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- PDB-4qns: Crystal structure of bromodomain from Plasmodium faciparum GCN5, ... -

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Basic information

Entry
Database: PDB / ID: 4qns
TitleCrystal structure of bromodomain from Plasmodium faciparum GCN5, PF3D7_0823300
ComponentsHistone acetyltransferase GCN5, putative
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / bromodomain / histone / malaria
Function / homology
Function and homology information


histone H3 acetyltransferase activity / histone acetyltransferase complex / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity ...histone H3 acetyltransferase activity / histone acetyltransferase complex / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / chromatin remodeling / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain profile. / bromo domain / Bromodomain ...Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Histone acetyltransferase GCN5
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.497 Å
AuthorsFonseca, M. / Tallant, C. / Knapp, S. / Loppnau, P. / von Delft, F. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of bromodomain from Plasmodium faciparum GCN5, PF3D7_0823300
Authors: Fonseca, M. / Tallant, C. / Knapp, S. / Loppnau, P. / Hui, R. / Wernimont, A.K. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C.
History
DepositionJun 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase GCN5, putative
B: Histone acetyltransferase GCN5, putative
C: Histone acetyltransferase GCN5, putative
D: Histone acetyltransferase GCN5, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,87022
Polymers50,4904
Non-polymers1,38018
Water8,179454
1
A: Histone acetyltransferase GCN5, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0016
Polymers12,6221
Non-polymers3785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone acetyltransferase GCN5, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1287
Polymers12,6221
Non-polymers5056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone acetyltransferase GCN5, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8774
Polymers12,6221
Non-polymers2543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone acetyltransferase GCN5, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8655
Polymers12,6221
Non-polymers2424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: Histone acetyltransferase GCN5, putative
hetero molecules

C: Histone acetyltransferase GCN5, putative
hetero molecules

A: Histone acetyltransferase GCN5, putative
D: Histone acetyltransferase GCN5, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,87022
Polymers50,4904
Non-polymers1,38018
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_447-x-1,y-1/2,-z+21
crystal symmetry operation2_548-x,y-1/2,-z+31
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-126 kcal/mol
Surface area21450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.217, 98.871, 50.439
Angle α, β, γ (deg.)90.000, 109.630, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS HAVE INDICATED THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein
Histone acetyltransferase GCN5, putative


