACTION	99
2.8618-3.1498	0.3247	118	0.2639	2381	X-RAY DIFFRACTION	99
3.1498-3.6054	0.2371	127	0.2197	2388	X-RAY DIFFRACTION	100
3.6054-4.5417	0.1993	127	0.176	2429	X-RAY DIFFRACTION	100
4.5417-44.7538	0.192	135	0.1726	2558	X-RAY DIFFRACTION	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	5.3326	-0.7153	-5.9653	0.9908	2.3829	9.5352	-0.0906	0.6438	0.2863	-1.2533	0.9624	0.2804	0.0769	0.172	-0.7039	0.8413	0.2964	-0.2832	0.7559	0.1178	0.9752	6.0706	53.8127	57.578
2	4.9242	-0.1847	0.498	4.2465	-0.3278	3.3612	0.2477	-0.0012	0.1143	-0.3685	-0.1975	0.3136	0.0965	-0.3313	0.058	0.3759	-0.007	0.0332	0.3383	-0.0102	0.3699	15.7051	36.9526	62.4027
3	4.7672	-0.2259	0.1316	5.3961	-1.1315	4.3291	0.4002	-0.3566	-0.3258	0.0341	0.3225	1.1196	0.0075	0.14	-0.8218	0.3614	0.0459	0.0618	0.334	-0.0194	0.4505	22.4582	32.3427	67.5653
4	5.0446	-1.0015	4.4344	3.281	0.8162	9.8789	-0.4057	0.7418	2.0836	0.0585	-1.8601	-0.1912	-0.2737	1.2394	1.5684	0.8083	0.0236	0.0869	0.6407	0.3308	0.9435	21.5736	54.1745	55.9261
5	3.8041	-1.1141	1.394	4.5945	-5.345	8.0271	-0.2611	-0.1314	-0.359	0.1894	0.3149	-1.1427	-0.5285	0.2128	-0.074	0.5733	-0.0111	0.0257	0.4362	-0.126	0.7324	21.0666	45.2523	70.3185
6	0.9016	-0.6277	1.9544	5.6404	1.98	6.3826	-0.183	-1.8302	0.3283	0.5977	0.3103	0.621	0.1695	-0.1066	0.0303	0.494	0.0499	0.0658	0.8339	-0.0703	0.3759	22.5298	38.8018	77.6627
7	5.2022	0.3989	2.2683	5.2153	-0.1718	4.14	-0.4182	0.5657	0.5533	-0.6835	-0.2977	-1.2727	-0.1019	-0.0547	0.6756	0.4393	-0.015	0.1309	0.4745	0.1002	0.4828	29.154	41.0847	60.7036
8	5.1647	-0.2303	-0.9221	3.7808	0.5925	2.2589	-0.0191	-1.1711	-0.4351	0.8597	-0.1707	0.6403	-0.2982	0.4252	0.1118	0.3584	-0.0052	0.0245	0.648	0.0425	0.3471	17.7735	35.4341	75.7254
9	5.5704	-0.8893	1.1651	5.1884	-1.4105	2.7932	0.5108	-0.2511	0.0446	0.9668	-0.9738	0.96	0.2357	0.0474	0.4166	0.4017	-0.0325	0.0994	0.4486	0.0845	0.4109	10.8084	35.0595	68.8582
10	7.4986	-2.2896	0.4557	6.674	1.7146	4.3947	0.0946	0.5679	-0.57	-0.3819	-0.1011	0.418	0.2488	-0.1881	0.0296	0.4773	0.0005	-0.0718	0.2966	-0.0213	0.2842	15.5342	31.4205	58.3726
11	4.4811	-1.1319	0.7294	4.7999	-2.5833	7.008	-0.4683	-0.6724	-0.6341	0.468	0.0765	-0.2037	0.4438	-0.5585	0.2956	0.4776	-0.0612	0.0562	0.4282	0.1142	0.4399	43.132	16.0268	75.8432
12	3.9687	-0.5129	-2.3178	0.451	0.8018	3.1578	0.296	-0.4013	-0.2231	0.1907	-0.3383	-0.07	0.1698	0.7761	-0.0302	0.3321	-0.0713	-0.0869	0.6245	0.1705	0.5153	47.9636	20.0309	80.4583
