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- PDB-5e11: Second PDZ domain of Ligand of Numb protein X 2 by Laue crystallo... -

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Basic information

Entry
Database: PDB / ID: 500000000000
TitleSecond PDZ domain of Ligand of Numb protein X 2 by Laue crystallography (no electric field)
ComponentsLigand of Numb protein X 2
KeywordsPROTEIN BINDING / Unperturbed / OFF state.
Function / homology
Function and homology information


neural precursor cell proliferation / PDZ domain binding / neuron differentiation / ubiquitin-protein transferase activity / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Zinc finger, C3HC4 type (RING finger) / PDZ domain / Pdz3 Domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain ...Zinc finger, C3HC4 type (RING finger) / PDZ domain / Pdz3 Domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
Ligand of Numb protein X 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHekstra, D.R. / White, K.I. / Socolich, M.A. / Henning, R.W. / Srajer, V. / Ranganathan, R.
Funding support1items
OrganizationGrant numberCountry
Robert A. Welch FoundationI-1366
CitationJournal: Nature / Year: 2016
Title: Electric-field-stimulated protein mechanics.
Authors: Hekstra, D.R. / White, K.I. / Socolich, M.A. / Henning, R.W. / Srajer, V. / Ranganathan, R.
History
DepositionSep 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Ligand of Numb protein X 2


Theoretical massNumber of molelcules
Total (without water)10,3111
Polymers10,3111
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.300, 39.450, 39.010
Angle α, β, γ (deg.)90.00, 117.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ligand of Numb protein X 2 / Numb-binding protein 2 / PDZ domain-containing RING finger protein 1


Mass: 10310.739 Da / Num. of mol.: 1 / Fragment: Second PDZ domain (UNP residues 336-424) / Mutation: F338L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LNX2, PDZRN1 / Plasmid: pNic28 / Details (production host): SGC Construct ID: LNX2A-c033 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8N448
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAuthors state that the C-terminal extension (residues 425-428) contains a putative ligand motif.

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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: 2.16 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 27-31% PEG 300, 48 mM citric acid, 35 mM NaH2PO4

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Data collection

DiffractionMean temperature: 289 K / Ambient temp details: cryostream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.02-1.16
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Mar 20, 2015 / Details: U23 and U27; KB mirror system
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.021
21.161
ReflectionResolution: 1.8→50 Å / Num. obs: 6565 / % possible obs: 79.3 % / Observed criterion σ(F): 2 / Redundancy: 9.8 % / Biso Wilson estimate: 11.49 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 19.6
Reflection shellResolution: 1.797→1.861 Å / Mean I/σ(I) obs: 5.9 / % possible all: 34.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Precognitiondata reduction
Epinormdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SSRL structure at 277 K (to be deposited)

Resolution: 1.8→30.1 Å / Rfactor Rfree error: 0.008 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.28 / Phase error: 12.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1483 328 5 %PHENIX default
Rwork0.1316 ---
obs0.1325 6565 78.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→30.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms719 0 0 94 813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02840
X-RAY DIFFRACTIONf_angle_d1.631142
X-RAY DIFFRACTIONf_dihedral_angle_d13.172326
X-RAY DIFFRACTIONf_chiral_restr0.102136
X-RAY DIFFRACTIONf_plane_restr0.009154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7965-2.26330.1291330.12452498X-RAY DIFFRACTION64
2.2633-30.08040.15591950.13423739X-RAY DIFFRACTION94

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