Mass: 12622.471 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: gcn5, PF08_0034, PFNF54_02299 / Plasmid: pet15mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8IB67
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 2.0 M Ammonium sulfate 0.1 M sodium acetate pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.5→29 Å / Num. all: 74520 / Num. obs: 74224 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 11.74 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.9 / Scaling rejects: 42
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.5-1.526.10.4873.921749356795.8
8.2-296.30.06232.5296646897.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.3.5data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.14data extraction
ADSCQuantumdata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.497→28.999 Å / SU ML: 0.12 / σ(F): 1.34 / Phase error: 17.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1868 3595 4.85 %random
Rwork0.1563 ---
obs0.1578 74191 99.59 %-
all-74496 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.09 Å2 / Biso mean: 16.5608 Å2 / Biso min: 5.18 Å2
Refinement stepCycle: LAST / Resolution: 1.497→28.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3493 0 80 454 4027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063856
X-RAY DIFFRACTIONf_angle_d1.055233
X-RAY DIFFRACTIONf_chiral_restr0.044538
X-RAY DIFFRACTIONf_plane_restr0.006673
X-RAY DIFFRACTIONf_dihedral_angle_d12.6221489
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4968-1.51650.23661240.22172606273095
1.5165-1.53730.18031210.179126942815100
1.5373-1.55920.22351070.174627352842100
1.5592-1.58250.20491450.16527332878100
1.5825-1.60720.2031520.171227252877100
1.6072-1.63360.22611360.170226612797100
1.6336-1.66170.2051370.169827172854100
1.6617-1.69190.20121320.16262706283899
1.6919-1.72450.17491630.163326772840100
1.7245-1.75970.21671420.152327272869100
1.7597-1.79790.17021130.143927522865100
1.7979-1.83980.17161420.146527042846100
1.8398-1.88580.19991320.147527182850100
1.8858-1.93670.19391580.156527362894100
1.9367-1.99370.20231250.156426852810100
1.9937-2.0580.18521390.155527552894100
2.058-2.13160.1771300.151627142844100
2.1316-2.21690.16551650.143227142879100
2.2169-2.31770.18111360.150227102846100
2.3177-2.43990.16591410.153927302871100
2.4399-2.59270.2311570.163827082865100
2.5927-2.79270.20371280.169927512879100
2.7927-3.07340.17511420.168827232865100
3.0734-3.51750.20121550.15712699285499
3.5175-4.42920.15861250.13432751287699
4.4292-29.00410.17051480.15432765291399
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)
14.4353-1.7386-2.73333.08711.46793.7039-0.10190.0809-0.06420.0152-0.01340.1073-0.0162-0.10450.00790.07540.0074-0.01990.0910.02230.1181-44.815137.428751.9799
21.1623-0.17480.07511.9493-0.52731.3395-0.0143-0.0289-0.0966-0.0096-0.0816-0.09940.1490.10680.02750.10930.00860.00060.11380.01260.1132-30.102621.214452.1418
31.6282-0.759-2.22352.86490.22993.32150.0070.1938-0.0252-0.07750.02950.15290.0837-0.211-0.0270.1104-0.0111-0.01230.09540.02990.1269-42.499627.471454.1908
41.1787-0.1029-0.03991.3867-0.03520.6907-0.0928-0.2024-0.01430.15310.0662-0.09940.05320.0263-0.01190.0939-0.0038-0.00230.08140.01040.1103-31.050531.50856.1559
51.3507-0.8046-0.24632.66090.13951.00430.03420.08270.1058-0.2079-0.0082-0.1120.0249-0.0849-0.00760.0865-0.00460.01220.05970.00040.0966-28.864835.685246.5863
63.0883-1.4862-1.62551.23891.07551.7966-0.03880.05920.1798-0.01590.0656-0.112-0.08820.0904-0.02230.07860.0074-0.01220.11560.01050.0742-26.236163.037124.6597
72.48480.0343-1.19870.28020.23972.63760.004-0.29120.00630.1634-0.04050.08490.21230.13230.07180.16280.0012-0.0010.15180.01610.1573-38.781760.315241.615
80.9586-0.3629-0.13140.45540.2991.0503-0.03550.04960.01730.0488-0.0334-0.01550.00580.02110.06420.08770.0121-0.00950.0868-0.00830.0689-34.955660.374227.4403
93.8632-0.81471.93852.8328-1.11853.0858-0.0706-0.3660.31390.11180.05090.0849-0.4038-0.2590.07470.12430.03530.00190.1592-0.03150.1274-28.509968.349566.3287
100.93040.4276-0.26730.7589-0.34321.8073-0.0014-0.03650.06350.0112-0.0503-0.0632-0.15660.11470.04390.09860.0021-0.00920.08260.00040.0809-10.482765.891759.2222
114.3279-2.04210.69632.3818-0.88391.702-0.134-0.19430.44670.0381-0.03150.135-0.28-0.07740.05080.14520.0185-0.03750.0999-0.03770.1804-22.863574.355462.1263
121.44492.28580.64715.29382.21521.3739-0.25360.22090.5016-0.2768-0.01970.2987-0.3406-0.09050.13890.20190.0577-0.07750.17490.01510.2465-29.563875.76156.1614
131.17180.3293-0.11090.7195-0.08790.8936-0.0173-0.00950.04810.0445-0.00050.0126-0.0304-0.06450.02030.06820.0057-0.00720.0688-0.01090.0597-20.142458.839559.1932
143.9311.7661-1.11222.5198-0.99852.6615-0.03650.1797-0.5742-0.30220.0561-0.24710.20580.13760.0410.12560.01330.02230.1114-0.04130.2344-5.526338.448342.734
154.2219-0.27770.0191.47481.32081.22440.0009-0.231-0.33520.25210.0419-0.14140.1511-0.063-0.02420.1126-0.0018-0.0050.07370.00790.1171-19.572438.746949.9147
162.2244-0.93230.35532.7290.21441.3839-0.01680.0259-0.0484-0.22540.04140.2982-0.0616-0.25640.03790.110.0281-0.02340.13190.02270.0916-25.495651.171540.6357
175.51870.579-2.8472.1461-1.2753.3343-0.06780.4943-0.4123-0.43460.1881-0.16880.13440.0586-0.01290.1805-0.00680.00420.1526-0.0610.1406-11.898642.505336.2689
181.20650.1279-0.02651.00450.25810.7567-0.02510.0919-0.0629-0.06580.0175-0.10460.07070.0271-0.02830.07110.00430.00690.0615-0.00490.0766-12.711748.077148.3094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1355 through 1374 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1375 through 1402 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1403 through 1411 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1412 through 1440 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1441 through 1460 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 1355 through 1381 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 1382 through 1402 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 1403 through 1460 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 1360 through 1373 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 1374 through 1402 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 1403 through 1411 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 1412 through 1417 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 1418 through 1460 )C0
14X-RAY DIFFRACTION14chain 'D' and (resid 1359 through 1374 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 1375 through 1381 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 1382 through 1402 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 1403 through 1411 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 1412 through 1460 )D0

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