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- PDB-3kuz: Crystal structure of the ubiquitin like domain of PLXNC1 -

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Basic information

Entry
Database: PDB / ID: 3kuz
TitleCrystal structure of the ubiquitin like domain of PLXNC1
ComponentsPlexin-C1
KeywordsSIGNALING PROTEIN / plexin / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of synapse pruning / cerebellar climbing fiber to Purkinje cell synapse / Other semaphorin interactions / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / positive regulation of axonogenesis / regulation of cell migration / regulation of cell shape ...regulation of synapse pruning / cerebellar climbing fiber to Purkinje cell synapse / Other semaphorin interactions / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / positive regulation of axonogenesis / regulation of cell migration / regulation of cell shape / cell adhesion / signaling receptor binding / membrane / plasma membrane
Similarity search - Function
Plexin-C1, Sema domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family / Plexin repeat / Plexin repeat / semaphorin domain / Sema domain ...Plexin-C1, Sema domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family / Plexin repeat / Plexin repeat / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / Rho GTPase activation protein / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / WD40/YVTN repeat-like-containing domain superfamily / Roll / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsWang, H. / Li, B. / Tempel, W. / Tong, Y. / Guan, X. / Zhong, N. / Crombet, L. / MacKenzie, F. / Buck, M. / Arrowsmith, C.H. ...Wang, H. / Li, B. / Tempel, W. / Tong, Y. / Guan, X. / Zhong, N. / Crombet, L. / MacKenzie, F. / Buck, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the ubiquitin like domain of PLXNC1
Authors: Wang, H. / Li, B. / Tempel, W. / Tong, Y. / Guan, X. / Zhong, N. / Crombet, L. / MacKenzie, F. / Buck, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionNov 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plexin-C1
B: Plexin-C1


Theoretical massNumber of molelcules
Total (without water)28,20014
Polymers28,2002
Non-polymers012
Water79344
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-7 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.246, 72.246, 116.235
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 1197 - 1305 / Label seq-ID: 18 - 126

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
Detailsauthors state that the biological assembly is not known.

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Components

#1: Protein Plexin-C1 / Virus-encoded semaphorin protein receptor


Mass: 14099.886 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNC1, VESPR / Plasmid: pET28-mhl (GI:134105571) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: O60486
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0M ammonium sulfate, 0.2M sodium chloride, 0.1M HEPES, 1:100 w/w chymotrypsin, pH 7.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 14277 / % possible obs: 99.6 % / Redundancy: 9 % / Rmerge(I) obs: 0.187 / Χ2: 1.208 / Net I/σ(I): 4.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.346.20.9636971.23598.3
2.34-2.387.10.9366841.1599
2.38-2.4380.9256941.22599.7
2.43-2.4890.9397001.185100
2.48-2.539.50.8896991.138100
2.53-2.599.50.7627161.07100
2.59-2.659.70.5836801.053100
2.65-2.739.70.5547071.084100
2.73-2.819.50.4227051.009100
2.81-2.99.50.3147060.988100
2.9-39.60.2787041.009100
3-3.129.60.2217061.002100
3.12-3.269.50.1817201.01799.9
3.26-3.439.40.1457211.05799.7
3.43-3.659.40.1156961.17199.7
3.65-3.939.40.1067261.40199.7
3.93-4.329.20.0997301.5999.6
4.32-4.939.10.0847291.5499.6
4.93-6.188.80.0817541.16499.3
6.18-208.50.0578032.08498.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: superimposed ensemble of PDB entries 3h6n and 3ig3

3h6n

3ig3


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.884 / WRfactor Rfree: 0.254 / WRfactor Rwork: 0.222 / SU B: 7.178 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. The programs COOT and MOLPROBITY were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 501 3.521 %thin shells (sftools)
Rwork0.25 ---
obs0.251 14229 99.762 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.04 Å2
Baniso -1Baniso -2Baniso -3
1-1.393 Å20 Å20 Å2
2--1.393 Å20 Å2
3----2.787 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1608 0 12 44 1664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221626
X-RAY DIFFRACTIONr_bond_other_d0.0010.021032
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.9762204
X-RAY DIFFRACTIONr_angle_other_deg0.84332576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8335219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.39427.37761
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93715283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.823151
X-RAY DIFFRACTIONr_chiral_restr0.0850.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02278
X-RAY DIFFRACTIONr_mcbond_it0.8891.51083
X-RAY DIFFRACTIONr_mcbond_other0.1391.5451
X-RAY DIFFRACTIONr_mcangle_it1.69521732
X-RAY DIFFRACTIONr_scbond_it2.1723543
X-RAY DIFFRACTIONr_scangle_it3.7324.5471
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1279 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.220.5
BMEDIUM THERMAL0.492
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.35900.3291006102398.338
2.359-2.4230.382520.31193899599.497
2.423-2.4920.386490.316927976100
2.492-2.5670.238350.287888923100
2.567-2.650.279350.268882917100
2.65-2.7410.363360.262846882100
2.741-2.84300.256858858100
2.843-2.9560.277340.254784818100
2.956-3.0850.366270.252777804100
3.085-3.2310.284540.26771577099.87
3.231-3.4010.249360.254698734100
3.401-3.6010.214200.232680700100
3.601-3.8410.244130.21464065499.847
3.841-4.1360.25170.191606623100
4.136-4.5110.242230.20155157599.826
4.511-5.0120.164150.251052699.81
5.012-5.7280.272240.245458482100
5.728-6.8760.599120.28240141499.758
6.876-9.1950.218140.28432834599.13
9.195-200.45350.27723524498.361

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