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- PDB-3igm: A 2.2A crystal structure of the AP2 domain of PF14_0633 from P. f... -

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Basic information

Entry
Database: PDB / ID: 3igm
TitleA 2.2A crystal structure of the AP2 domain of PF14_0633 from P. falciparum, bound as a domain-swapped dimer to its cognate DNA
Components
  • 5'-D(*TP*GP*CP*AP*TP*GP*CP*A)-3'
  • PF14_0633 protein
KeywordsTranscription/DNA / AP2 domain / Plasmodium falciparum / specific transcription factor / PROTEIN-DNA COMPLEX / Transcription-DNA COMPLEX
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity / nucleus
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2050 / AP2 domain / AP2/ERF domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / AP2 domain transcription factor AP2-EXP
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsLindner, S.E. / De Silva, E. / Keck, J.L. / Llinas, M.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural Determinants of DNA Binding by a P. falciparum ApiAP2 Transcriptional Regulator.
Authors: Lindner, S.E. / De Silva, E.K. / Keck, J.L. / Llinas, M.
History
DepositionJul 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
B: PF14_0633 protein
W: 5'-D(*TP*GP*CP*AP*TP*GP*CP*A)-3'
X: 5'-D(*TP*GP*CP*AP*TP*GP*CP*A)-3'
A: PF14_0633 protein
C: 5'-D(*TP*GP*CP*AP*TP*GP*CP*A)-3'
D: 5'-D(*TP*GP*CP*AP*TP*GP*CP*A)-3'


Theoretical massNumber of molelcules
Total (without water)27,3376
Polymers27,3376
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-62 kcal/mol
Surface area11040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.810, 58.821, 177.296
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsBIOLOGICAL ASSEMBLY OF PROTEIN IS DIMER

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Components

#1: Protein PF14_0633 protein


Mass: 8815.056 Da / Num. of mol.: 2 / Fragment: UNP residues 63-123, AP2 domain
Source method: isolated from a genetically manipulated source
Details: GST-tagged derivative of the AP2 domain of PF14_0633. GST removed by thrombin cleavage.
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: FP14_0633, PF14_0633 / Plasmid: pSURE, a pGEX4T-1 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon plus / References: UniProt: Q8IKH2
#2: DNA chain
5'-D(*TP*GP*CP*AP*TP*GP*CP*A)-3'


Mass: 2426.617 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: This sequence occurs naturally in P. falciparum. DNA produced for this study was chemically synthesized.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 0.5M-1.25M 1,6-hexanediol 100mM NaOAc pH 5.1 @295K 10mM CoCl2 10-20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97886 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97886 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 11402 / Num. obs: 10478 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Rsym value: 0.075 / Net I/σ(I): 32.1
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 9 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.381 / % possible all: 72.4

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Processing

Software
NameVersionClassification
MAR345data collection
MLPHAREphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→29.55 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 15.931 / SU ML: 0.18 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26268 526 4.8 %RANDOM
Rwork0.21448 ---
obs0.21681 10478 91.78 %-
all-10478 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.953 Å2
Baniso -1Baniso -2Baniso -3
1-2.84 Å20 Å20 Å2
2---1.48 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 623 0 97 1691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0211695
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3482.3942400
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0755116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.05221.0249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45815179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1111511
X-RAY DIFFRACTIONr_chiral_restr0.0730.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021090
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6171.5585
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1842927
X-RAY DIFFRACTIONr_scbond_it1.12731110
X-RAY DIFFRACTIONr_scangle_it1.8054.51473
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 27 -
Rwork0.279 581 -
obs--69.25 %
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)
11.4607-0.2373.50980.54450.01329.68320.17290.0021-0.120.08890.04120.12980.40240.0549-0.21410.0926-0.01180.04170.0398-0.0240.06814.4456-5.615-20.314
21.1839-0.3432.37680.2593-1.5699.8892-0.03280.08870.0878-0.01850.06680.01150.2432-0.2973-0.0340.111-0.04230.01540.0943-0.03380.10399.9642-1.0769-27.3083
32.8765-1.0093-0.66424.83391.80285.30280.04140.17070.1645-0.18230.0789-0.9101-0.13620.6339-0.12040.1512-0.05070.07090.1328-0.02980.262727.6921-1.3296-13.2621
44.7050.5541-0.61242.80980.60063.9339-0.18990.1890.47520.29970.1868-0.0628-0.30090.26160.00310.1029-0.0353-0.02210.0643-0.01440.090413.709212.1749-33.7973
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A62 - 123
2X-RAY DIFFRACTION2B62 - 117
3X-RAY DIFFRACTION3C1 - 8
4X-RAY DIFFRACTION3D1 - 7
5X-RAY DIFFRACTION4W1 - 8
6X-RAY DIFFRACTION4X1 - 8

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