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- PDB-7e0w: Crystal Structure of BCH domain from S. pombe -

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Basic information

Entry
Database: PDB / ID: 7e0w
TitleCrystal Structure of BCH domain from S. pombe
ComponentsPutative Rho GTPase-activating protein C1565.02c
KeywordsLIPID BINDING PROTEIN / Intertwined / Anti-parallel / Dimeric structure
Function / homology
Function and homology information


: / phospholipid transfer activity / intermembrane phospholipid transfer / GTPase activator activity / Golgi apparatus / signal transduction
Similarity search - Function
Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein
Similarity search - Domain/homology
Putative Rho GTPase-activating protein C1565.02c
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsChichili, V.P.R. / Jobichen, C. / Sivaraman, J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)R154-000-625-112 Singapore
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: A novel intertwined anti-parallel dimeric structure of scaffold BCH domain regulates RhoA and RhoGAP functions
Authors: Chichili, V.P.R. / Chew, T.W. / Er, S.Y. / Chin, C.F. / Shankar, S. / Jobichen, C. / Pan, Q.C. / Zhou, Y.T. / Yeong, F.M. / Low, B.C. / Sivaraman, J.
History
DepositionJan 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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: Putative Rho GTPase-activating protein C1565.02c
B: Putative Rho GTPase-activating protein C1565.02c
C: Putative Rho GTPase-activating protein C1565.02c
D: Putative Rho GTPase-activating protein C1565.02c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6438
Polymers74,8664
Non-polymers7774
Water0
1
A: Putative Rho GTPase-activating protein C1565.02c
D: Putative Rho GTPase-activating protein C1565.02c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8214
Polymers37,4332
Non-polymers3882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-36 kcal/mol
Surface area15810 Å2
MethodPISA
2
B: Putative Rho GTPase-activating protein C1565.02c
C: Putative Rho GTPase-activating protein C1565.02c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8214
Polymers37,4332
Non-polymers3882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-38 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.390, 108.390, 250.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Putative Rho GTPase-activating protein C1565.02c


Mass: 18716.518 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Strain: 972 / ATCC 24843 / Gene: SPAC1565.02c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P3B1
#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
Has ligand of interestN

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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: 5.67 Å3/Da / Density % sol: 78.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris propane pH 7.0 and 2.1M NaCl.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 36910 / % possible obs: 87.7 % / Redundancy: 5.5 % / Rsym value: 0.089 / Net I/σ(I): 12.6
Reflection shellResolution: 2.8→2.93 Å / Num. unique obs: 2453 / Rsym value: 0.338

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→49.736 Å / Cross valid method: FREE R-VALUE / σ(F): 146.76 / Phase error: 25.71
RfactorNum. reflection% reflection
Rfree0.2603 2143 5.94 %
Rwork0.2284 --
obs0.2317 36099 88.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→49.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4856 0 52 0 4908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055038
X-RAY DIFFRACTIONf_angle_d0.8386806
X-RAY DIFFRACTIONf_dihedral_angle_d4.2982922
X-RAY DIFFRACTIONf_chiral_restr0.048736
X-RAY DIFFRACTIONf_plane_restr0.004844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8003-2.87040.488660.43081106X-RAY DIFFRACTION38
2.8704-2.9480.48431080.39511842X-RAY DIFFRACTION64
2.948-3.03470.38951300.35732235X-RAY DIFFRACTION76
3.0347-3.13260.34981390.32042372X-RAY DIFFRACTION82
3.1326-3.24460.31921460.28622440X-RAY DIFFRACTION84
3.2446-3.37440.28511410.26772502X-RAY DIFFRACTION86
3.3744-3.5280.27261500.24962516X-RAY DIFFRACTION87
3.528-3.71390.26971580.24112655X-RAY DIFFRACTION91
3.7139-3.94640.25571650.21842675X-RAY DIFFRACTION92
3.9464-4.2510.21321640.19912721X-RAY DIFFRACTION93
4.251-4.67840.20681570.17412738X-RAY DIFFRACTION94
4.6784-5.35450.20391550.18762744X-RAY DIFFRACTION94
5.3545-6.74270.25361600.21662758X-RAY DIFFRACTION94
6.7427-46.13720.25941600.22432787X-RAY DIFFRACTION94

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