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- PDB-4e71: Crystal structure of the RHO GTPASE binding domain of Plexin B2 -

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Basic information

Entry
Database: PDB / ID: 4.0E+71
TitleCrystal structure of the RHO GTPASE binding domain of Plexin B2
ComponentsPlexin-B2
KeywordsSIGNALING PROTEIN / plexin / transmembrane / signaling / rbd / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


excitatory synapse assembly / regulation of neuron migration / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor activity / negative regulation of cell adhesion / semaphorin receptor complex / positive regulation of axonogenesis / regulation of GTPase activity / plasma membrane => GO:0005886 / homophilic cell adhesion via plasma membrane adhesion molecules ...excitatory synapse assembly / regulation of neuron migration / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor activity / negative regulation of cell adhesion / semaphorin receptor complex / positive regulation of axonogenesis / regulation of GTPase activity / plasma membrane => GO:0005886 / homophilic cell adhesion via plasma membrane adhesion molecules / semaphorin-plexin signaling pathway / neuroblast proliferation / regulation of cell migration / neural tube closure / positive regulation of translation / regulation of protein phosphorylation / brain development / positive regulation of neuron projection development / regulation of cell shape / cell surface / extracellular exosome
Similarity search - Function
Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain ...Plexin, TIG domain 1 / TIG 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.26 Å
AuthorsGuan, X. / Wang, H. / Tempel, W. / Tong, Y. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the RHO GTPASE binding domain of Plexin B2
Authors: Guan, X. / Wang, H. / Tempel, W. / Tong, Y. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H.
History
DepositionMar 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plexin-B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3732
Polymers12,3501
Non-polymers231
Water1629
1
A: Plexin-B2
hetero molecules

A: Plexin-B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7464
Polymers24,7002
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area1230 Å2
ΔGint-21 kcal/mol
Surface area9960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.380, 48.380, 157.360
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1601-

NA

DetailsBIOLOGICAL ASSEMBLY IS UNKNOWN AS PER AUTHORS

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Components

#1: Protein Plexin-B2 / MM1


Mass: 12350.050 Da / Num. of mol.: 1 / Fragment: UNP residues 1452-1562
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLXNB2, KIAA0315 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: O15031
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.6
Details: 2.5M sodium formate, 0.1M glycine, pH 9.6, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 5712 / % possible obs: 99.7 % / Redundancy: 19.6 % / Rmerge(I) obs: 0.098 / Χ2: 1.915 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.26-2.3210.9992740.961100
2.3-2.3420.60.8082651.0111100
2.34-2.39210.8112771.0131100
2.39-2.4320.40.7842770.9881100
2.43-2.4920.90.6552671.0411100
2.49-2.5520.90.5492831.0821100
2.55-2.6120.60.3962721.1141100
2.61-2.6820.40.3322821.1531100
2.68-2.7620.50.2752591.1761100
2.76-2.8520.60.2432921.2241100
2.85-2.9520.60.1712671.384199.3
2.95-3.07200.1482891.554199.7
3.07-3.2120.40.132811.7571100
3.21-3.38200.1082852.2881100
3.38-3.5919.40.0972852.7881100
3.59-3.8619.30.0892902.9691100
3.86-4.2518.60.0722973.5381100
4.25-4.8717.70.0653073.8131100
4.87-6.13170.073143.8331100
6.13-5014.20.0643494.294196.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.11data extraction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2R2O

2r2o


Resolution: 2.26→32.74 Å / Cor.coef. Fo:Fc: 0.9285 / Cor.coef. Fo:Fc free: 0.9208 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0
Details: ANISOTROPY IN RESOLUTION LIMITS OF DIFFRACTION WAS OBSERVED. APPEARANCE OF ELECTRON DENSITY MAPS IS POOR GIVEN THE HIGH RESOLUTION LIMIT OF DIFFRACTION DATA. AVERAGE ATOMIC B-FACTOR ...Details: ANISOTROPY IN RESOLUTION LIMITS OF DIFFRACTION WAS OBSERVED. APPEARANCE OF ELECTRON DENSITY MAPS IS POOR GIVEN THE HIGH RESOLUTION LIMIT OF DIFFRACTION DATA. AVERAGE ATOMIC B-FACTOR SIGNIFICANTLY EXCEEDS VALUE DERIVED FROM WILSON PLOT. DENSITY FOR SOME PROTEIN LOOPS IS NOT INTERPRETABLE IN TERMS OF GOOD PEPTIDE GEOMETRY. UNMERGED REFLECTION INTENSITIES ARE INCLUDED IN ADDITION TO STRUCTURE FACTORS FROM LAST REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2853 254 4.5 %RANDOM
Rwork0.2441 ---
obs0.2459 5645 99.88 %-
Displacement parametersBiso max: 152.4 Å2 / Biso mean: 72.5111 Å2 / Biso min: 38.4 Å2
Baniso -1Baniso -2Baniso -3
1--5.0156 Å20 Å20 Å2
2---5.0156 Å20 Å2
3---10.0312 Å2
Refine analyzeLuzzati coordinate error obs: 0.497 Å
Refinement stepCycle: LAST / Resolution: 2.26→32.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms650 0 1 9 660
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d210SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes16HARMONIC2
X-RAY DIFFRACTIONt_gen_planes92HARMONIC5
X-RAY DIFFRACTIONt_it655HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion99SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact721SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d655HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg896HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion15.03
LS refinement shellResolution: 2.26→2.53 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2416 78 5.06 %
Rwork0.2081 1464 -
all0.2098 1542 -
obs--99.88 %
Refinement TLS params.Method: refined / Origin x: -16.3709 Å / Origin y: 15.5125 Å / Origin z: 2.0833 Å
111213212223313233
T0.0115 Å20.0967 Å20.059 Å2-0.1855 Å20.2069 Å2---0.0658 Å2
L9.4369 °23.3919 °2-2.9905 °2-6.3021 °2-5.4746 °2--7.8396 °2
S-0.0884 Å °0.7336 Å °0.2369 Å °-0.6255 Å °0.0839 Å °0.2001 Å °0.7194 Å °0.1274 Å °0.0045 Å °
Refinement TLS groupSelection details: { A|* }

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