PDB-4ye7: N-terminal domain of Orf22, a Cydia pomonella granulovirus envelo...

ID or keywords:

Entry

Database: PDB / ID: 4ye7

Title

N-terminal domain of Orf22, a Cydia pomonella granulovirus envelope protein

Components

ORF22 similar to XcGV ORF19

Keywords

VIRAL PROTEIN / envelope / calyx

Function / homology

Baculovirus polyhedron envelope protein PEP, N-terminal / Baculovirus polyhedron envelope protein PEP, C-terminal / Baculovirus polyhedron envelope protein, PEP, N terminus / Baculovirus polyhedron envelope protein, PEP, C terminus / viral capsid / viral envelope / structural molecule activity / ACETATE ION / ORF22 similar to XcGV ORF19

Function and homology information

Biological species

Cydia pomonella granulosis virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.4 Å

Authors

Busby, J.N. / Metcalf, P.

Funding support

New Zealand, 1items

Citation

Journal: To Be Published
Title: Structural studies of granulovirus envelope fibres.
Authors: Busby, J.N. / Goldie, K.N. / Metcalf, P.

#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.

#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...

History

Deposition	Feb 23, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / diffrn_source / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ye7.cif.gz	135.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4ye7.ent.gz	88.9 KB	Display	PDB format
PDBx/mmJSON format	4ye7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4ye7_validation.pdf.gz	445.1 KB	Display	wwPDB validaton report
Full document	4ye7_full_validation.pdf.gz	447.4 KB	Display
Data in XML	4ye7_validation.xml.gz	15.7 KB	Display
Data in CIF	4ye7_validation.cif.gz	21.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ye/4ye7 ftp://data.pdbj.org/pub/pdb/validation_reports/ye/4ye7	HTTPS FTP

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Related structure data

Similar structure data	5lam-d 7aby-d 1rax-d 4zr7-3 2hqt-11 1jl3-3 2id1-2 7lgo-1 2p6v-d 4kuo-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ORF22 similar to XcGV ORF19

B: ORF22 similar to XcGV ORF19

hetero molecules

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

1

A: ORF22 similar to XcGV ORF19

hetero molecules

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

2

B: ORF22 similar to XcGV ORF19

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

Unit cell

Length a, b, c (Å)	59.565, 61.212, 75.283
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	ORF22 similar to XcGV ORF19 Mass: 12147.304 Da / Num. of mol.: 2 / Fragment: N-terminal domain residues 2-106 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cydia pomonella granulosis virus / Strain: isolate Mexico/1963 / Gene: orf22 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P87582
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 268 / 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: 1

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Sample preparation

Crystal	Density Matthews: 2.86 Å³/Da / Density % sol: 56.97 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% PEG 8000, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.0612 M MES, 0.0388 M imidazole, 20% ethylene glycol

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Australian Synchrotron

/ Beamline: MX1 / Wavelength: 0.9779, 0.9794, 0.9537

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 16, 2014

Radiation

Monochromator: Double Si crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9779	1
2	0.9794	1
3	0.9537	1

Reflection

Redundancy: 14.7 % / Number: 792724 / R_merge(I) obs: 0.092 / D res high: 1.4 Å / D res low: 47.49 Å / Num. obs: 53927 / % possible obs: 98.3

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	ID	R_merge(I) obs	Redundancy
1.4	1.42	1	3.252	14.3
7.66	47.49	1	0.021	10.9

Reflection

Resolution: 1.4→47.49 Å / Num. obs: 53936 / % possible obs: 98.2 % / Redundancy: 14.7 % / B_iso Wilson estimate: 17.116 Å² / CC_1/2: 1 / R_merge(I) obs: 0.092 / R_pim(I) all: 0.025 / Net I/σ(I): 25.3 / Num. measured all: 792724

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	CC_1/2	R_pim(I) all	% possible all
1.4-1.42	14.5	3.104	1	37051	2596	0.339	0.877	93.7
7.66-47.49	10.9	0.021	127.1	4296	393	1	0.007	97.8

