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- PDB-9fcr: Crystal structure of RBBP9 with spacegroup p212121 -

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Basic information

Entry
Database: PDB / ID: 9fcr
TitleCrystal structure of RBBP9 with spacegroup p212121
ComponentsSerine hydrolase RBBP9
KeywordsCELL CYCLE / regulation of cell proliferation and differentiation
Function / homology
Function and homology information


type II pneumocyte differentiation / serine hydrolase activity / response to nematode / xenobiotic metabolic process / Hydrolases; Acting on ester bonds / positive regulation of gene expression / nucleoplasm
Similarity search - Function
: / Putative hydrolase RBBP9/YdeN / Serine hydrolase / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Serine hydrolase RBBP9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsGorrec, F. / Bellini, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: J.Appl.Crystallogr. / Year: 2025
Title: A generic cross-seeding approach to protein crystallization.
Authors: Caspy, I. / Tang, S. / Bellini, D. / Gorrec, F.
History
DepositionMay 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Apr 16, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine hydrolase RBBP9
B: Serine hydrolase RBBP9


Theoretical massNumber of molelcules
Total (without water)42,0522
Polymers42,0522
Non-polymers00
Water6,936385
1
A: Serine hydrolase RBBP9


Theoretical massNumber of molelcules
Total (without water)21,0261
Polymers21,0261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine hydrolase RBBP9


Theoretical massNumber of molelcules
Total (without water)21,0261
Polymers21,0261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.740, 82.550, 58.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Serine hydrolase RBBP9 / B5T-overexpressed gene protein / Protein BOG / Retinoblastoma-binding protein 10 / RBBP-10 / ...B5T-overexpressed gene protein / Protein BOG / Retinoblastoma-binding protein 10 / RBBP-10 / Retinoblastoma-binding protein 9 / RBBP-9


Mass: 21025.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP9, BOG, RBBP10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75884, Hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.95 Å3/Da / Density % sol: 37.01 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: PEG 3350/PEG 1K/MPD (1:1:1) 37.5%, 0.1 M MES/imidazole pH 6.5, 4mM Morpheus II Alkalis, 2.5% (w/v) Morpheus Fusion Cryopolyols

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.37→44.38 Å / Num. obs: 65671 / % possible obs: 89.6 % / Redundancy: 1.9 % / Biso Wilson estimate: 18.27 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Net I/σ(I): 5.3
Reflection shellResolution: 1.37→1.42 Å / Rmerge(I) obs: 0.95 / Num. unique obs: 4570 / CC1/2: 0.54

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Processing

Software
NameVersionClassification
REFMAC1.17.1_3660refinement
PHENIX1.17.1_3660refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→44.38 Å / SU ML: 0.205 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.3094
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2335 3077 4.92 %
Rwork0.2017 59498 -
obs0.2032 62575 89.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.39 Å2
Refinement stepCycle: LAST / Resolution: 1.37→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2922 0 0 385 3307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063007
X-RAY DIFFRACTIONf_angle_d0.81654087
X-RAY DIFFRACTIONf_chiral_restr0.0748438
X-RAY DIFFRACTIONf_plane_restr0.0056521
X-RAY DIFFRACTIONf_dihedral_angle_d10.7263388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.503550.4992815X-RAY DIFFRACTION28.09
1.39-1.410.4223630.45861124X-RAY DIFFRACTION38.24
1.41-1.440.4131050.4231840X-RAY DIFFRACTION61.88
1.44-1.460.38491200.40182177X-RAY DIFFRACTION72.9
1.46-1.490.37631310.37462481X-RAY DIFFRACTION83.74
1.49-1.520.35911590.33012734X-RAY DIFFRACTION91.38
1.52-1.560.3411590.2992865X-RAY DIFFRACTION96.52
1.56-1.590.2731580.27222974X-RAY DIFFRACTION99.4
1.59-1.630.31821520.26422964X-RAY DIFFRACTION99.27
1.63-1.680.28381420.25433005X-RAY DIFFRACTION99.75
1.68-1.730.28581520.2442998X-RAY DIFFRACTION99.84
1.73-1.780.29521310.2363034X-RAY DIFFRACTION99.97
1.78-1.850.27541420.2293008X-RAY DIFFRACTION99.94
1.85-1.920.25021620.23572982X-RAY DIFFRACTION99.97
1.92-2.010.24141570.21383009X-RAY DIFFRACTION99.87
2.01-2.110.2221410.20393051X-RAY DIFFRACTION99.91
2.11-2.240.26991460.1933028X-RAY DIFFRACTION99.97
2.25-2.420.1981520.19943032X-RAY DIFFRACTION99.78
2.42-2.660.22281770.19533019X-RAY DIFFRACTION99.69
2.66-3.050.22551540.18613068X-RAY DIFFRACTION99.66
3.05-3.840.19761540.16193077X-RAY DIFFRACTION99.6
3.84-44.380.18361650.15593213X-RAY DIFFRACTION98.74

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