PDB-4z24: Mimivirus R135 (residues 51-702)

ID or keywords:

Entry

Database: PDB / ID: 4z24

Title

Mimivirus R135 (residues 51-702)

Components

GMC-type oxidoreductase R135

Keywords

OXIDOREDUCTASE / GMC oxidoreductase / FAD / fiber

Function / homology

Function and homology information

oxidoreductase activity, acting on CH-OH group of donors / Oxidoreductases / host cell membrane / virion component / flavin adenine dinucleotide binding / identical protein binding / membrane
Similarity search - Function

Biological species

Acanthamoeba polyphaga mimivirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Klose, T. / Rossmann, M.G.

Funding support

United States, 1items

Citation

Journal: Structure / Year: 2015
Title: A Mimivirus Enzyme that Participates in Viral Entry.
Authors: Klose, T. / Herbst, D.A. / Zhu, H. / Max, J.P. / Kenttamaa, H.I. / Rossmann, M.G.

History

Deposition	Mar 28, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 15, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jun 3, 2015	Group: Database references / Structure summary
Revision 1.2	Jun 10, 2015	Group: Database references
Revision 1.3	Jun 17, 2015	Group: Database references
Revision 1.4	Sep 13, 2017	Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6	Sep 27, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4z24.cif.gz	542.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4z24.ent.gz	442.9 KB	Display	PDB format
PDBx/mmJSON format	4z24.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4z24_validation.pdf.gz	965.1 KB	Display	wwPDB validaton report
Full document	4z24_full_validation.pdf.gz	976.3 KB	Display
Data in XML	4z24_validation.xml.gz	63.5 KB	Display
Data in CIF	4z24_validation.cif.gz	96.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z2/4z24 ftp://data.pdbj.org/pub/pdb/validation_reports/z2/4z24	HTTPS FTP

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Related structure data

Related structure data	4z25C 4z26C 3q9tS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4z25-4 4z25-6 4z25-1 4z26-3 4z26-4 4z25-5 4z26-1 4z25-3 4z25-2 4z26-2 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	#77 - May 2006 Glucose Oxidase similarity (6)

Deposited unit

A: GMC-type oxidoreductase R135

B: GMC-type oxidoreductase R135

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	64.760, 77.500, 94.340
Angle α, β, γ (deg.)	111.22, 109.64, 94.56
Int Tables number	1
Space group name H-M	P1

#1: Protein	GMC-type oxidoreductase R135 Mass: 71355.430 Da / Num. of mol.: 2 / Fragment: UNP residues 51-702 Source method: isolated from a genetically manipulated source Details: FAD cofactor bound to the enzyme / Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_R135 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5UPL2, Oxidoreductases
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1650 / 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: 2.84 Å³/Da / Density % sol: 56.63 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: HEPES, PEG 8000, calcium chloride

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 10, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. obs: 105150 / % possible obs: 99.2 % / Redundancy: 3.4 % / R_merge(I) obs: 0.209 / Net I/σ(I): 6.3
Reflection shell	Resolution: 2→2.07 Å / R_merge(I) obs: 0.992 / Mean I/σ(I) obs: 1.6 / % possible all: 99.3

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3Q9T

3q9t

Resolution: 2→47.707 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 20.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2037	5247	4.99 %	Random selection
R_work	0.163	-	-	-
obs	0.165	105097	99.19 %	-

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→47.707 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10092	0	0	1650	11742

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	10348
X-RAY DIFFRACTION	f_angle_d	1.087	14140
X-RAY DIFFRACTION	f_dihedral_angle_d	11.865	3686
X-RAY DIFFRACTION	f_chiral_restr	0.044	1570
X-RAY DIFFRACTION	f_plane_restr	0.006	1842

