PDB-7r5z: Monocot chimeric jacalin JAC1 from Oryza sativa: dirigent domain ...

ID or keywords:

Entry

Database: PDB / ID: 7r5z

Title

Monocot chimeric jacalin JAC1 from Oryza sativa: dirigent domain (crystal form 1)

Components

Dirigent protein

Keywords

PLANT PROTEIN / Monocot chimeric jacalin / Dirigent protein / Lectin / Pathogen resistance

Function / homology

Function and homology information

phenylpropanoid biosynthetic process / apoplast / carbohydrate binding / metal ion binding
Similarity search - Function

Biological species

Oryza sativa (Asian cultivated rice)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Huwa, N. / Classen, T. / Weiergraeber, O.H.

Funding support

Germany, 2items

Citation

Journal: Biomolecules / Year: 2022
Title: The Crystal Structure of the Defense Conferring Rice Protein Os JAC1 Reveals a Carbohydrate Binding Site on the Dirigent-like Domain.
Authors: Huwa, N. / Weiergraber, O.H. / Fejzagic, A.V. / Kirsch, C. / Schaffrath, U. / Classen, T.

History

Deposition	Feb 12, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 4, 2022	Provider: repository / Type: Initial release
Revision 1.1	Sep 14, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
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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Download

PDBx/mmCIF format	7r5z.cif.gz	211.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7r5z.ent.gz	150.7 KB	Display	PDB format
PDBx/mmJSON format	7r5z.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7r5z_validation.pdf.gz	444.3 KB	Display	wwPDB validaton report
Full document	7r5z_full_validation.pdf.gz	446.3 KB	Display
Data in XML	7r5z_validation.xml.gz	18.4 KB	Display
Data in CIF	7r5z_validation.cif.gz	25.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r5/7r5z ftp://data.pdbj.org/pub/pdb/validation_reports/r5/7r5z	HTTPS FTP

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Related structure data

Related structure data	7yweC 7ywfC 7ywgC 7ywwC 6oodS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	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: Dirigent protein

B: Dirigent protein

C: Dirigent protein

hetero molecules

52.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	48.990, 87.360, 93.730
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	Dirigent protein Mass: 17452.025 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: JAC1, LOC_Os12g14440, Os12g0247700, OSNPB_120247700 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q306J3
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 120 / 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: 1.92 Å³/Da / Density % sol: 35.79 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: PEG 3350, calcium chloride, Tris-HCl, dithiothreitol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 11, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9677 Å / Relative weight: 1
Reflection	Resolution: 1.75→43.68 Å / Num. obs: 41085 / % possible obs: 99.4 % / Redundancy: 13.72 % / B_iso Wilson estimate: 31.87 Å² / CC_1/2: 0.998 / Net I/σ(I): 10.11
Reflection shell	Resolution: 1.75→1.8 Å / Redundancy: 13 % / Mean I/σ(I) obs: 0.69 / Num. unique obs: 2914 / CC_1/2: 0.346 / % possible all: 97.6

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Processing

Software

Name	Version	Classification
XDS		data reduction
MoRDa		phasing
PHENIX	1.19.2_4158	refinement
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6OOD

6ood

Resolution: 1.75→43.68 Å / SU ML: 0.2553 / Cross valid method: FREE R-VALUE / Phase error: 27.3662
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.229	2055	5.01 %
R_work	0.191	38995	-
obs	0.1929	41050	99.32 %

Solvent computation

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

Displacement parameters

B_iso mean: 55.22 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→43.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3221	0	6	120	3347

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0063	3434
X-RAY DIFFRACTION	f_angle_d	0.863	4683
X-RAY DIFFRACTION	f_chiral_restr	0.0588	523
X-RAY DIFFRACTION	f_plane_restr	0.0057	614
X-RAY DIFFRACTION	f_dihedral_angle_d	13.9271	1169

