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- PDB-7c2p: Structure of Egk Peptide -

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Basic information

Entry
Database: PDB / ID: 7c2p
TitleStructure of Egk Peptide
ComponentsPlant defensing Egk
KeywordsPROTEIN BINDING / Plant Defensin
Biological speciesElaeis guineensis (African oil palm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsEl Sahili, A.
CitationJournal: Acs Pharmacol Transl Sci / Year: 2020
Title: Modulation of Lymphocyte Potassium Channel KV1.3 by Membrane-Penetrating, Joint-Targeting Immunomodulatory Plant Defensin.
Authors: Ong, S.T. / Bajaj, S. / Tanner, M.R. / Chang, S.C. / Krishnarjuna, B. / Ng, X.R. / Morales, R.A.V. / Chen, M.W. / Luo, D. / Patel, D. / Yasmin, S. / Ng, J.J.H. / Zhuang, Z. / Nguyen, H.M. / ...Authors: Ong, S.T. / Bajaj, S. / Tanner, M.R. / Chang, S.C. / Krishnarjuna, B. / Ng, X.R. / Morales, R.A.V. / Chen, M.W. / Luo, D. / Patel, D. / Yasmin, S. / Ng, J.J.H. / Zhuang, Z. / Nguyen, H.M. / El Sahili, A. / Lescar, J. / Patil, R. / Charman, S.A. / Robins, E.G. / Goggi, J.L. / Tan, P.W. / Sadasivam, P. / Ramasamy, B. / Hartimath, S.V. / Dhawan, V. / Bednenko, J. / Colussi, P. / Wulff, H. / Pennington, M.W. / Kuyucak, S. / Norton, R.S. / Beeton, C. / Chandy, K.G.
History
DepositionMay 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plant defensing Egk
B: Plant defensing Egk
C: Plant defensing Egk
D: Plant defensing Egk


Theoretical massNumber of molelcules
Total (without water)21,4054
Polymers21,4054
Non-polymers00
Water43224
1
A: Plant defensing Egk


Theoretical massNumber of molelcules
Total (without water)5,3511
Polymers5,3511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Plant defensing Egk


Theoretical massNumber of molelcules
Total (without water)5,3511
Polymers5,3511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Plant defensing Egk


Theoretical massNumber of molelcules
Total (without water)5,3511
Polymers5,3511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Plant defensing Egk


Theoretical massNumber of molelcules
Total (without water)5,3511
Polymers5,3511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.84, 37.92, 54.77
Angle α, β, γ (deg.)83.76, 78.35, 70.22
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
Plant defensing Egk


Mass: 5351.280 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elaeis guineensis (African oil palm) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium tartrate dibasic dehydrate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.000034 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000034 Å / Relative weight: 1
ReflectionResolution: 2.1→65 Å / Num. obs: 9535 / % possible obs: 88.3 % / Redundancy: 1.7 % / CC1/2: 0.902 / Rmerge(I) obs: 0.16 / Net I/σ(I): 3.11
Reflection shellResolution: 2.1→2.22 Å / Num. unique obs: 1392 / CC1/2: 0.67

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UJ0

4uj0


Resolution: 2.1→35.65 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.9 / SU R Cruickshank DPI: 0.326 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.312 / SU Rfree Blow DPI: 0.221 / SU Rfree Cruickshank DPI: 0.226
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 476 -RANDOM
Rwork0.2295 ---
obs0.2311 9514 88.7 %-
Displacement parametersBiso mean: 52.06 Å2
Baniso -1Baniso -2Baniso -3
1--3.8592 Å22.9341 Å20.0943 Å2
2--1.3433 Å20.8145 Å2
3---2.5159 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.1→35.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1472 0 0 24 1496
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081528HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.892029HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d567SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes263HARMONIC5
X-RAY DIFFRACTIONt_it1528HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion181SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact982SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion17.35
LS refinement shellResolution: 2.1→2.13 Å
RfactorNum. reflection% reflection
Rfree0.3273 21 -
Rwork0.2859 --
obs0.2882 414 82.94 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
13.9477-0.1555-0.62626.1829-0.95190.42060.24310.1838-0.14280.1838-0.21810.1019-0.14280.1019-0.025-0.13490.0667-0.0852-0.472-0.0144-0.488931.201856.3775-8.9333
23.11281.0137-0.33686.1003-1.29161.310.13950.1425-0.22470.1425-0.2744-0.0507-0.2247-0.05070.1348-0.14480.10790.0066-0.49450.0119-0.472323.891639.3943-9.2669
35.0616-3.31912.80049.78520.0254-0.7671-0.1350.00060.25520.00060.20030.0350.25520.035-0.0653-0.20940.12150.0155-0.45980.0285-0.406225.493456.5206-36.1229
43.336-2.55520.04188.3507-0.6947-0.0683-0.2091-0.0438-0.3142-0.04380.0269-0.0608-0.3142-0.06080.1822-0.22460.1409-0.0133-0.4139-0.0644-0.414232.740238.7264-36.0847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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