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- PDB-2r2o: Crystal structure of the effector domain of human Plexin B1 -

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Basic information

Entry
Database: PDB / ID: 2r2o
TitleCrystal structure of the effector domain of human Plexin B1
ComponentsPlexin-B1
KeywordsSIGNALING PROTEIN / Plexin / effector domain / structural genomics / Structural Genomics Consortium / SGC / Glycoprotein / Membrane / Phosphorylation / Receptor / Secreted / Transmembrane
Function / homology
Function and homology information


semaphorin receptor binding / semaphorin-plexin signaling pathway involved in axon guidance / negative regulation of osteoblast proliferation / inhibitory synapse assembly / semaphorin receptor complex / semaphorin receptor activity / RHOD GTPase cycle / negative regulation of cell adhesion / Sema4D induced cell migration and growth-cone collapse / GTPase activating protein binding ...semaphorin receptor binding / semaphorin-plexin signaling pathway involved in axon guidance / negative regulation of osteoblast proliferation / inhibitory synapse assembly / semaphorin receptor complex / semaphorin receptor activity / RHOD GTPase cycle / negative regulation of cell adhesion / Sema4D induced cell migration and growth-cone collapse / GTPase activating protein binding / Sema4D mediated inhibition of cell attachment and migration / ossification involved in bone maturation / regulation of cytoskeleton organization / positive regulation of Rho protein signal transduction / positive regulation of axonogenesis / semaphorin-plexin signaling pathway / regulation of cell migration / GTPase activator activity / neuron projection morphogenesis / positive regulation of GTPase activity / G alpha (12/13) signalling events / transmembrane signaling receptor activity / cell migration / regulation of cell shape / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / extracellular region / plasma membrane
Similarity search - Function
Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family / Plexin repeat ...Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG 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 / Sema domain / 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) / Immunoglobulin E-set / 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 / SAD / sad / Resolution: 2 Å
AuthorsTong, Y. / Tempel, W. / Shen, L. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Binding of Rac1, Rnd1, and RhoD to a novel Rho GTPase interaction motif destabilizes dimerization of the plexin-B1 effector domain.
Authors: Tong, Y. / Chugha, P. / Hota, P.K. / Alviani, R.S. / Li, M. / Tempel, W. / Shen, L. / Park, H.W. / Buck, M.
History
DepositionAug 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plexin-B1
B: Plexin-B1


Theoretical massNumber of molelcules
Total (without water)31,06914
Polymers31,0692
Non-polymers012
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.979, 56.571, 99.366
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Plexin-B1 / Semaphorin receptor SEP


Mass: 15534.260 Da / Num. of mol.: 2 / Fragment: Effector domain: Residues 1743-1862
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNB1, KIAA0407, PLXN5, SEP / Plasmid: pET28a-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O43157
#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.: 48 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8
Details: 2.6M Sodium chloride, 18% Ethylene glycol, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B10.97918
SYNCHROTRONAPS 19-ID20.97937
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJun 10, 2007
ADSC QUANTUM 3152CCDJun 10, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979181
20.979371
ReflectionResolution: 2→50 Å / Num. obs: 19206 / % possible obs: 94.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.067 / Χ2: 1.854 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.072.70.43512480.5991,262.5
2.07-2.154.20.36117400.5731,288
2.15-2.255.70.28819430.6351,297.2
2.25-2.376.70.21919940.6881,299.7
2.37-2.527.20.17919760.7531,2100
2.52-2.717.30.12420340.9531,2100
2.71-2.997.30.09220111.3791,2100
2.99-3.427.30.07120292.3651,2100
3.42-4.317.10.05820643.6041,2100
4.31-506.70.0521674.8261,299.3

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Phasing

PhasingMethod: sad

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RESOLVEphasing
REFMACrefmac_5.3.0037refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: SAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.274 / WRfactor Rwork: 0.224 / SU B: 7.771 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. TLS parameters were refined. 3. Atomic temperature factors are residuals. 4. Resolve, coot, molprobity programs have also been used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 842 4.4 %thin shells
Rwork0.222 ---
all0.224 ---
obs0.224 19071 95.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.328 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20 Å2
2---0.58 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1509 0 12 48 1569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221541
X-RAY DIFFRACTIONr_bond_other_d0.0010.021001
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.9932110
X-RAY DIFFRACTIONr_angle_other_deg0.92632483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6855201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28824.90251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6315250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.163157
X-RAY DIFFRACTIONr_chiral_restr0.0830.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021674
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02257
X-RAY DIFFRACTIONr_nbd_refined0.2020.2242
X-RAY DIFFRACTIONr_nbd_other0.1890.2985
X-RAY DIFFRACTIONr_nbtor_refined0.1610.2707
X-RAY DIFFRACTIONr_nbtor_other0.0860.2778
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.247
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1760.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.25
X-RAY DIFFRACTIONr_mcbond_it1.031.51113
X-RAY DIFFRACTIONr_mcbond_other0.2011.5403
X-RAY DIFFRACTIONr_mcangle_it1.32321649
X-RAY DIFFRACTIONr_scbond_it2.0423575
X-RAY DIFFRACTIONr_scangle_it2.9424.5460
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 (%)
2-2.05100.331877144360.776
2.051-2.1070.3041160.2891046140882.528
2.107-2.16700.2571270137492.431
2.167-2.2330.2851230.2431172133297.222
2.233-2.30600.2321284129199.458
2.306-2.3850.242930.2241163125799.92
2.385-2.47400.23712091209100
2.474-2.5730.2791000.23410741174100
2.573-2.68600.23211291129100
2.686-2.8140.275820.2519921074100
2.814-2.9630.284670.2419551022100
2.963-3.13900.233974974100
3.139-3.350.238580.221876934100
3.35-3.610.261520.21812864100
3.61-3.9410.211360.213769805100
3.941-4.3850.278340.18869372899.863
4.385-5.0240.238220.17864967299.851
5.024-6.0580.355200.236545565100
6.058-8.1990.321310.253441472100
8.199-200.26380.20929931497.771
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.5693-0.5527-2.25871.29460.82273.25170.06790.16-0.07330.0146-0.05050.00320.0790.1998-0.01740.00630.0757-0.03950.0314-0.0485-0.0742-3.083-7.143227.2181
22.8097-0.13731.52490.82260.00591.7933-0.0133-0.14570.0860.10330.01250.091-0.1449-0.09480.0008-0.0303-0.00630.0231-0.08320.0145-0.0341.0336-34.115252.4617
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1746 - 1852 / Label seq-ID: 22 - 128

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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