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- PDB-7y77: Crystal structure of rice NAL1 -

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Basic information

Entry
Database: PDB / ID: 7y77
TitleCrystal structure of rice NAL1
ComponentsProtein NARROW LEAF 1
KeywordsHYDROLASE / Serine protease / NAL1
Function / homologystem vascular tissue pattern formation / internode patterning / regulation of leaf development / leaf vascular tissue pattern formation / Peptidase S1, PA clan / nucleoplasm / cytoplasm / ADENOSINE-5'-TRIPHOSPHATE / Protein NARROW LEAF 1
Function and homology information
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYan, J.J. / Guan, Z.Y. / Yin, P. / Xiong, L.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31700203 China
Citation
Journal: Nat.Plants / Year: 2023
Title: Serine protease NAL1 exerts pleiotropic functions through degradation of TOPLESS-related corepressor in rice.
Authors: Li, W. / Yan, J. / Zhang, Y. / Zhang, F. / Guan, Z. / Yao, Y. / Chang, Y. / Tu, H. / Li, X. / Wang, H. / Xiong, H. / Lai, X. / Yin, P. / Xiong, L.
#1: Journal: Nat Plants / Year: 2023
Title: Serine protease NAL1 exerts pleiotropic functions through degradation of TOPLESS-related corepressor in rice.
Authors: Li, W. / Yan, J. / Zhang, Y. / Zhang, F. / Guan, Z. / Yao, Y. / Chang, Y. / Tu, H. / Li, X. / Wang, H. / Xiong, H. / Lai, X. / Yin, P. / Xiong, L.
History
DepositionJun 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: 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 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein NARROW LEAF 1
B: Protein NARROW LEAF 1
C: Protein NARROW LEAF 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,0596
Polymers142,5373
Non-polymers1,5223
Water46826
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


Theoretical massNumber of molelcules
Total (without water)288,11712
Polymers285,0746
Non-polymers3,0436
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Unit cell
Length a, b, c (Å)89.413, 194.400, 173.374
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 60 through 78 or resid 83...
d_2ens_1(chain "B" and (resid 60 through 78 or resid 83 through 172 or resid 182 through 501))
d_3ens_1(chain "C" and (resid 60 through 145 or (resid 146...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11HISHISLEULEUAA60 - 7830 - 48
d_12GLYGLYTYRTYRAA83 - 17253 - 142
d_13GLUGLUGLNGLNAA182 - 457152 - 427
d_14ARGARGPHEPHEAA464 - 465428 - 429
d_15ATPATPATPATPAD501
d_21HISHISLEULEUBB60 - 7830 - 48
d_22GLYGLYTYRTYRBB83 - 17253 - 142
d_23GLUGLUPHEPHEBB182 - 459152 - 429
d_24ATPATPATPATPBE501
d_31HISHISPHEPHECC60 - 45930 - 429
d_32ATPATPATPATPCF501

NCS oper:
IDCodeMatrixVector
1given(0.602306359924, 0.441008505723, 0.665386013285), (-0.449120682788, -0.501888338989, 0.739187870219), (0.659937619088, -0.744056176016, -0.104224497339)-31.1327917894, -104.584562725, 51.8552245702
2given(0.60467579958, -0.451330633626, 0.656252875463), (0.440835459106, -0.496583927699, -0.747708834203), (0.66334853237, 0.741420974819, -0.101309736457)-61.8221194646, 0.380561332089, 103.929997231

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Components

#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: 47512.398 Da / Num. of mol.: 3 / Mutation: C31S,C163S,C168S,C296S,C307S,C334S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice)
Gene: NAL1, GFP, LSCHL4, SPIKE, Os04g0615000, LOC_Os04g52479, OsJ_16147
Production host: Escherichia coli BL21(DE3) (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 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: MES, calcium acetate, PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 46791 / % possible obs: 99.91 % / Redundancy: 2 % / Biso Wilson estimate: 66.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02128 / Rpim(I) all: 0.02128 / Rrim(I) all: 0.03009 / Net I/σ(I): 20.36
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 2 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 2.86 / Num. unique obs: 4592 / CC1/2: 0.901 / CC star: 0.974 / Rpim(I) all: 0.248 / Rrim(I) all: 0.3507 / % possible all: 99.67

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF2

Resolution: 2.6→49.67 Å / SU ML: 0.389 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.1083
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2679 2279 4.87 %
Rwork0.224 44501 -
obs0.2262 46780 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.28 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8889 0 115 26 9030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00499190
X-RAY DIFFRACTIONf_angle_d0.828112471
X-RAY DIFFRACTIONf_chiral_restr0.05711392
X-RAY DIFFRACTIONf_plane_restr0.00491611
X-RAY DIFFRACTIONf_dihedral_angle_d18.42593303
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.05089587734
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.913210297597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.34491540.30562698X-RAY DIFFRACTION99.48
2.66-2.720.33271390.30022769X-RAY DIFFRACTION100
2.72-2.790.36811360.29032757X-RAY DIFFRACTION99.93
2.79-2.860.41131240.32582760X-RAY DIFFRACTION100
2.86-2.950.4661310.36032756X-RAY DIFFRACTION99.93
2.95-3.040.36051310.31312795X-RAY DIFFRACTION100
3.04-3.150.32221480.27492733X-RAY DIFFRACTION99.86
3.15-3.280.34321520.27952742X-RAY DIFFRACTION99.93
3.28-3.420.29511260.26662799X-RAY DIFFRACTION99.97
3.42-3.610.30861380.26552769X-RAY DIFFRACTION100
3.61-3.830.26741470.22242781X-RAY DIFFRACTION99.97
3.83-4.130.26511550.21382755X-RAY DIFFRACTION100
4.13-4.540.23821360.18072800X-RAY DIFFRACTION100
4.54-5.20.1971600.17562807X-RAY DIFFRACTION100
5.2-6.550.24791480.21212826X-RAY DIFFRACTION99.97
6.55-49.670.22671540.18062954X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: -27.9424229838 Å / Origin y: -34.9287281163 Å / Origin z: 53.6978777417 Å
111213212223313233
T0.341825201172 Å20.0206875080843 Å2-0.116192258934 Å2-0.519984311488 Å2-0.0213317498113 Å2--0.462773758157 Å2
L0.506664649363 °20.0726965542014 °2-0.25582624567 °2-0.551799715822 °2-0.0351200489305 °2--1.06360463603 °2
S-0.00599963942956 Å °-0.0402352007375 Å °0.111998436146 Å °0.0437041274948 Å °0.022962430363 Å °-0.0322919295893 Å °0.0325527958722 Å °0.0723802743463 Å °-0.0208376333086 Å °
Refinement TLS groupSelection details: all

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