PDB-7pab: Varicella zoster Orf24-Orf27 nuclear egress complex

ID or keywords:

Entry

Database: PDB / ID: 7pab

Title

Varicella zoster Orf24-Orf27 nuclear egress complex

Components

Nuclear egress protein 2,Nuclear egress protein 1

Keywords

VIRAL PROTEIN / VZV / varicella zoster virus / Orf24 / Orf27 / Orf24-Orf27 / herpesvirus / nuclear egress / nuclear egress complex / NEC

Function / homology

Function and homology information

host cell nuclear inner membrane / viral budding from nuclear membrane / membrane => GO:0016020 / membrane / metal ion binding
Similarity search - Function

Biological species

Human herpesvirus 3 (Varicella-zoster virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Schweininger, J. / Muller, Y.A.

Funding support

Germany, 1items

Citation

Journal: J.Biol.Chem. / Year: 2022
Title: The crystal structure of the varicella-zoster Orf24-Orf27 nuclear egress complex spotlights multiple determinants of herpesvirus subfamily specificity.
Authors: Schweininger, J. / Kriegel, M. / Hage, S. / Conrad, M. / Alkhashrom, S. / Losing, J. / Weiler, S. / Tillmanns, J. / Egerer-Sieber, C. / Decker, A. / Lenac Rovis, T. / Eichler, J. / Sticht, H. ...

History

Deposition	Jul 29, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 19, 2022	Provider: repository / Type: Initial release
Revision 1.1	Aug 3, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7pab.cif.gz	588.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7pab.ent.gz	409.7 KB	Display	PDB format
PDBx/mmJSON format	7pab.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7pab_validation.pdf.gz	455.9 KB	Display	wwPDB validaton report
Full document	7pab_full_validation.pdf.gz	473.8 KB	Display
Data in XML	7pab_validation.xml.gz	30.7 KB	Display
Data in CIF	7pab_validation.cif.gz	42.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pa/7pab ftp://data.pdbj.org/pub/pdb/validation_reports/pa/7pab	HTTPS FTP

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Related structure data

Related structure data	4zxsS S: Starting model for refinement
Similar structure data	6h5c-d 4cnn-d 4gug-d 4guj-d 1l9w-1 3oex-1 4cnp-d 6ku0-2 3o1n-d 4j5l-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

Deposited unit

A: Nuclear egress protein 2,Nuclear egress protein 1

C: Nuclear egress protein 2,Nuclear egress protein 1

hetero molecules

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

1

A: Nuclear egress protein 2,Nuclear egress protein 1

hetero molecules

defined by author&software
Evidence: gel filtration, Orf24-Orf27 fusion protein behaves like a heterodimer of Orf24 and Orf27
50.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Nuclear egress protein 2,Nuclear egress protein 1

hetero molecules

defined by author&software
Evidence: gel filtration, Orf24-Orf27 fusion protein behaves like a heterodimer of Orf24 and Orf27
50.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	76.010, 35.050, 158.220
Angle α, β, γ (deg.)	90.000, 93.694, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Nuclear egress protein 2,Nuclear egress protein 1 Mass: 49932.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Fusion protein of residues 16 to 189 of VZV Orf24 (Uniprot entry: Q6QCN1) and residues 77 to 333 of VZV Orf27 (Uniprot entry: Q6QCM8),Fusion protein of residues 16 to 189 of VZV Orf24 ...Details: Fusion protein of residues 16 to 189 of VZV Orf24 (Uniprot entry: Q6QCN1) and residues 77 to 333 of VZV Orf27 (Uniprot entry: Q6QCM8),Fusion protein of residues 16 to 189 of VZV Orf24 (Uniprot entry: Q6QCN1) and residues 77 to 333 of VZV Orf27 (Uniprot entry: Q6QCM8) Source: (gene. exp.) Human herpesvirus 3 (Varicella-zoster virus) Gene: ORF24, NEC2, HHV3_E_SVETAgp26, HHV3gp26, HHV3M2gp26, ORF 27, NEC1, ORF27, HHV3_gp29, HHV3gp29, HHV3M2gp29 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6QCN1, UniProt: Q6QCM8
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.11 Å³/Da / Density % sol: 41.6 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris, ammonium sulfate, PEG 3350, formamide

