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- PDB-4rz0: Crystal Structure of Plasmodium falciparum putative histone methy... -

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Basic information

Entry
Database: PDB / ID: 4rz0
TitleCrystal Structure of Plasmodium falciparum putative histone methyltransferase PFL0690c
ComponentsPFL0690c
KeywordsTRANSFERASE / Structural Genomics Consortium / SGC / Putative Histone Methyltransferase / PFL0690c
Function / homologyBeta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain / Beta Complex / Mainly Beta / SET domain-containing protein
Function and homology information
Biological speciesPlasmodium (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.487 Å
AuthorsJiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / He, H. / Ravichandran, M. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Jiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / He, H. / Ravichandran, M. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Hutchinson, A. / Lin, Y.H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Plasmodium falciparum putative histone methyltransferase PFL0690c
Authors: Jiang, D.Q. / Tempel, W. / Loppnau, P. / Graslund, S. / He, H. / Ravichandran, M. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Hui, R. / Hutchinson, A. / Lin, Y.H.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PFL0690c
B: PFL0690c


Theoretical massNumber of molelcules
Total (without water)33,5619
Polymers33,5612
Non-polymers07
Water1448
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-15 kcal/mol
Surface area12110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.730, 53.474, 111.592
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ILEILELYSLYSchain AAA3 - 1463 - 146
2LYSLYSTRPTRPchain BBB6 - 1446 - 144

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Components

#1: Protein PFL0690c


Mass: 16780.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium (eukaryote) / Strain: Laverania / Gene: PFAG_03779, PFL0690c / Plasmid: PFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: W7FLI1
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 20% PEG3350, 0.2M NH4Cl, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.487→50 Å / Num. all: 10729 / Num. obs: 10658 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Biso Wilson estimate: 55.32 Å2 / Rmerge(I) obs: 0.097 / Χ2: 1.351 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.5460.844940.742194.6
2.54-2.596.70.8285070.748197.7
2.59-2.646.80.6465050.839198.1
2.64-2.697.30.6575160.853198.5
2.69-2.757.50.5415220.836199.6
2.75-2.827.70.55190.832199.8
2.82-2.8980.4615400.8731100
2.89-2.968.30.3565210.9111100
2.96-3.058.20.2725271.0051100
3.05-3.158.20.2385310.9961100
3.15-3.268.20.1685291.1421100
3.26-3.398.10.1475251.2231100
3.39-3.558.10.125361.3491100
3.55-3.738.10.0975321.5361100
3.73-3.9780.0875371.7931100
3.97-4.277.90.0745462.173199.8
4.27-4.77.70.0655382.459199.8
4.7-5.387.40.0595572.1841100
5.38-6.787.10.0565641.9541100
6.78-506.60.0416122.201199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.9-1692refinement
PDB_EXTRACT3.15data extraction
APSdata collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.487→48.223 Å / SU ML: 0.52 / σ(F): 1.34 / Phase error: 34.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.275 523 4.95 %RANDOM
Rwork0.2198 ---
all0.2225 10573 --
obs0.2225 10573 98.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.17 Å2 / Biso mean: 52.4588 Å2 / Biso min: 26.59 Å2
Refinement stepCycle: LAST / Resolution: 2.487→48.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1654 0 7 8 1669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121688
X-RAY DIFFRACTIONf_angle_d1.3362308
X-RAY DIFFRACTIONf_chiral_restr0.063271
X-RAY DIFFRACTIONf_plane_restr0.007290
X-RAY DIFFRACTIONf_dihedral_angle_d12.888560
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A862X-RAY DIFFRACTION4.536TORSIONAL
12B862X-RAY DIFFRACTION4.536TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4865-2.73670.40751130.31032328244193
2.7367-3.13270.33971440.279224982642100
3.1327-3.94650.29551300.224125522682100
3.9465-48.23230.22571360.189226722808100

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