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 (%)
1.75-1.79	0.3813	132	0.3948	2492	X-RAY DIFFRACTION	97.51
1.79-1.84	0.3399	133	0.3357	2539	X-RAY DIFFRACTION	98.93
1.84-1.89	0.3214	137	0.2919	2592	X-RAY DIFFRACTION	99.49
1.89-1.94	0.3095	134	0.2859	2559	X-RAY DIFFRACTION	99.7
1.94-2	0.2888	137	0.2785	2584	X-RAY DIFFRACTION	99.38
2-2.07	0.2726	135	0.2542	2560	X-RAY DIFFRACTION	99.67
2.07-2.16	0.2712	136	0.2264	2594	X-RAY DIFFRACTION	99.67
2.16-2.26	0.2459	136	0.2064	2578	X-RAY DIFFRACTION	99.52
2.26-2.38	0.22	138	0.1936	2605	X-RAY DIFFRACTION	99.75
2.38-2.52	0.2469	137	0.2067	2606	X-RAY DIFFRACTION	99.78
2.52-2.72	0.2562	138	0.2082	2626	X-RAY DIFFRACTION	99.96
2.72-2.99	0.2492	138	0.1998	2609	X-RAY DIFFRACTION	99.96
2.99-3.43	0.2368	135	0.1804	2567	X-RAY DIFFRACTION	96.71
3.43-4.31	0.1924	140	0.1499	2671	X-RAY DIFFRACTION	99.93
4.31-43.68	0.1905	149	0.164	2813	X-RAY DIFFRACTION	99.87