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97627 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97627 Å / Relative weight: 1
Reflection	Resolution: 2.1→19.96 Å / Num. obs: 49198 / % possible obs: 98.97 % / Redundancy: 11.9 % / B_iso Wilson estimate: 51.07 Å² / CC_1/2: 0.999 / R_pim(I) all: 0.041 / R_rim(I) all: 0.143 / Net I/σ(I): 10.2
Reflection shell	Resolution: 2.1→2.175 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 0.72 / Num. unique obs: 4890 / CC_1/2: 0.463 / R_pim(I) all: 1.05 / R_rim(I) all: 3.78 / % possible all: 99.53

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
Coot		model building
XSCALE		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4ZXS

4zxs

Resolution: 2.1→19.96 Å / SU ML: 0.3057 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2185
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2543	3678	7.48 %
R_work	0.2152	45519	-
obs	0.2181	49197	99.13 %

Solvent computation

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

Displacement parameters

B_iso mean: 79.36 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→19.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6495	0	12	168	6675

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0018	6654
X-RAY DIFFRACTION	f_angle_d	0.4891	9027
X-RAY DIFFRACTION	f_chiral_restr	0.0399	1003
X-RAY DIFFRACTION	f_plane_restr	0.003	1163
X-RAY DIFFRACTION	f_dihedral_angle_d	14.4265	2444

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 (%)
2.1-2.13	0.4061	143	0.3983	1708	X-RAY DIFFRACTION	99.57
2.13-2.16	0.3629	122	0.3868	1788	X-RAY DIFFRACTION	99.43
2.16-2.19	0.3938	144	0.3597	1758	X-RAY DIFFRACTION	99.69
2.19-2.22	0.3637	141	0.3562	1699	X-RAY DIFFRACTION	99.73
2.22-2.25	0.3561	134	0.3497	1718	X-RAY DIFFRACTION	98.15
2.25-2.29	0.352	143	0.336	1712	X-RAY DIFFRACTION	99.09
2.29-2.33	0.368	140	0.3153	1800	X-RAY DIFFRACTION	99.85
2.33-2.37	0.3235	140	0.2886	1703	X-RAY DIFFRACTION	99.68
2.37-2.42	0.2688	140	0.2911	1713	X-RAY DIFFRACTION	99.84
2.42-2.47	0.297	140	0.2899	1797	X-RAY DIFFRACTION	99.74
2.47-2.52	0.339	146	0.2834	1736	X-RAY DIFFRACTION	99.84
2.52-2.58	0.3543	140	0.2833	1723	X-RAY DIFFRACTION	99.68
2.58-2.64	0.2707	144	0.2719	1767	X-RAY DIFFRACTION	99.38
2.64-2.72	0.2809	135	0.2721	1635	X-RAY DIFFRACTION	91.95
2.72-2.8	0.285	138	0.2571	1730	X-RAY DIFFRACTION	99.73
2.8-2.89	0.2905	146	0.249	1760	X-RAY DIFFRACTION	99.58
2.89-2.99	0.2942	136	0.2565	1746	X-RAY DIFFRACTION	99.74
2.99-3.11	0.274	147	0.2344	1742	X-RAY DIFFRACTION	99.68
3.11-3.25	0.2817	142	0.2469	1783	X-RAY DIFFRACTION	99.9
3.25-3.42	0.2631	143	0.2234	1749	X-RAY DIFFRACTION	99.53
3.42-3.63	0.269	139	0.2069	1756	X-RAY DIFFRACTION	98.7
3.63-3.91	0.216	144	0.1885	1748	X-RAY DIFFRACTION	97.83
3.91-4.3	0.1978	146	0.1636	1789	X-RAY DIFFRACTION	99.64
4.3-4.92	0.2091	144	0.1509	1781	X-RAY DIFFRACTION	99.38
4.92-6.16	0.2339	146	0.1854	1790	X-RAY DIFFRACTION	99.18
6.16-19.96	0.2254	155	0.1824	1888	X-RAY DIFFRACTION	99.08