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
Aimless	0.3.11	data scaling
SOLVE		phasing
RESOLVE		phasing
PDB_EXTRACT	3.15	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MAD / Resolution: 1.4→37.13 Å / SU ML: 0.179252574456 / Cross valid method: FREE R-VALUE / Phase error: 22.5005368728

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2071	2467	4.928 %	Random selection
R_work	0.1817	97879	-	-
obs	0.183	53873	98.07 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 26.8896746069 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→37.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1655	0	4	268	1927

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0151324602193	1899
X-RAY DIFFRACTION	f_angle_d	1.6405897701	2602
X-RAY DIFFRACTION	f_chiral_restr	0.12019885625	285
X-RAY DIFFRACTION	f_plane_restr	0.0083538489538	338
X-RAY DIFFRACTION	f_dihedral_angle_d	12.3492324336	695

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 (%)
1.4-1.4149	0.328339466024	165	0.333061786759	3003	X-RAY DIFFRACTION	90.9038737446
1.4149-1.4316	0.384768457094	134	0.341633145333	3271	X-RAY DIFFRACTION	96.925704526
1.4316-1.449	0.355249361095	141	0.331751280761	3255	X-RAY DIFFRACTION	96.1767204758
1.449-1.4674	0.333965162211	152	0.312532834752	3190	X-RAY DIFFRACTION	97.2359615944
1.4674-1.4867	0.280453583927	169	0.295659788034	3230	X-RAY DIFFRACTION	97.1975979411
1.4867-1.507	0.314557923964	169	0.286014487857	3210	X-RAY DIFFRACTION	96.4877213021
1.507-1.5286	0.309082034034	179	0.26565081585	3303	X-RAY DIFFRACTION	97.6718092567
1.5286-1.5514	0.261696003839	147	0.252249031288	3212	X-RAY DIFFRACTION	97.2777295106
1.5514-1.5756	0.274096700539	180	0.261135767576	3225	X-RAY DIFFRACTION	97.2023979446
1.5756-1.6015	0.260940853609	178	0.24764327955	3270	X-RAY DIFFRACTION	97.5941126521
1.6015-1.6291	0.305485987317	228	0.238849456689	3159	X-RAY DIFFRACTION	97.8901734104
1.6291-1.6587	0.297162442717	152	0.239530457821	3291	X-RAY DIFFRACTION	97.8125
1.6587-1.6906	0.251773979649	144	0.218196470573	3287	X-RAY DIFFRACTION	98.0846197827
1.6906-1.7251	0.185581488677	145	0.202219738843	3291	X-RAY DIFFRACTION	98.0593607306
1.7251-1.7626	0.236750344724	165	0.199513873571	3258	X-RAY DIFFRACTION	98.2491389208
1.7626-1.8036	0.232174342687	112	0.194422519555	3354	X-RAY DIFFRACTION	98.2704848313
1.8036-1.8487	0.171675184449	186	0.182920863742	3226	X-RAY DIFFRACTION	98.4420080785
1.8487-1.8987	0.228615087323	161	0.180293931841	3318	X-RAY DIFFRACTION	98.5552407932
1.8987-1.9546	0.186683122027	195	0.184116332542	3228	X-RAY DIFFRACTION	98.7024221453
1.9546-2.0177	0.202356664952	153	0.173219860646	3286	X-RAY DIFFRACTION	98.7367212173
2.0177-2.0898	0.184231495513	190	0.172205359667	3277	X-RAY DIFFRACTION	98.6344238976
2.0898-2.1734	0.197554229911	161	0.172505353342	3307	X-RAY DIFFRACTION	99.2842828514
2.1734-2.2723	0.190387983536	250	0.16348815082	3236	X-RAY DIFFRACTION	99.203187251
2.2723-2.3921	0.211798375771	146	0.164700900723	3344	X-RAY DIFFRACTION	99.3170176437
2.3921-2.542	0.194510250243	152	0.175004276653	3302	X-RAY DIFFRACTION	99.4242947611
2.542-2.7382	0.171631861088	203	0.175556394688	3281	X-RAY DIFFRACTION	99.6282527881
2.7382-3.0136	0.219687566905	160	0.170081710988	3332	X-RAY DIFFRACTION	99.6575342466
3.0136-3.4494	0.223897679024	151	0.167106004105	3364	X-RAY DIFFRACTION	99.8295938654
3.4494-4.3448	0.194394543781	177	0.147680831521	3297	X-RAY DIFFRACTION	99.913718723
4.3448-37.1475	0.16075144451	228	0.146338542687	3272	X-RAY DIFFRACTION	99.8858447489