13	3.6532	-0.0521	-0.0226	3.9385	-1.4282	5.7145	0.2986	-0.0719	0.0315	0.0321	-0.6588	0.5273	0.1649	0.8281	0.3016	0.2876	-0.0722	0.0346	0.4064	0.0075	0.3201	38.1145	23.2821	74.8089
14	5.1985	1.1732	3.9476	4.3466	1.1903	7.4866	-2.1149	0.8209	-1.1409	-0.5833	0.3393	0.082	1.7974	1.0729	1.49	1.1591	-0.0861	0.107	0.8166	0.1849	0.7692	39.1019	7.2049	92.4499
15	4.2239	2.4675	-0.7924	2.3978	-2.2602	4.1152	-0.2661	-0.5539	0.5878	0.8574	0.3833	0.6302	-0.0942	-0.3124	-0.1672	0.5345	-0.0189	0.0287	0.5825	-0.0225	0.4123	40.4077	26.3711	85.9213
16	6.7604	0.1454	-0.6328	4.7038	0.0031	6.908	-0.3096	-0.7917	-1.6171	-0.4356	0.2575	-0.5059	0.102	-0.5152	0.213	0.4633	-0.0104	0.1	0.6141	0.1103	0.6668	32.7012	19.4484	83.1372
17	3.4427	0.5708	-0.2805	2.9997	-1.7252	4.2251	0.2721	-0.6852	0.395	0.6833	-0.3411	0.1353	-0.2117	0.3266	0.0126	0.4293	-0.0637	0.0056	0.4384	0.052	0.434	40.1756	28.0699	79.4501
18	2.1574	-0.8842	0.6876	1.8761	-2.2227	5.8429	0.0907	-0.9583	0.0823	0.5263	-0.22	-0.1202	-0.2231	0.0102	-0.3306	0.5519	-0.1171	-0.0933	0.8332	0.0989	0.594	51.0411	23.9453	82.1841
19	2.27	-1.7126	0.8972	3.0007	-2.8578	3.8511	0.6443	0.8194	-2.0735	1.7794	-0.7647	0.6281	-0.3127	-1.2573	-0.1355	0.5945	-0.0514	-0.0629	0.6804	0.0783	0.7067	47.5683	26.719	62.8562
20	5.4429	0.0339	0.6029	3.1343	0.0147	7.7868	-0.1962	-0.012	-0.5815	-0.249	-0.1985	-0.1819	0.6586	0.5861	0.3936	0.5113	0.0111	0.1486	0.4002	0.0442	0.4951	45.2427	15.0132	71.6758

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 0:4)
2	X-RAY DIFFRACTION	2	(chain A and resid 5:38)
3	X-RAY DIFFRACTION	3	(chain A and resid 39:54)
4	X-RAY DIFFRACTION	4	(chain A and resid 55:60)
5	X-RAY DIFFRACTION	5	(chain A and resid 61:67)
6	X-RAY DIFFRACTION	6	(chain A and resid 68:75)
7	X-RAY DIFFRACTION	7	(chain A and resid 76:89)
8	X-RAY DIFFRACTION	8	(chain A and resid 91:105)
9	X-RAY DIFFRACTION	9	(chain A and resid 106:124)
10	X-RAY DIFFRACTION	10	(chain A and resid 125:151)
11	X-RAY DIFFRACTION	11	(chain B and resid 3:21)
12	X-RAY DIFFRACTION	12	(chain B and resid 22:39)
13	X-RAY DIFFRACTION	13	(chain B and resid 40:54)
14	X-RAY DIFFRACTION	14	(chain B and resid 55:60)
15	X-RAY DIFFRACTION	15	(chain B and resid 61:70)
16	X-RAY DIFFRACTION	16	(chain B and resid 71:84)
17	X-RAY DIFFRACTION	17	(chain B and resid 85:105)
18	X-RAY DIFFRACTION	18	(chain B and resid 106:120)
19	X-RAY DIFFRACTION	19	(chain B and resid 121:125)
20	X-RAY DIFFRACTION	20	(chain B and resid 126:150)

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