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	6.09658695044	0.894641035709	-2.90154751028	1.92815118694	2.66833073249	2.01597356266	0.528508082173	-2.91543407188	-1.94491494751	0.0786464544723	0.771406528444	0.256414508835	1.40940751875	-0.373904885079	-0.924068803902	1.27350442215	-0.0652277296083	-0.254354276584	1.8026900482	0.546614606264	0.95871708541	49.1547720855	14.525348813	131.152480122
2	4.79796001782	1.2446289409	4.28576111996	4.50818389269	1.21556317339	5.42214862084	0.250791927698	-1.54967197482	-0.11592784764	0.268836557161	0.127017933081	-0.343033422397	-0.0574849112646	-0.438348318147	-0.326727755568	0.617077789237	0.116290488743	0.064335040249	1.05953295899	-0.0460393181106	0.549689356353	42.7349056769	23.3607259404	118.273693314
3	1.30735371273	-0.229992779344	0.0708224196649	5.69729082948	-0.862627568098	3.49605599648	-0.599201741038	-0.448540145281	0.318879633951	1.45586396145	-0.320537327868	-0.22020288243	-1.11793846188	-1.55798402597	0.610585357345	1.10938236875	-0.00466989778035	-0.2404927002	3.39941627002	-0.780571315299	1.20610648381	54.8245619463	29.0535265004	141.984423035
4	3.38061445163	-0.320523918704	0.170287181062	0.700299712367	1.19436558121	7.73611996627	-0.0721351542396	-1.78895456522	0.376867469496	0.603581076706	-0.0759415494396	-0.223202818651	0.151665408248	-0.00216299564612	-0.057334345721	0.547924666376	-0.0416374541619	-0.00568148437309	0.975927146735	-0.181081777596	0.498635285901	50.674926286	23.4403157613	119.500921126
5	8.49611583857	1.03977412282	5.16606756552	6.19511444354	-0.224276825188	3.44853615873	-0.0591129611601	0.448642125481	-0.267746916527	-0.31610854897	-0.207990829837	-0.422633550382	-0.724233284149	0.693280398413	0.379191885665	0.939265308121	0.0288032227678	0.161784297087	0.948333942186	0.00386104029783	1.03690313255	41.1481011141	31.9626224478	89.8665779189
6	8.85443888277	-0.470264921684	-1.51619472215	5.77295565261	-4.34515649975	4.02375401486	0.290705001003	-0.0841938429555	-0.549931687808	-0.450440476115	-0.000357691623098	-0.107049947601	0.0737437945113	0.210620557599	-0.388422367115	0.582812627455	-0.0762686883124	0.0542815178402	0.625328154791	-0.125396741977	0.561847207815	45.2378201689	17.6620273138	76.7666386503
7	5.47556278389	0.265819855811	1.08008736269	3.73236896178	2.34657269102	8.10688002663	-0.0316102601876	0.047351789182	0.24429513541	-0.0764378633519	-0.106586092019	0.212161947651	-0.107038464939	-0.0549870253066	0.150306124176	0.372551352132	0.00125284407619	0.0791412115324	0.272888558833	0.0205766378807	0.447647890332	47.1405747341	18.3081916882	92.3992759525
8	1.41460490533	-0.56848205391	-0.244110552643	3.47156568708	-1.22578571001	8.35221031011	0.0909437249263	0.39228097295	-0.246144583071	-0.0110554384499	0.144262863479	0.348610151063	-0.262968289887	-0.105664016295	-0.216986882955	0.430584801083	-0.0374360338967	0.0812413990887	0.430434223164	-0.0808655404774	0.554140684921	47.0368566606	15.1670569557	83.0733817849
9	8.42410987496	-6.85912168838	-5.9711641016	9.5878292245	4.45147820748	6.85654485463	0.650663497081	0.782709455992	0.0518131699412	-1.24645101184	-0.040314728094	-0.174154412848	-0.16283770687	-0.247361261783	-0.70701305792	0.980210878317	0.0830181051881	0.232973380505	0.589392211018	0.0119580593482	0.691560402596	72.9703071065	-0.587115311047	0.524834094151
10	2.3919950601	0.524205493457	-0.43050824159	9.72226370478	9.56897275721	9.8066715469	-0.349088688065	0.10516201701	-0.111229600522	0.123040655677	0.963984891615	-0.58825961037	0.313979589623	1.85273282661	-0.522602339645	0.883932309695	-0.00992309868689	0.26025835444	0.768183529474	-0.0592784159251	0.753341089633	75.9124163999	-2.16722351992	9.57953366931
11	1.99572274442	-0.539515190402	-1.00603203977	4.59628372168	3.19636045033	5.84477067675	-0.0785864323353	-0.0436241050663	-0.355387987609	0.195247511544	-0.103280212184	-0.0423349765496	0.594777318329	-0.238144218599	0.177610183707	0.638463356655	0.0149373628996	0.173249894905	0.393333253044	0.0267114618222	0.497859637183	65.3199142842	-5.5885525317	17.0807691114
12	4.98539127795	-0.000209426924645	0.467393321473	3.27455731844	1.85522109658	6.61288811116	0.137744892424	0.363385543211	0.30119649605	-0.500500943815	-0.214136859031	0.150479090141	-0.348337146421	-0.88816980239	0.0909600746074	0.63200716326	0.0777920146665	0.146970480097	0.604898988414	-0.0547055611276	0.465146327171	57.0282095688	6.25994222079	13.8460073851
