[English] 日本語
Yorodumi
- PDB-7y77: Crystal structure of rice NAL1 -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Adenosine 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 / Water


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more