PDB-8pmm: Structure of Nal1 protein, allele SPIKE from japonica rice, const...

ID or keywords:

Entry

Database: PDB / ID: 8pmm

Title

Structure of Nal1 protein, allele SPIKE from japonica rice, construct 31-458

Components

Protein NARROW LEAF 1

Keywords

PLANT PROTEIN / Serine protease

Function / homology

Function and homology information

stem vascular tissue pattern formation / internode patterning / regulation of leaf development / leaf vascular tissue pattern formation / nucleoplasm / cytoplasm
Similarity search - Function

Biological species

Oryza sativa Japonica Group (Japanese rice)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Huang, L.Y. / Rety, S. / Xi, X.G.

Funding support

China, 4items

Organization	Grant number	Country
National Natural Science Foundation of China (NSFC)	32071291	China
National Natural Science Foundation of China (NSFC)	32201042	China
National Natural Science Foundation of China (NSFC)	32071225	China
National Natural Science Foundation of China (NSFC)	31870788	China

Citation

Journal: Nat Plants / Year: 2024
Title: The catalytic triad of rice NARROW LEAF1 involves H234.
Authors: Ling-Yun Huang / Na-Nv Liu / Wei-Fei Chen / Xia Ai / Hai-Hong Li / Ze-Lin Zhang / Xi-Miao Hou / Philippe Fossé / Olivier Mauffret / Dong-Sheng Lei / Stephane Rety / Xu-Guang Xi /

Abstract: NARROW LEAF1 (NAL1) exerts a multifaceted influence on leaf morphology and crop yield. Recent crystal study proposed that histidine 233 (H233) is part of the catalytic triad. Here we report that ...

History

Deposition	Jun 29, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 17, 2024	Provider: repository / Type: Initial release
Revision 1.1	Apr 24, 2024	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jun 5, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8pmm.cif.gz	599.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8pmm.ent.gz		Display	PDB format
PDBx/mmJSON format	8pmm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8pmm_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	8pmm_full_validation.pdf.gz	2.6 MB	Display
Data in XML	8pmm_validation.xml.gz	49.8 KB	Display
Data in CIF	8pmm_validation.cif.gz	71.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pm/8pmm ftp://data.pdbj.org/pub/pdb/validation_reports/pm/8pmm	HTTPS FTP

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Related structure data

Related structure data	17766C 17768C 8pmeC 8pmgC 8pmiC 8pmlC 8pn1C 8pn2C C: citing same article (ref.)
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: Protein NARROW LEAF 1

B: Protein NARROW LEAF 1

C: Protein NARROW LEAF 1

hetero molecules

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

1

A: Protein NARROW LEAF 1

B: Protein NARROW LEAF 1

C: Protein NARROW LEAF 1

hetero molecules

A: Protein NARROW LEAF 1

B: Protein NARROW LEAF 1

C: Protein NARROW LEAF 1

hetero molecules

defined by author&software
Evidence: SAXS
287 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	89.967, 182.917, 172.510
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z+1/2 #4: -x,-y,z+1/2 #5: x+1/2,y+1/2,z #6: x+1/2,-y+1/2,-z #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	A-1332- HOH
2	1	B-1237- HOH
3	1	B-1303- HOH

#1: Protein	Protein NARROW LEAF 1 / Protein GREEN FOR PHOTOSYNTHESIS / Protein QUANTITATIVE TRAIT LOCUS FOR FLAG LEAF WIDTH 4 / qFLW4 / ...Protein GREEN FOR PHOTOSYNTHESIS / Protein QUANTITATIVE TRAIT LOCUS FOR FLAG LEAF WIDTH 4 / qFLW4 / Protein SPIKELET NUMBER Mass: 47270.379 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Gene: NAL1, GFP, LSCHL4, SPIKE, Os04g0615000, LOC_Os04g52479, OsJ_16147 Plasmid: pET15b-SUMO / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: B4XT64
#2: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.5 Å³/Da / Density % sol: 50.85 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 4% tacsimate 12% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97869 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97869 Å / Relative weight: 1
Reflection	Resolution: 1.748→91.459 Å / Num. obs: 107716 / % possible obs: 94.9 % / Redundancy: 13.5 % / B_iso Wilson estimate: 31.94 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.077 / R_pim(I) all: 0.022 / R_rim(I) all: 0.08 / Net I/σ(I): 18.1
Reflection shell	Resolution: 1.748→1.91 Å / Redundancy: 13.7 % / R_merge(I) obs: 1.339 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5386 / CC_1/2: 0.8 / R_pim(I) all: 0.374 / R_rim(I) all: 1.391 / % possible all: 61.7