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	7.39280712361	-2.87829729026	0.114344026173	8.28616988807	-0.204585548629	5.09749907623	0.0207615494354	-0.326932171426	-0.711607727071	0.309228707782	-0.126727863644	-0.303719004346	0.942047780402	-0.189479487333	0.050697840856	0.301092830123	-0.0805456147541	-0.00552939019064	0.192611519176	-0.0240406056682	0.343311208579	32.4005762121	23.5680762531	22.1510946237
2	7.64206246429	-3.26809578135	3.84349918881	4.71396989932	-2.33413238815	3.06564630431	-0.045585057205	0.321658808885	-0.0940638444536	0.239162515806	-0.240469014072	0.354179537768	0.0775542923437	-0.256730479596	0.222684377781	0.18291901853	0.00149912214222	0.00399066598055	0.179286917886	-0.0557435423058	0.186413360371	31.2298372465	31.3406172178	17.867379508
3	1.28186074567	0.18027115356	0.0885121857932	0.0264438588768	0.0103778094228	0.00895241572521	-0.245664842513	-1.207756846	-0.405453454136	2.33251816575	0.536979242007	-0.455853602587	0.851897570588	-0.0942567650136	-0.206338631546	0.65879623737	0.0619299660404	-0.143173806185	0.250530101476	0.00535817152269	0.209873347199	38.7806518885	29.0323998658	31.3875418338
4	1.60405262713	-1.49801343298	0.794664297721	8.50310252481	-3.06192153973	6.0720632663	-0.0453866324242	0.133083416037	0.0505688691104	-0.111046334299	0.0488598272357	0.151178280842	-0.141045284878	-0.265892580652	0.00777890956959	0.07759843563	0.0171970235909	0.00214363243443	0.124886742155	-0.00826847541584	0.1379642653	34.888697866	38.3172491709	15.4574573356
5	7.89630602301	-2.85449178643	5.60149162066	4.37758603867	-1.54102672765	7.23829079695	-0.042695857336	0.771644798959	0.327661879632	-0.429797358119	-0.216895306908	-0.517949606582	-0.716023361628	0.818020785595	0.204991421426	0.194035580837	-0.00410635490387	0.0426091548231	0.18424811191	0.0283136013289	0.182047546116	40.9530501067	45.0497626862	13.4403815103
6	0.0185720491008	0.15392000227	-0.0180196920711	8.67364512027	5.99374880205	4.85175635535	-0.0636078558569	0.0134782532085	-0.0651281086283	0.0691945194153	0.126512375879	-0.422619435732	0.291977310158	0.517117517593	-0.0737908336215	0.152851354186	0.0757998989518	-0.00777768445284	0.207059681513	-0.0198438862667	0.236694071032	46.3016401347	34.1232626056	20.895903665
7	2.79233323781	-1.22779978135	1.14082443507	4.8854840673	-0.904962402696	0.581207781279	-0.373668132341	0.0192070219953	-0.329635723433	0.300264929031	0.166762559673	-0.223754288529	0.824484650699	0.299690564233	0.107950517586	0.305397718543	0.0896588440255	0.0839884193882	0.168075673923	-0.0466386135173	0.235841403997	43.4776142988	25.4862478818	14.0512489857
8	1.17577301988	-0.248244364303	-0.165873443111	3.06223421437	0.381979996408	2.05284982532	0.068356890892	0.0795607778825	0.159772092401	-0.091719651751	0.030441841883	0.112313654191	-0.300711729481	-0.249555025576	-0.0258427376118	0.107412951537	0.0353094912184	0.00351159975162	0.111350449643	0.0199799616287	0.160143180047	35.3976689581	45.2092989723	21.3658971431
9	3.28663694574	0.945329361732	-0.266484370653	3.97669440023	2.2754913567	1.62722100114	0.0510627770542	0.0685029280491	0.0735148949543	0.812579058751	-0.343298998785	0.542318040608	0.156057021697	-0.406835894982	0.249012393952	0.18887554714	-0.0679529181782	0.0642796849525	0.281911436754	-0.0748377830306	0.212467962851	27.1628788862	36.6877676303	25.2935046219