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 (%)
2-2.0227	0.3165	172	0.2586	3390	X-RAY DIFFRACTION	99
2.0227-2.0465	0.3087	160	0.2486	3329	X-RAY DIFFRACTION	99
2.0465-2.0715	0.2714	173	0.2436	3277	X-RAY DIFFRACTION	99
2.0715-2.0977	0.2708	199	0.229	3381	X-RAY DIFFRACTION	100
2.0977-2.1253	0.2852	176	0.2271	3253	X-RAY DIFFRACTION	100
2.1253-2.1544	0.2727	165	0.2199	3436	X-RAY DIFFRACTION	99
2.1544-2.1852	0.2824	186	0.2119	3265	X-RAY DIFFRACTION	99
2.1852-2.2178	0.2501	182	0.2	3332	X-RAY DIFFRACTION	99
2.2178-2.2524	0.2339	179	0.1983	3294	X-RAY DIFFRACTION	99
2.2524-2.2894	0.2474	187	0.192	3333	X-RAY DIFFRACTION	99
2.2894-2.3288	0.2323	172	0.1886	3321	X-RAY DIFFRACTION	99
2.3288-2.3712	0.2401	187	0.1818	3344	X-RAY DIFFRACTION	99
2.3712-2.4168	0.2356	194	0.1819	3344	X-RAY DIFFRACTION	100
2.4168-2.4661	0.2016	177	0.1775	3279	X-RAY DIFFRACTION	99
2.4661-2.5197	0.2246	149	0.1678	3381	X-RAY DIFFRACTION	99
2.5197-2.5784	0.2476	191	0.1629	3357	X-RAY DIFFRACTION	99
2.5784-2.6428	0.1921	154	0.1596	3321	X-RAY DIFFRACTION	99
2.6428-2.7143	0.2089	166	0.1616	3333	X-RAY DIFFRACTION	100
2.7143-2.7941	0.2003	174	0.1593	3359	X-RAY DIFFRACTION	99
2.7941-2.8843	0.2252	175	0.163	3315	X-RAY DIFFRACTION	99
2.8843-2.9874	0.1963	192	0.1541	3331	X-RAY DIFFRACTION	99
2.9874-3.107	0.1968	171	0.1563	3323	X-RAY DIFFRACTION	99
3.107-3.2484	0.1819	153	0.1456	3378	X-RAY DIFFRACTION	99
3.2484-3.4196	0.1716	184	0.143	3294	X-RAY DIFFRACTION	99
3.4196-3.6337	0.1737	160	0.1389	3357	X-RAY DIFFRACTION	99
3.6337-3.9142	0.1649	175	0.1369	3292	X-RAY DIFFRACTION	99
3.9142-4.3079	0.1409	168	0.1178	3337	X-RAY DIFFRACTION	99
4.3079-4.9307	0.1497	181	0.1198	3269	X-RAY DIFFRACTION	98
4.9307-6.21	0.1742	169	0.1398	3311	X-RAY DIFFRACTION	99
6.21-47.7202	0.1595	176	0.1423	3314	X-RAY DIFFRACTION	99