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS	BUILT 20200417	data reduction
Aimless	0.7.4	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.75→46.84 Å / SU ML: 0.1722 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.0567
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2305	5202	4.83 %
R_work	0.2004	102499	-
obs	0.2019	107701	75.19 %

Solvent computation

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

Displacement parameters

B_iso mean: 43.65 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→46.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9360	0	101	618	10079

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0048	9664
X-RAY DIFFRACTION	f_angle_d	0.9739	13139
X-RAY DIFFRACTION	f_chiral_restr	0.0575	1464
X-RAY DIFFRACTION	f_plane_restr	0.0081	1702
X-RAY DIFFRACTION	f_dihedral_angle_d	17.3841	3458

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 (%)
1.75-1.77	0.3709	1	0.5167	59	X-RAY DIFFRACTION	1.27
1.77-1.79	0.5981	17	0.4757	252	X-RAY DIFFRACTION	5.7
1.79-1.81	0.4132	23	0.4023	447	X-RAY DIFFRACTION	10.03
1.81-1.83	0.3132	23	0.3409	622	X-RAY DIFFRACTION	13.67
1.83-1.86	0.271	29	0.315	817	X-RAY DIFFRACTION	17.91
1.86-1.88	0.3187	53	0.2981	1080	X-RAY DIFFRACTION	23.86
1.88-1.91	0.3884	99	0.2984	1794	X-RAY DIFFRACTION	40.11
1.91-1.94	0.3268	139	0.2803	2556	X-RAY DIFFRACTION	56.99
1.94-1.97	0.3016	158	0.271	3004	X-RAY DIFFRACTION	66.74
1.97-2	0.3048	158	0.2564	3292	X-RAY DIFFRACTION	72.36
2-2.04	0.2814	179	0.2464	3564	X-RAY DIFFRACTION	78.77
2.04-2.07	0.2729	170	0.2361	3726	X-RAY DIFFRACTION	82.75
2.07-2.11	0.274	196	0.2343	4034	X-RAY DIFFRACTION	88.77
2.11-2.16	0.263	219	0.23	4341	X-RAY DIFFRACTION	95.8
2.16-2.2	0.268	241	0.2352	4463	X-RAY DIFFRACTION	98.97
2.2-2.25	0.3076	235	0.2318	4506	X-RAY DIFFRACTION	100
2.25-2.31	0.2528	220	0.2272	4553	X-RAY DIFFRACTION	99.98
2.31-2.37	0.2437	213	0.2299	4545	X-RAY DIFFRACTION	99.83
2.37-2.44	0.2624	247	0.2203	4507	X-RAY DIFFRACTION	99.73
2.44-2.52	0.2665	243	0.2245	4429	X-RAY DIFFRACTION	98.82
2.52-2.61	0.2353	226	0.2185	4569	X-RAY DIFFRACTION	100
2.61-2.72	0.2687	226	0.2124	4519	X-RAY DIFFRACTION	100
2.72-2.84	0.2397	236	0.2114	4561	X-RAY DIFFRACTION	100
2.84-2.99	0.2494	221	0.2199	4587	X-RAY DIFFRACTION	100
2.99-3.18	0.2215	229	0.2068	4533	X-RAY DIFFRACTION	99.64
3.18-3.42	0.2129	244	0.1925	4551	X-RAY DIFFRACTION	99.61
3.42-3.77	0.222	230	0.1782	4610	X-RAY DIFFRACTION	99.96
3.77-4.31	0.2058	251	0.1693	4575	X-RAY DIFFRACTION	99.9
4.31-5.43	0.1799	234	0.1588	4618	X-RAY DIFFRACTION	99.24
5.43-46.84	0.2167	242	0.1934	4785	X-RAY DIFFRACTION	99.43

