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- PDB-7oex: Crystal structure of RBBP9 in complex with phenylalanine -

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Basic information

Entry
Database: PDB / ID: 7oex
TitleCrystal structure of RBBP9 in complex with phenylalanine
ComponentsSerine hydrolase RBBP9
KeywordsHYDROLASE / Retinoblastoma-binding protein 9
Function / homology
Function and homology information


type II pneumocyte differentiation / response to nematode / Hydrolases / hydrolase activity / positive regulation of gene expression / nucleoplasm
Similarity search - Function
Putative hydrolase RBBP9/YdeN / Serine hydrolase / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
PHENYLALANINE / Serine hydrolase RBBP9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsFiedler, M. / Tang, S. / Chin, J.W.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105181009 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_A024_1008 United Kingdom
CitationJournal: Nature / Year: 2022
Title: Mechanism-based traps enable protease and hydrolase substrate discovery.
Authors: Tang, S. / Beattie, A.T. / Kafkova, L. / Petris, G. / Huguenin-Dezot, N. / Fiedler, M. / Freeman, M. / Chin, J.W.
History
DepositionMay 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Mar 9, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,5244
Polymers44,1942
Non-polymers3302
Water5,260292
1
A: Serine hydrolase RBBP9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2622
Polymers22,0971
Non-polymers1651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine hydrolase RBBP9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2622
Polymers22,0971
Non-polymers1651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.956, 130.127, 38.993
Angle α, β, γ (deg.)90.000, 115.240, 90.000
Int Tables number4
Space group name H-MP1211

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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: 22097.057 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: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C9H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.92 Å3/Da / Density % sol: 35.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 30% w/v PEG 4K, 0.1 M MES sodium salt pH 6.5

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Data collection

DiffractionMean temperature: 130 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.51→29.75 Å / Num. obs: 49673 / % possible obs: 96.1 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Net I/σ(I): 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.51-1.545.10.669939218410.8130.3120.7422.372
8.29-29.7370.03422323200.9990.0130.03642.296.3

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QS9

2qs9


Resolution: 1.51→29.73 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.688 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0785 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1972 2383 4.8 %RANDOM
Rwork0.161 ---
obs0.1627 47250 95.93 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 134.29 Å2 / Biso mean: 20.106 Å2 / Biso min: 7.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20.08 Å2
2--0.02 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.51→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3006 0 24 292 3322
Biso mean--21.77 29.06 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0183121
X-RAY DIFFRACTIONr_bond_other_d0.0010.0192852
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.8424241
X-RAY DIFFRACTIONr_angle_other_deg1.1632.7356605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9235374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25723.013156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.44215509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3631512
X-RAY DIFFRACTIONr_chiral_restr0.0940.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023492
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02704
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.513→1.552 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.317 154 -
Rwork0.317 2829 -
obs--78.03 %

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