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- PDB-9gjr: Crystal Structure of the Leishmania Bromodomain LmxBDF5.1 in comp... -

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Basic information

Entry
Database: PDB / ID: 9gjr
TitleCrystal Structure of the Leishmania Bromodomain LmxBDF5.1 in complex with OXFBD06
ComponentsBromo domain-containing protein
KeywordsTRANSCRIPTION / Bromodomain / Leishmania / Protein-inhibitor complex
Function / homology: / Bromodomain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / : / (R,R)-2,3-BUTANEDIOL / : / Bromo domain-containing protein
Function and homology information
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsAmann, M. / Huegle, M. / Carter, J. / Einsle, O. / Guenther, S. / Conway, S.
Funding support Germany, 2items
OrganizationGrant numberCountry
Other governmentEP/R513295/1
German Research Foundation (DFG)RTG2202 Germany
CitationJournal: To Be Published
Title: Crystal Structure of the Leishmania Bromodomain LmxBDF5.1 in complex with OXFBD06
Authors: Amann, M. / Huegle, M. / Carter, J. / Einsle, O. / Guenther, S. / Conway, S.
History
DepositionAug 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromo domain-containing protein
C: Bromo domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3496
Polymers25,1962
Non-polymers1,1524
Water5,314295
1
A: Bromo domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1102
Polymers12,5981
Non-polymers5121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Bromo domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2394
Polymers12,5981
Non-polymers6413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.794, 49.646, 85.634
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bromo domain-containing protein


Mass: 12598.044 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Gene: LMXM_09_1260 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: E9AMX7
#2: Chemical ChemComp-A1IMI / 5-[2-[5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[2-(4-ethanoylpiperazin-1-ium-1-yl)ethyl]benzimidazol-2-yl]ethyl]-2-methyl-benzenecarbonitrile


Mass: 511.638 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H35N6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.89 Å3/Da / Density % sol: 34.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Potassium thiocyanate, 30% PEG monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.45→44.79 Å / Num. obs: 34606 / % possible obs: 99.9 % / Redundancy: 10.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.035 / Rrim(I) all: 0.115 / Χ2: 1.02 / Net I/σ(I): 12.6 / Num. measured all: 359193
Reflection shellResolution: 1.45→1.47 Å / % possible obs: 100 % / Redundancy: 10.7 % / Rmerge(I) obs: 1.205 / Num. measured all: 17859 / Num. unique obs: 1669 / CC1/2: 0.823 / Rpim(I) all: 0.382 / Rrim(I) all: 1.266 / Χ2: 1.06 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→42.95 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1698 1710 4.95 %
Rwork0.1364 --
obs0.1381 34538 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→42.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 83 295 2130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042067
X-RAY DIFFRACTIONf_angle_d0.6972852
X-RAY DIFFRACTIONf_dihedral_angle_d16.664814
X-RAY DIFFRACTIONf_chiral_restr0.072296
X-RAY DIFFRACTIONf_plane_restr0.007419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.26431390.18522697X-RAY DIFFRACTION100
1.49-1.540.20151350.15242679X-RAY DIFFRACTION100
1.54-1.60.17871470.14072701X-RAY DIFFRACTION100
1.6-1.660.19181410.13212692X-RAY DIFFRACTION100
1.66-1.740.17671550.1342698X-RAY DIFFRACTION100
1.74-1.830.18451220.12632727X-RAY DIFFRACTION100
1.83-1.940.16871400.12022731X-RAY DIFFRACTION100
1.94-2.090.18871570.1252718X-RAY DIFFRACTION100
2.09-2.30.17021340.1252739X-RAY DIFFRACTION100
2.3-2.630.19151420.13742736X-RAY DIFFRACTION99
2.63-3.320.16051520.14192786X-RAY DIFFRACTION100
3.32-42.950.14371460.13982924X-RAY DIFFRACTION100

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