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- PDB-6nek: Crystal structure of a consensus PDZ domain -

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Basic information

Entry
Database: PDB / ID: 6nek
TitleCrystal structure of a consensus PDZ domain
ComponentsConsensus PDZ domain
KeywordsDE NOVO PROTEIN / Consensus design / PDZ domain
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsSun, Y.J. / Gakhar, L. / Fuentes, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart Association15GRNT25740021 United States
CitationJournal: To be published
Title: Consensus PDZ domain
Authors: Sun, Y.J. / Sternke, M. / Barrick, D. / Fuentes, E.J.
History
DepositionDec 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

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Assembly

Deposited unit
A: Consensus PDZ domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9443
Polymers9,8201
Non-polymers1242
Water1,27971
1
A: Consensus PDZ domain
hetero molecules

A: Consensus PDZ domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8886
Polymers19,6402
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area6520 Å2
ΔGint-19 kcal/mol
Surface area8620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.620, 60.090, 73.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1620-

HOH

21A-1668-

HOH

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Components

#1: Protein Consensus PDZ domain


Mass: 9820.028 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MET A1, GLY A2, TRP A3, GLY A85, GLY A86, GLY A87, HIS A88, HIS A89, HIS A90, HIS A91, HIS A92, HIS A93 are expression tags
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.1 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.5M LiSO4 2% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Mar 19, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0003 Å / Relative weight: 1
ReflectionResolution: 1.63→46.49 Å / Num. obs: 15141 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.016 / Rpim(I) all: 0.016 / Rrim(I) all: 0.023 / Net I/σ(I): 27.5
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 2 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1488 / CC1/2: 0.704 / Rpim(I) all: 0.471 / Rrim(I) all: 0.666 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Blu-Icedata collection
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W4F

2w4f


Resolution: 1.63→46.47 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 720 4.76 %
Rwork0.197 --
obs0.198 15125 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms616 0 8 71 695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019637
X-RAY DIFFRACTIONf_angle_d1.921857
X-RAY DIFFRACTIONf_dihedral_angle_d8.975503
X-RAY DIFFRACTIONf_chiral_restr0.085102
X-RAY DIFFRACTIONf_plane_restr0.012112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.75590.28371560.22942837X-RAY DIFFRACTION100
1.7559-1.93260.25931350.21262837X-RAY DIFFRACTION100
1.9326-2.21220.23591240.1932865X-RAY DIFFRACTION100
2.2122-2.78720.22751460.21052884X-RAY DIFFRACTION100
2.7872-46.48950.21671590.18892982X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 1.1407 Å / Origin y: 26.3951 Å / Origin z: 12.0446 Å
111213212223313233
T0.2447 Å2-0.0968 Å2-0.0253 Å2-0.2863 Å20.037 Å2--0.1916 Å2
L3.556 °2-1.6642 °20.1894 °2-2.9976 °2-0.4171 °2--1.6122 °2
S0.1895 Å °-0.5213 Å °-0.1518 Å °0.1163 Å °-0.1551 Å °0.0285 Å °0.094 Å °0.0896 Å °-0.0291 Å °
Refinement TLS groupSelection details: ALL

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