10	7.82897406766	1.01825676139	-0.142734377842	6.00718554672	0.551687110976	7.16845804401	0.086999342984	-0.386138246687	-0.390163127619	0.449919891657	0.0373599074475	0.0347761507537	0.243298605961	-0.0287591645222	-0.0617800137792	0.112491072247	0.0281821485338	-0.0418155126091	0.210453768064	0.0676790805191	0.173578225946	39.0368848788	42.7596360659	47.8726724464
11	4.58427641219	-1.03608043861	1.4536007983	0.779222930361	0.219156664621	6.66817366475	-0.133871646693	0.00334066415191	-0.289425583295	-0.205968477718	-0.00565965697501	-0.298309751719	0.303340278976	0.290162234197	0.099472081666	0.113486006482	0.00252358516023	0.00343793831624	0.169591859101	-0.00698531784818	0.156213320451	37.7892358668	46.8248444695	41.2468937507
12	3.12412187441	1.61151963058	-1.67947208467	7.47756908682	1.04008645384	3.90311445676	0.129862676594	-0.0354197876667	1.33125562668	0.135618216052	0.140596178505	1.20896734023	-1.4892684169	-0.529441078233	0.243050272977	0.464526161191	0.057253703053	0.0316922921695	0.171601543091	-0.00674217167622	0.391855001533	34.1172803184	58.5406565228	33.4806143627
13	1.96071578551	-0.381693641119	0.316923925353	0.549311477821	0.477386917755	2.83674015255	0.0407248630589	-0.771476859836	0.00685883996286	-0.0271937779214	0.108036408071	0.217644841435	0.362787867316	-1.19989961015	0.117207290255	0.0371019685161	0.0357475237052	0.0412423163663	0.575581468251	-0.0410058705001	0.190050265711	27.4046618716	48.7053590979	45.2181583809
14	5.50981125314	0.841536100361	-2.47701439593	3.73686180083	1.5834514559	8.33983698792	-0.0256173100933	0.100496756707	0.172442535079	-0.188017614417	0.0668933474778	-0.110958887431	-0.32940072133	-0.248987540345	-0.0584444791318	0.0949130394386	0.0187546995257	-0.0248261102723	0.0864547838463	0.00280757716458	0.138969090739	35.9725022803	49.4755620395	32.2083665507
15	8.20832509529	-4.92901925147	-1.88521927955	6.84330899826	5.04848061347	4.38743607139	0.187399695727	0.512272755525	1.22291394645	-1.06766295184	-0.345119786346	-0.116308578561	-1.26258885913	0.0485470597912	0.278979612763	0.3614590507	-0.0905116630361	-0.0340456394847	0.305959860113	0.0484659003676	0.462147855772	46.1023862384	52.983747673	26.4089967389
16	1.69386230508	-0.439053771346	0.734651943732	0.802375773976	-0.854821991681	3.40623033292	0.114119971167	-0.225563531063	0.230323618543	0.0613201599305	0.133374514891	-0.0300220369003	0.463468330328	1.13501787594	0.0268718112881	0.152610636407	0.087697142398	-0.0398350049182	0.238144406153	-0.0314201065371	0.192383289772	45.2119984538	42.2733361816	36.8208126487

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 11 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 12 through 20 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 21 through 28 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 29 through 39 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 40 through 50 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 51 through 60 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 61 through 71 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 72 through 90 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 91 through 106 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 3 through 11 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 12 through 39 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 40 through 50 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 51 through 71 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 72 through 85 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 86 through 90 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 91 through 106 )

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