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- PDB-6bya: Crystal structure of LdBPK_091320 with inhibitor bound -

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Basic information

Entry
Database: PDB / ID: 6bya
TitleCrystal structure of LdBPK_091320 with inhibitor bound
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Leishmania / bromodomain / parasitology / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


lysine-acetylated histone binding / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain profile. / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-2LO / Bromodomain family protein
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsDong, A. / Lin, Y.H. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of LdBPK_091320.1 with with inhibitor bound
Authors: Lin, Y.H. / Dong, A. / Loppnau, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hui, R. / Structural Genomics Consortium (SGC)
History
DepositionDec 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,52611
Polymers59,4904
Non-polymers2,0367
Water2,324129
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3823
Polymers14,8731
Non-polymers5092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3823
Polymers14,8731
Non-polymers5092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3823
Polymers14,8731
Non-polymers5092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3822
Polymers14,8731
Non-polymers5091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.615, 82.615, 177.235
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Uncharacterized protein


Mass: 14872.503 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (strain BPK282A1) (eukaryote)
Strain: BPK282A1 / Gene: LDBPK_091320 / Plasmid: pET15-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: E9BA17
#2: Chemical
ChemComp-2LO / 2-[2-(3-chloro-4-methoxyphenyl)ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(2S)-2-(morpholin-4-yl)propyl]-1H-benzimidazole


Mass: 509.040 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H33ClN4O3
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.51 Å3/Da / Density % sol: 51.03 % / Mosaicity: 0.309 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2.64 M NaFormate and 0.1M Tris 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 29431 / % possible obs: 99.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 46.42 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.05 / Rrim(I) all: 0.123 / Χ2: 1.085 / Net I/σ(I): 5.9 / Num. measured all: 166490
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.26-2.35.70.90214520.7180.4090.9940.49799.6
2.3-2.345.70.75414290.7760.3420.8310.69999.7
2.34-2.395.80.76514500.7620.3490.8440.556100
2.39-2.435.70.56114590.870.2580.620.53399.6
2.43-2.495.40.50514210.8580.2380.5610.52399.5
2.49-2.555.50.44614370.9090.2080.4940.57199.2
2.55-2.6160.38414620.9350.1710.4220.61799.8
2.61-2.6860.30614510.9440.1370.3370.61299.7
2.68-2.765.90.25914560.9590.1170.2850.63199.8
2.76-2.855.80.26114640.9560.1170.2870.86999.5
2.85-2.955.70.18414500.9740.0850.2040.81699.7
2.95-3.075.30.14714640.980.0690.1640.93499.4
3.07-3.215.80.12914440.9890.0570.1421.04199.4
3.21-3.385.90.11314760.9890.050.1241.192100
3.38-3.595.80.09114940.9920.040.11.4999.9
3.59-3.865.60.0814780.9940.0350.0871.67699.7
3.86-4.255.40.0714880.9950.0310.0771.79199.3
4.25-4.875.80.07115280.9940.0310.0782.15299.7
4.87-6.135.20.0715220.9940.0320.0771.92599.1
6.13-505.30.06316060.9950.0290.072.52495.6

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TCM

5tcm


Resolution: 2.26→28.37 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.236 / SU Rfree Blow DPI: 0.196 / SU Rfree Cruickshank DPI: 0.195
RfactorNum. reflection% reflectionSelection details
Rfree0.239 868 2.96 %RANDOM
Rwork0.195 ---
obs0.197 29356 99.3 %-
Displacement parametersBiso mean: 50.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.8366 Å20 Å20 Å2
2---3.8366 Å20 Å2
3---7.6731 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 2.26→28.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3541 0 139 129 3809
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013782HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.965166HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1204SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes83HARMONIC2
X-RAY DIFFRACTIONt_gen_planes687HARMONIC5
X-RAY DIFFRACTIONt_it3782HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion16.52
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion489SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4476SEMIHARMONIC4
LS refinement shellResolution: 2.26→2.34 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.237 -3.27 %
Rwork0.219 2695 -
all0.22 2786 -
obs--97.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6461-0.7383-0.17851.55980.72952.23740.04280.019-0.12920.0436-0.09050.04910.2801-0.18780.0477-0.067-0.01940.0092-0.00510.0144-0.1103-37.00382.7636-17.2638
21.66840.8009-0.88482.1228-0.63652.3275-0.0112-0.0344-0.07580.04660.0095-0.06730.05970.17320.0017-0.06330.0032-0.02940.0040.0092-0.0952-12.798110.1999-16.4403
31.72420.09540.46451.28980.36243.6740.053-0.0115-0.20380.08850.0221-0.09280.38590.1567-0.07510.02090.0604-0.0131-0.1161-0.0082-0.0925-19.7265-10.4718-30.506
40.43561.3293-0.15063.9385-1.28412.98440.0579-0.05090.38860.0536-0.15050.3587-0.18050.0210.0926-0.0160.02640.0542-0.204-0.02450.026-21.5606-40.8343-12.3739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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