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	6.75747409243	2.64627054009	-0.626826032617	7.13730679398	1.66060196057	4.2662330839	0.238487565653	0.000269530893962	-1.34868546125	0.566849461004	0.275119536487	-1.32244379379	0.48630457982	0.0102434780843	-0.386516139538	0.557051815872	0.0581060685476	0.00756061688868	0.40857830529	0.0979395335216	0.443174147262	6.756	-5.242	66.972
2	2.68171835402	-0.485420060123	2.27822550526	1.99039903847	0.420515373089	4.61500094249	0.153322425789	-0.0530705760855	-0.206954023003	-0.166524607725	-0.013833063745	0.0549441715619	0.289706093254	-0.121613741151	-0.120705448503	0.25438168769	-0.0603567427541	-0.019814438983	0.191682388288	0.0332587727851	0.235652604962	-14.877	-4.545	60.964
3	1.16224237889	0.818503672364	-0.0265727248704	4.2596661841	1.19466143277	1.78086817946	0.038551575748	0.0574158832126	-0.0499031095185	-0.138321837259	0.159860817969	-0.430351585753	-0.126453470478	0.0659541107893	-0.149840661507	0.152224653291	0.00484140143638	0.0297293589031	0.205550949655	0.0257465880639	0.202653870825	-2.746	16.555	75.339
4	3.15050215972	-0.509888712688	0.90910203488	6.95894407576	-2.34460661992	3.33896548199	0.0649571050373	0.112875980708	-0.213256001029	0.00685059169519	-0.359864238881	-0.0884006756138	-0.0847849683815	-0.10598574438	0.317163147588	0.398685856703	-0.00141362368041	-0.0538819887512	0.416031592702	0.0364425037564	0.218431604182	-29	29.103	10.064
5	1.03401889098	-0.905431876633	0.627812346018	4.85472906104	-1.64754227355	1.78417349582	0.115964410379	0.0456180203783	0.0204477627749	-0.207589948386	-0.184610243673	0.128172754205	-0.0724266813102	-0.030197458159	0.0665571998855	0.1111891592	0.0297200710621	0.0253103877381	0.29302045848	-0.0178909810113	0.149731083889	-32.908	30.592	29.616
6	0.789507358136	-0.424288283002	0.717544151413	3.50562208811	-2.20550760138	2.10767211037	0.114882856129	0.0791503901223	-0.0439214592824	-0.359055099826	-0.268146191407	-0.153104063961	0.234116556889	0.0919157699084	0.121943560056	0.151737077006	0.0199786956777	0.00607003909321	0.260017376571	0.00277559769534	0.230748813123	-28.574	18.799	29.806
7	2.40817185992	-0.313209133183	0.168071533396	7.37953431146	0.908422053637	3.35450846295	0.26747879019	0.0471297461968	-0.197466779377	-0.213504582874	-0.0879498010461	-0.0466692207394	0.1558747022	-0.157091828894	-0.190362633277	0.17427117349	0.0204016845291	-0.0745498174193	0.298084632062	0.0390050093127	0.207691897312	-34.853	17.648	31.592
8	2.13088037862	0.352005280028	-1.61398114692	1.28171381824	-0.767132451364	4.15004006817	0.306472768936	-0.355649065448	0.265378342327	0.221693960111	0.0480521556127	-0.0658877122166	-1.13842986823	0.669845364536	-0.0745327377369	0.558332744383	-0.0751072059372	0.0252705963122	0.29462262298	-0.0926898675624	0.317679252482	1.742	69.014	62.449
9	1.49024874099	-0.189459608813	2.28138620769	0.547212815877	-0.541520391528	4.17144371654	0.00647723869812	-0.0142643439945	-0.117603234767	0.028322592714	0.110056627025	-0.0583291524553	-0.111351690953	0.0681388933042	-0.118736372703	0.293637846738	0.0560624827348	0.0733356305869	0.225256144395	-0.0681153276124	0.240927185692	-9.322	52.368	71.277
10	1.69731879068	0.28256397703	0.878735306162	0.81074269066	-0.261946563254	3.55103002938	-0.0324180777789	0.0465812940104	0.00586776949336	0.00890938888417	0.0392670264428	0.0267716310771	-0.0760255740415	0.113885295619	-0.0104017353276	0.345519374561	0.0737680304607	0.0606219180356	0.1676126793	-0.0167656861494	0.237817150228	-14.607	61.07	53.361
11	0.644399079791	-1.13116925455	1.16810199278	2.33015351907	-2.44846085397	3.2454688794	0.0720268875412	0.0522663533805	0.00105623525976	-0.477448835627	0.00693645332793	0.260631312875	0.271043010009	-0.0151070170498	0.0506054028679	0.428675121055	0.096470342853	0.0133999558079	0.255998996579	-0.0290212941619	0.28217079912	-15.745	60.287	58.616

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 41:86 )	A	41 - 86
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 87:169 )	A	87 - 169
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 170:457 )	A	170 - 457
4	X-RAY DIFFRACTION	4	( CHAIN B AND RESID 41:86 )	B	41 - 86
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 87:236 )	B	87 - 236
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 237:387 )	B	237 - 387
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 388:458 )	B	388 - 458
8	X-RAY DIFFRACTION	8	( CHAIN C AND RESID 40:103 )	C	40 - 103
9	X-RAY DIFFRACTION	9	( CHAIN C AND RESID 104:203 )	C	104 - 203
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 204:399 )	C	204 - 399
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 400:457 )	C	400 - 457

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