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- PDB-5y09: Crystal structure of Deg9 at 295 K -

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Basic information

Entry
Database: PDB / ID: 5y09
TitleCrystal structure of Deg9 at 295 K
ComponentsProtease Do-like 9
KeywordsHYDROLASE / Protease
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / serine-type endopeptidase activity / nucleolus / proteolysis / nucleus
Similarity search - Function
Protease Do-like, PDZ domain / Protease Do-like, PDZ domain superfamily / PDZ domain / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / PDZ superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.449 Å
AuthorsOuyang, M. / Li, X.Y. / Liu, L. / Zhang, L.X.
CitationJournal: To Be Published
Title: Crystal structure of Deg9 at 295 K
Authors: Ouyang, M. / Li, X.Y. / Zhao, S. / Zhang, L.X.
History
DepositionJul 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease Do-like 9
B: Protease Do-like 9


Theoretical massNumber of molelcules
Total (without water)124,7652
Polymers124,7652
Non-polymers00
Water3,135174
1
A: Protease Do-like 9
B: Protease Do-like 9

A: Protease Do-like 9
B: Protease Do-like 9

A: Protease Do-like 9
B: Protease Do-like 9

A: Protease Do-like 9
B: Protease Do-like 9


Theoretical massNumber of molelcules
Total (without water)499,0598
Polymers499,0598
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area24540 Å2
ΔGint-78 kcal/mol
Surface area138110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.372, 132.372, 154.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Protease Do-like 9


Mass: 62382.383 Da / Num. of mol.: 2 / Fragment: UNP residues 65-592
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: Deg9, DEGP9, At5g40200, MSN9.10, MSN9.100 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9FL12, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium acetate, 0.1M HEPES pH 7.5, 45% v/v MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.449→50 Å / Num. obs: 48768 / % possible obs: 99.7 % / Redundancy: 7.6 % / Biso Wilson estimate: 34.55 Å2 / Net I/σ(I): 26.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IL9

5il9


Resolution: 2.449→38.888 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.35
RfactorNum. reflection% reflection
Rfree0.2533 2379 5.09 %
Rwork0.206 --
obs0.2084 46781 95.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.84 Å2 / Biso mean: 27.87 Å2 / Biso min: 6.25 Å2
Refinement stepCycle: final / Resolution: 2.449→38.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6502 0 0 174 6676
Biso mean---22.29 -
Num. residues----834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046649
X-RAY DIFFRACTIONf_angle_d0.8949014
X-RAY DIFFRACTIONf_chiral_restr0.0641034
X-RAY DIFFRACTIONf_plane_restr0.0041153
X-RAY DIFFRACTIONf_dihedral_angle_d12.6242437
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4486-2.49860.307810.2271637171860
2.4986-2.55290.28291120.23912047215976
2.5529-2.61220.34751340.23452565269995
2.6122-2.67760.28911530.23292698285198
2.6776-2.74990.29671670.239327072874100
2.7499-2.83080.30231480.229927012849100
2.8308-2.92220.29091450.240526952840100
2.9222-3.02660.28361560.233227112867100
3.0266-3.14770.27881540.224427402894100
3.1477-3.29090.27131340.211727462880100
3.2909-3.46430.25541460.203527232869100
3.4643-3.68120.22841410.191427322873100
3.6812-3.96520.21341310.198927082839100
3.9652-4.36370.23721530.177827442897100
4.3637-4.9940.2141400.176227422882100
4.994-6.28760.24591390.207427552894100
6.2876-38.89250.22971450.20122751289699
Refinement TLS params.Method: refined / Origin x: -30.5119 Å / Origin y: 24.4671 Å / Origin z: -11.1218 Å
111213212223313233
T0.0901 Å20.0446 Å2-0.0085 Å2-0.0545 Å20.0158 Å2--0.0795 Å2
L0.1763 °20.02 °20.1268 °2-0.09 °20.0112 °2--0.1949 °2
S0.0269 Å °0.0449 Å °0.0068 Å °0.0417 Å °0.0228 Å °0.0083 Å °0.0253 Å °-0.0059 Å °0.0172 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA123 - 587
2X-RAY DIFFRACTION1allB129 - 587
3X-RAY DIFFRACTION1allS1 - 174

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