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	1.72631592774	0.10844877188	1.57817024562	1.57939299338	0.079964484808	4.00015150032	-0.0899799137399	-0.107066494841	0.0225048863695	-0.0460931254271	0.182282888539	-0.567085061456	0.238032409377	1.15945731831	-0.467260488949	0.31883871624	0.0436835161095	-0.0114277767623	0.738038857139	-0.139256983985	0.497192282694	52.6186584406	39.6331974581	47.3976091806
2	0.283680157052	0.547860379451	-0.346471751814	2.20188438149	-0.0999612160069	6.11356803018	-0.0930189376611	0.368363669774	-0.032535137663	-0.373371876867	0.0990882182519	-0.0194787987204	0.126603234473	-0.113967056366	-0.041610579769	0.251951689154	-0.0141267579417	0.0118189813007	0.324379608802	-0.0180977522697	0.258426512552	41.8851260092	39.7240330151	46.075822872
3	0.98147933743	-1.58654131399	1.71592702175	2.57922625384	-2.76583066537	2.97878426809	1.13386627988	2.11744587409	-1.00260012958	-0.39528523963	0.805353084667	-2.29859544607	2.74410546585	3.0810540175	-1.18381276768	1.13921967336	0.429052461488	-0.0271987596683	1.277660578	-0.263132133178	0.948324838762	57.3730500482	29.4321248788	54.9211371796
4	6.97237252914	1.08678632708	0.581740736297	3.47872743131	2.54081201185	1.89999450049	-0.0896667581564	0.191064292246	0.0553562013375	-0.272583793753	-0.0677194947636	-0.352056120416	-0.257661658495	1.10841305455	0.265038902791	0.22991791692	-0.00849420683466	0.0416536597137	0.504191054659	-0.0150878781993	0.326608353746	49.9630893259	43.248518452	53.4031039687
5	4.37626062457	1.78788622305	-0.509400080992	3.77091893711	0.0697400645505	2.68179804605	-0.360304803694	0.627106599849	-0.0645495222295	-0.568479528505	0.289551657124	-0.20507654272	-0.123175354436	1.33063000336	0.11028265369	0.303520074162	-0.0268143831099	0.0564278135602	0.679129232955	-0.0304016831062	0.400274293953	52.790721961	43.4664704686	45.2502627928
6	1.00790566699	-0.498614813927	-1.5802333114	2.01201002523	-0.426657540804	8.93686051905	-0.195643710977	1.09456092132	0.509668719897	-0.0583183564273	-0.650575357175	0.876466406235	-1.00968514352	-0.0386149969834	0.488861023908	0.436974311277	-0.0352956912074	-0.0572538847995	1.39570479047	-0.16801286292	0.858530794621	64.2077277802	46.7833946304	60.3601889545
7	6.09186518132	-2.6154906137	-3.16377796534	2.05442460677	-0.554252243885	7.25911714906	0.527998249903	-0.54255689516	1.40021414055	-0.0562136148315	0.16167958929	-0.872905808872	-2.83383831575	0.473640025737	0.577044063281	1.0508819038	0.122115613865	0.0835227359518	0.406879587249	-0.0946768297187	0.652631863196	40.3970684345	63.1013244434	62.5434144611
8	3.70781405185	-0.157946662921	0.472821485284	3.35967603252	0.729445386794	3.5634622302	0.343859086093	0.286691936889	0.498149851102	0.300202910754	-0.00534640627083	0.824149362641	-1.44153184051	-1.98256217742	0.922483157414	0.659952756136	0.367515991088	0.0860076378365	0.782070741003	0.0611102876634	0.446124997437	26.9401779705	52.9956619088	55.7301486656
9	3.10861885516	1.89462648212	1.09599370136	2.34986016702	1.88421828496	1.5458376778	0.0652469980773	-0.188980210082	-0.295481421088	-0.030241258697	-0.166133764009	0.0517268158676	-0.830213636199	-0.690457129089	0.0529492295748	0.342886670465	0.109477966396	-0.00214924997279	0.356391236152	0.00564760376494	0.281410447971	34.5114097118	51.3008274754	57.4433589675
10	7.69282177131	-0.0910427873134	4.31885465283	6.60950585542	3.84615087965	4.72473722762	0.0013888881631	1.80845720426	3.26434797443	-0.298379748982	-2.1969726325	-0.552954549798	-2.6153538001	1.59930262908	-0.733853846567	1.98654213468	-0.227269882327	0.316846840193	0.970846516599	0.301768016771	1.11310017457	45.9882406586	63.350828478	50.2417755806
11	4.92266415246	1.58980509657	2.67436309169	6.01183139405	-0.961153020304	3.60588094643	0.154766926382	-0.498887647062	0.696520824465	-0.215531167909	0.16964000637	0.0586255192005	-1.71222312653	0.0842920494015	-0.0796823451589	0.432074482007	-0.0375418527344	0.0159224420106	0.18149782979	-0.0536203597814	0.29900516004	40.6390972735	52.5960427882	62.1348092432
12	1.73789460073	-0.56794483088	2.64425990301	2.75594362338	-2.32044673153	5.74650820192	-0.50171972404	-0.637703206233	-0.371103921505	-0.00489954433802	0.45264997931	0.859775466294	-2.38240722886	-1.05555222278	-0.0167324583537	0.761860413043	0.0813267531206	0.0209535023105	0.39918326273	-0.117697578849	0.455819350545	37.1596674255	58.2676941685	65.7240553106
13	0.163860437221	0.34294289277	-0.644143615952	1.66618859296	-0.624707407961	3.11886851738	0.661207027169	0.645013846574	-0.084389155779	-0.377801448314	-0.28233622711	-0.287629238938	-1.44739829937	0.103474760682	0.357724034127	0.677109081018	0.0997555863331	0.107425335121	0.52587371107	-0.109433158818	0.48812233818	39.4974422027	58.9443238743	62.889491854
14	3.37763787951	-3.00988151251	2.11275264408	3.2285270475	0.0830303742076	8.53564616168	0.358896684717	-0.464881450589	-0.582842515822	0.901293668538	0.519031347351	-0.611920680026	1.70216594279	-0.0450071661655	-0.799645935162	0.993636975153	-0.334892621133	-0.400667622848	1.06136759766	0.114804479115	0.638776751789	50.1325036556	39.9940054095	78.5739846067
15	6.27489056685	-0.175183075345	-4.23859282088	4.14240132327	1.80012116729	3.84548679509	-0.749128780096	0.0482764155443	-0.270401391127	0.577412482655	0.423048062782	0.332021853467	1.75444075158	-1.30223237777	0.0333642360778	0.784391790138	-0.207938414463	-0.00766146450091	0.459148141772	0.0690350811916	0.438077928122	31.6956099347	27.2015870923	69.8295637707
16	2.60578755663	-0.00619285338414	-0.507370297199	2.77217196501	-0.144495069207	2.19478828796	-0.0718443383285	-0.0386382425531	-0.3449597631	0.152405917801	-0.050829230972	0.107007001456	1.13624316175	-0.72505274702	0.0612466959098	0.419187070651	-0.125711975818	0.0154957057391	0.38868966418	0.0021851421677	0.392886498837	34.6601706545	32.8402391224	63.1872923036
17	2.91695659287	1.80487538206	-2.37527324777	7.68493538433	0.778335450649	2.68862987094	0.0645746399034	0.0449154624785	-0.411496806309	0.321765119967	-0.315514754888	-0.473328743137	0.760792772089	-0.294851750864	0.113280442045	0.431856957386	7.24823031787E-5	0.0217701788093	0.734965275453	-0.031821319152	0.406574530254	36.9820843814	43.7321165811	80.9467771439
18	4.74714613962	-0.718939943546	-1.18212335942	4.13969553475	3.9548905924	6.31970868573	-0.221910151032	-0.165435268852	-0.214110669995	0.862821325528	-0.0445760738927	0.326341460171	0.883287043703	0.141639179425	0.243965649307	0.272224432302	0.055169462009	0.008539053287	0.257572751101	0.0594735565248	0.221330557866	42.9089552268	35.2211015295	63.769233249
19	4.32163063033	0.276807421091	-0.263701136458	1.51294786952	-1.02376776337	4.93195344653	-0.1054599071	-0.450221543967	-0.48928543355	0.597657897661	0.0690554225753	-0.481108928341	0.800286024761	0.667037255315	0.20603467769	0.366488229175	0.06190536056	0.0048497154624	0.419937119636	0.064831175721	0.330142432096	45.4443860709	36.0643626566	69.7600708412
20	2.50845362759	5.91178026121	0.54111822111	7.58754985462	0.982098917369	5.03107416385	-0.688790145714	-0.694311660707	-0.813854081275	-0.0558439592721	0.297822764783	-0.217658169709	0.618276367327	0.641086341804	-0.0439662456558	0.805917581243	0.0986736330266	-0.110009257411	0.531246281419	0.0401611963966	0.497063471245	42.7245967998	31.2432497001	71.9468142955