13	3.11444198443	2.59437344192	-1.9552287753	4.0685942034	-1.41540371749	9.1343722217	0.0283255769218	1.24541266128	0.338797709548	-1.50633114717	-0.270902805119	0.317133065699	0.137352230089	-0.416023604488	0.177972032579	0.736399116876	0.205906780241	0.156828650112	0.636744710713	0.0531880744345	0.544038909313	60.6176719558	6.63147760966	1.62184067453
14	2.89025369033	-1.03823065689	-0.973541873491	2.99844626013	-1.93603646387	7.18568120927	0.200383054328	0.391078328164	0.242028106757	-0.595128988067	-0.0195657514853	-0.351069831584	-0.0557931556012	0.0308160765167	-0.18122074073	0.43767128859	0.014417301774	0.0856236960365	0.433207454276	-0.0790552717594	0.418395067502	54.3321882145	9.13112577477	33.2661452233
15	7.69329905667	-2.01992830094	3.12859541709	1.61298538175	0.627387672598	7.07259425736	-0.132301933822	-0.134236963516	0.311422621377	0.152394707785	0.0366416921227	-0.551905739175	-0.131755578212	0.468474126254	0.0805632088033	0.59790930753	-0.0356905049497	0.0477128397088	0.44321162773	-0.027970860545	0.575541151399	64.5687175053	12.0952876647	59.0288086004
16	5.20045063806	-2.98725741435	2.42207633869	6.08905117768	-2.62949845342	8.55285547611	-0.0271598495599	0.154432674089	0.101539042711	-0.0586381052941	-0.0564247409007	-0.17399976533	0.18500347754	0.405119496371	0.118203688902	0.450541566787	-0.0415573852154	0.0747581887302	0.351438270811	-0.142504563383	0.432043894411	58.8191667373	7.97559416193	47.7135232117
17	7.94407026653	-1.19620292535	4.21183252651	1.76464307679	-1.43158126348	5.66858287712	0.311643883453	-0.226020233523	-0.304303842248	0.0470266094641	-0.125730480161	-0.214499712801	0.345768696698	0.249336945847	-0.3088460985	0.634807716376	0.0105100479888	0.0867876308394	0.447711130858	-0.0424117442471	0.512385511868	60.5790798194	3.39591165159	51.3402041925
18	6.82133123663	1.14141941424	1.17260068954	5.61516278912	2.25199483586	7.25545016733	-0.0307621187953	-0.394173141068	0.266497039441	-0.234682046584	0.0112889301066	0.0436833372512	0.142367335468	-0.11476789264	-0.00874934662972	0.610646211488	-0.0582041398144	0.119565710659	0.640805665997	0.0696932589174	0.414949299897	56.1509674271	11.3922001438	64.1280668245
19	5.01847949896	-2.5248928989	-3.7364809333	6.06432630191	0.73796723212	8.10346039102	0.496505493581	-3.17216896304	0.118833617696	0.27560747865	0.359684862071	0.660087038999	-1.46715998445	-0.338927204543	-1.10627350121	0.755259237743	0.150627169901	0.00484895060151	2.13269176478	-0.444613413632	1.10690418818	34.5186618903	33.4154057444	135.270676855
20	1.61142289996	-0.510465732354	-2.43987082256	2.43148762807	2.71258503318	4.9664559027	-0.0759879913106	-2.30128265231	0.368863542585	0.65574364772	-0.119070876531	0.22518223423	0.497370004865	-0.62681563115	-0.442548176386	0.823485233883	-0.0354205027011	0.137661432716	1.99438303268	-0.168349730757	0.706660248067	33.559692887	26.7620947122	129.440690521
21	0.627529390388	0.584691642057	-0.979536389015	4.04658136531	1.233736124	4.04756679544	0.0730544963506	-2.05306179782	-0.783112255138	0.931827835421	-0.133171883043	0.0584644328787	1.11057517217	-0.633902779948	0.18134229671	0.750884909714	-0.159367819427	0.0374541156611	1.46814637319	0.283712900918	0.727873077961	32.9829316866	16.8654844092	121.678934384

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 130 through 149 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 150 through 173 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 174 through 189 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 83 through 150 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 151 through 173 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 174 through 208 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 209 through 274 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 275 through 333 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 9 through 26 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 27 through 43 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 44 through 140 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 141 through 189 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 81 through 102 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 103 through 159 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 160 through 232 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 233 through 263 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 264 through 298 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 299 through 333 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 16 through 26 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 27 through 76 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 77 through 129 )

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