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- PDB-2vsv: Crystal structure of the PDZ domain of human rhophilin-2 -

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Basic information

Entry
Database: PDB / ID: 2vsv
TitleCrystal structure of the PDZ domain of human rhophilin-2
ComponentsRHOPHILIN-2
KeywordsPROTEIN BINDING / SCAFFOLD PROTEIN / RHO GTPASE BINDING / PROTEIN-BINDING / RHOB / NITRATION / CYTOPLASM / PDZ DOMAIN / CASP8
Function / homology
Function and homology information


RHO GTPases Activate Rhotekin and Rhophilins / perinuclear region of cytoplasm / signal transduction / cytosol
Similarity search - Function
Hr1 repeat / Rho effector or protein kinase C-related kinase homology region 1 homologues / HR1 repeat superfamily / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / HR1 rho-binding domain / REM-1 domain profile. ...Hr1 repeat / Rho effector or protein kinase C-related kinase homology region 1 homologues / HR1 repeat superfamily / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / HR1 rho-binding domain / REM-1 domain profile. / PDZ domain / Pdz3 Domain / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsPike, A.C.W. / Kochan, G. / Sun, Z. / Shafqat, N. / Pilka, E.S. / Roos, A. / Elkins, J. / Burgess-Brown, N. / Murray, J.W. / von Delft, F. ...Pike, A.C.W. / Kochan, G. / Sun, Z. / Shafqat, N. / Pilka, E.S. / Roos, A. / Elkins, J. / Burgess-Brown, N. / Murray, J.W. / von Delft, F. / Wikstrom, M. / Edwards, A. / Arrowsmith, C.H. / Bountra, C. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of the Pdz Domain of Human Rhophilin-2
Authors: Pike, A.C.W. / Kochan, G. / Sun, Z. / Shafqat, N. / Pilka, E.S. / Roos, A. / Elkins, J. / Burgess-Brown, N. / Murray, J.W. / von Delft, F. / Wikstrom, M. / Edwards, A. / Arrowsmith, C.H. / ...Authors: Pike, A.C.W. / Kochan, G. / Sun, Z. / Shafqat, N. / Pilka, E.S. / Roos, A. / Elkins, J. / Burgess-Brown, N. / Murray, J.W. / von Delft, F. / Wikstrom, M. / Edwards, A. / Arrowsmith, C.H. / Bountra, C. / Oppermann, U.
History
DepositionApr 29, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RHOPHILIN-2
B: RHOPHILIN-2


Theoretical massNumber of molelcules
Total (without water)24,5642
Polymers24,5642
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-22.3 kcal/mol
Surface area13270 Å2
MethodPQS
2
A: RHOPHILIN-2


Theoretical massNumber of molelcules
Total (without water)12,2821
Polymers12,2821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: RHOPHILIN-2


Theoretical massNumber of molelcules
Total (without water)12,2821
Polymers12,2821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.250, 39.890, 73.480
Angle α, β, γ (deg.)90.00, 115.78, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2047-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A499 - 520
2112B499 - 520
1212A526 - 593
2212B526 - 593

NCS oper: (Code: given
Matrix: (0.625, 0.781), (0.002, -1, -0.002), (0.781, 0.002, -0.625)
Vector: -8.54858, 40.8257, 17.81877)

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Components

#1: Protein RHOPHILIN-2 / GTP-RHO-BINDING PROTEIN 2 / 76 KDA RHOB EFFECTOR PROTEIN / P76RBE


Mass: 12281.888 Da / Num. of mol.: 2 / Fragment: PDZ DOMAIN, RESIDUES 514-595
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q8IUC4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2M SODIUM ACETATE, 20% PEG3350; 10% ETHYLENE GLYCOL, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99186
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99186 Å / Relative weight: 1
ReflectionResolution: 1.82→38.9 Å / Num. obs: 18177 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 10.28 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.8
Reflection shellResolution: 1.82→1.92 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.2 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2F5Y,2OCS,2V90

2f5y

2ocs

2v90


Resolution: 1.82→66.23 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.895 / SU B: 3.645 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 939 5.2 %RANDOM
Rwork0.22 ---
obs0.222 17238 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.21 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å20 Å20.72 Å2
2---0.39 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 1.82→66.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1538 0 0 93 1631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211577
X-RAY DIFFRACTIONr_bond_other_d0.0030.021039
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.962133
X-RAY DIFFRACTIONr_angle_other_deg0.90232549
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1185199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.62224.30865
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52515270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.991156
X-RAY DIFFRACTIONr_chiral_restr0.0850.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021744
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02312
X-RAY DIFFRACTIONr_nbd_refined0.2170.2303
X-RAY DIFFRACTIONr_nbd_other0.190.21021
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2753
X-RAY DIFFRACTIONr_nbtor_other0.0870.2813
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2109
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8113995
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.10151598
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.7248582
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.23611535
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A530tight positional0.030.05
2B530tight positional0.030.05
1A622medium positional0.030.5
2B622medium positional0.030.5
1A530tight thermal0.230.5
2B530tight thermal0.230.5
1A622medium thermal0.142
2B622medium thermal0.142
LS refinement shellResolution: 1.82→1.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.349 74
Rwork0.256 1223

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