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- PDB-4nxj: Crystal Structure of PF3D7_1475600, a bromodomain from Plasmodium... -

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Basic information

Entry
Database: PDB / ID: 4nxj
TitleCrystal Structure of PF3D7_1475600, a bromodomain from Plasmodium Falciparum
ComponentsBromodomain protein
KeywordsDNA BINDING PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC / bromodomain
Function / homology
Function and homology information


Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain protein, putative
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsWernimont, A.K. / Loppnau, P. / Knapp, S. / Fonseca, M. / Brennan, P.E. / Dong, A. / Walker, J.R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Wernimont, A.K. / Loppnau, P. / Knapp, S. / Fonseca, M. / Brennan, P.E. / Dong, A. / Walker, J.R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Hutchinson, A. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of PF3D7_1475600, a bromodomain from Plasmodium Falciparum
Authors: Wernimont, A.K. / Loppnau, P. / Knapp, S. / Fonseca, M. / Brennan, P.E. / Dong, A. / Walker, J.R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Hutchinson, A.
History
DepositionDec 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Other
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain protein
B: Bromodomain protein
C: Bromodomain protein


Theoretical massNumber of molelcules
Total (without water)43,2983
Polymers43,2983
Non-polymers00
Water2,774154
1
A: Bromodomain protein


Theoretical massNumber of molelcules
Total (without water)14,4331
Polymers14,4331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bromodomain protein


Theoretical massNumber of molelcules
Total (without water)14,4331
Polymers14,4331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Bromodomain protein


Theoretical massNumber of molelcules
Total (without water)14,4331
Polymers14,4331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.240, 41.352, 107.432
Angle α, β, γ (deg.)90.000, 93.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bromodomain protein


Mass: 14432.708 Da / Num. of mol.: 3 / Fragment: UNP residues 8-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PF14_0724 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IK82
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 25% PEG3350, 0.3 M KAcetate, pH 7.5, microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Sep 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.18→35.75 Å / Num. all: 19612 / Num. obs: 18730 / % possible obs: 95.5 % / Redundancy: 1.7 % / Biso Wilson estimate: 36.35 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.18-2.251.30.3573.13938130766
9-35.751.80.02136.698930698.2

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Processing

Software
NameVersionClassificationNB
Aimless0.2.8data scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
PHASERphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FFAS03 model of 3g0l

3g0l


Resolution: 2.18→29.89 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.8693 / Occupancy max: 1 / Occupancy min: 0.2 / SU R Cruickshank DPI: 0.319 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 959 5.12 %RANDOM
Rwork0.2028 ---
all0.2051 19180 --
obs0.2051 18719 97.59 %-
Displacement parametersBiso max: 118.51 Å2 / Biso mean: 36.5454 Å2 / Biso min: 7.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.2704 Å20 Å2-2.2894 Å2
2--8.397 Å20 Å2
3----8.6674 Å2
Refine analyzeLuzzati coordinate error obs: 0.337 Å
Refinement stepCycle: LAST / Resolution: 2.18→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 0 154 3106
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1104SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes101HARMONIC2
X-RAY DIFFRACTIONt_gen_planes422HARMONIC5
X-RAY DIFFRACTIONt_it3066HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion409SEMIHARMONIC5
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_contact3942SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3066HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4160HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion19.34
LS refinement shellResolution: 2.18→2.31 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3428 154 5.8 %
Rwork0.2852 2503 -
all0.2885 2657 -
obs--97.59 %
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)
12.2016-0.990.74042.5201-1.28822.2516-0.1078-0.24830.20840.06320.0744-0.09730.0735-0.03680.0334-0.06380.0282-0.02450.0413-0.0217-0.156348.60450.856146.1529
22.87650.7891-0.14821.53020.21222.0655-0.0578-0.1283-0.1442-0.0063-0.0406-0.0552-0.03450.07640.0984-0.0946-0.02430.0845-0.0129-0.0044-0.082241.71587.276673.2152
31.81610.1808-1.03482.29690.29351.7746-0.05340.1148-0.2172-0.1892-0.02790.0315-0.00280.05490.0814-0.12250.01820.00020.0334-0.0172-0.064448.38560.8165104.8686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 118
2X-RAY DIFFRACTION2{ B|* }B1 - 117
3X-RAY DIFFRACTION3{ C|* }C1 - 117

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