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 14 through 41 )	A	A	14 - 41	1 - 28
2	2	chain 'A' and (resid 42 through 93 )	A	A	42 - 93	29 - 80
3	3	chain 'A' and (resid 94 through 101 )	A	A	94 - 101	81 - 88
4	4	chain 'A' and (resid 102 through 124 )	A	A	102 - 124	89 - 111
5	5	chain 'A' and (resid 125 through 155 )	A	A	125 - 155	112 - 142
6	6	chain 'B' and (resid 6 through 18 )	B	E	6 - 18	1 - 13
7	7	chain 'B' and (resid 19 through 30 )	B	E	19 - 30	14 - 25
8	8	chain 'B' and (resid 31 through 70 )	B	E	31 - 70	26 - 65
9	9	chain 'B' and (resid 71 through 93 )	B	E	71 - 93	66 - 88
10	10	chain 'B' and (resid 94 through 101 )	B	E	94 - 101	89 - 96
11	11	chain 'B' and (resid 102 through 124 )	B	E	102 - 124	97 - 119
12	12	chain 'B' and (resid 125 through 138 )	B	E	125 - 138	120 - 133
13	13	chain 'B' and (resid 139 through 159 )	B	E	139 - 159	134 - 154
14	14	chain 'C' and (resid 17 through 25 )	C	G	17 - 25	1 - 9
15	15	chain 'C' and (resid 26 through 38 )	C	G	26 - 38	10 - 22
16	16	chain 'C' and (resid 39 through 93 )	C	G	39 - 93	23 - 77
17	17	chain 'C' and (resid 94 through 101 )	C	G	94 - 101	78 - 85
18	18	chain 'C' and (resid 102 through 112 )	C	G	102 - 112	86 - 96
19	19	chain 'C' and (resid 113 through 138 )	C	G	113 - 138	97 - 122
20	20	chain 'C' and (resid 139 through 155 )	C	G	139 - 155	123 - 139

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