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	0.9571	0.1497	0.0392	0.3679	-0.307	1.0292	-0.0326	0.1173	0.0168	-0.0499	0.0059	0.014	0.0655	-0.098	0.0275	0.1163	0.0008	-0.011	0.1054	-0.0139	0.0819	10.969	26.3735	40.32
2	0.7017	-0.2863	-0.0789	0.925	-0.1578	0.4182	-0.1458	0.2366	0.2459	-0.103	-0.1474	-0.0505	-0.2907	0.3121	-0.3478	0.2823	-0.183	-0.0178	0.3383	0.2807	0.1117	32.5369	46.0518	26.1912
3	1.8218	0.6464	-0.3221	0.8796	-0.3996	1.3894	-0.1133	0.266	0.1297	-0.13	0.1034	0.0951	-0.0423	-0.1611	-0.0152	0.15	0.006	-0.0453	0.1923	0.0254	0.0974	9.8044	32.7087	28.7469
4	0.8192	0.1287	0.012	0.3912	-0.2533	1.1611	-0.015	0.0578	-0.004	-0.0048	-0.0449	-0.0288	0.0657	0.098	0.047	0.0962	0.0252	-0.0067	0.0991	-0.0179	0.1019	19.2458	25.6813	44.307
5	0.8636	0.5243	-0.2675	0.4337	-0.3499	1.2477	-0.0287	0.002	0.026	0.0383	-0.0654	-0.08	-0.1076	0.1376	0.0894	0.0921	0.011	-0.0242	0.1055	0.0155	0.1037	24.1628	32.9107	50.9665
6	1.5933	-0.5697	0.1606	0.4049	0.0529	0.729	-0.1214	0.0722	0.1664	0.0038	0.0676	-0.0202	-0.2784	0.2436	0.037	0.1787	-0.095	-0.0408	0.2401	0.0634	0.1872	38.9512	42.1548	40.8666
7	1.3955	-0.0428	-0.7705	1.6787	0.327	0.6754	-0.0622	-0.0049	0.2818	0.025	0.0655	-0.2544	-0.171	0.3364	-0.0202	0.1871	-0.0915	-0.0444	0.282	0.0385	0.2195	43.8355	44.2782	47.704
8	1.216	-0.1138	-0.0392	1.0065	-0.0825	1.1055	0.0491	0.2589	-0.1224	-0.1666	-0.0939	-0.0454	0.2297	0.0986	0.0289	0.1762	0.0295	0.0099	0.1442	-0.0399	0.1011	15.2899	17.3819	34.4073
9	0.3783	0.2612	0.0573	0.8568	-0.3717	1.0234	0.0351	-0.1694	-0.0061	0.237	-0.1112	-0.0652	-0.1207	0.15	0.003	0.1954	-0.0359	-0.0333	0.1942	0.0005	0.0994	19.1562	26.1938	82.4195
10	0.5803	0.3781	0.0512	2.0679	1.1688	1.2617	0.0446	-0.2815	-0.0353	0.4391	-0.072	-0.1985	-0.1705	0.4415	-0.1209	0.4012	-0.1483	-0.0794	0.3871	0.0329	0.1342	26.6802	29.571	94.2346
11	2.6483	-0.2599	1.1124	0.974	-0.5066	2.3542	0.0231	-0.0185	-0.294	-0.1017	0.0687	0.0535	0.3513	-0.0622	-0.0999	0.1865	-0.0276	0.0343	0.1225	0.0257	0.1396	6.5032	7.5286	77.8826
12	6.5396	-1.774	-6.4701	2.3289	3.1247	8.0913	-0.26	0.0455	-0.2148	0.0682	0.0594	0.1067	0.4551	-0.2236	0.1929	0.1833	-0.0021	-0.0233	0.1343	0.0789	0.172	1.9689	7.1442	70.0699
13	0.6516	0.3237	-0.0666	0.8007	-0.2757	1.1747	0.0403	-0.1586	0.1361	0.2063	-0.0995	-0.0488	-0.3159	0.1731	0.0539	0.2269	-0.0417	-0.0126	0.1695	-0.0225	0.1329	19.1325	36.1823	77.1346
14	1.2161	0.5684	-0.0822	1.3173	-0.1008	1.2748	0.1495	-0.1836	0.3705	0.2388	-0.2002	0.0091	-0.6186	0.1596	0.0901	0.4454	-0.1052	-0.0263	0.1616	-0.0506	0.2152	22.3462	50.3661	74.3819
15	7.2434	2.1816	-3.0042	2.0838	-0.9101	4.0745	0.128	0.2356	0.31	0.1101	0.1405	-0.0213	-0.5386	0.0195	-0.2343	0.2923	-0.022	-0.0104	0.1839	-0.0047	0.0905	10.4823	32.6757	76.7857
16	1.4358	-0.0573	0.077	1.174	-0.606	1.5294	-0.0187	-0.3126	-0.066	0.2934	0.0429	0.0892	-0.1567	-0.058	-0.0145	0.2041	0.0137	0.0282	0.2119	-0.0093	0.1067	6.5007	21.4488	88.0795

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 5:148)
2	X-RAY DIFFRACTION	2	(chain A and resid 149:178)
3	X-RAY DIFFRACTION	3	(chain A and resid 179:256)
4	X-RAY DIFFRACTION	4	(chain A and resid 257:413)
5	X-RAY DIFFRACTION	5	(chain A and resid 414:462)
6	X-RAY DIFFRACTION	6	(chain A and resid 463:515)
7	X-RAY DIFFRACTION	7	(chain A and resid 516:573)
8	X-RAY DIFFRACTION	8	(chain A and resid 574:651)
9	X-RAY DIFFRACTION	9	(chain B and resid 5:178)
10	X-RAY DIFFRACTION	10	(chain B and resid 179:236)
11	X-RAY DIFFRACTION	11	(chain B and resid 237:277)
12	X-RAY DIFFRACTION	12	(chain B and resid 278:293)
13	X-RAY DIFFRACTION	13	(chain B and resid 294:419)
14	X-RAY DIFFRACTION	14	(chain B and resid 420:573)
15	X-RAY DIFFRACTION	15	(chain B and resid 574:587)
16	X-RAY DIFFRACTION	16	(chain B and resid 588:651)

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