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- PDB-2ghi: Crystal Structure of Plasmodium yoelii Multidrug Resistance Protein 2 -

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Basic information

Entry
Database: PDB / ID: 2ghi
TitleCrystal Structure of Plasmodium yoelii Multidrug Resistance Protein 2
Componentstransport protein
KeywordsTRANSPORT PROTEIN / Plasmodium yoelii / Multidrug Resistance Protein / MDR / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


ABC-type transporter activity / ATP hydrolysis activity / ATP binding / metal ion binding / membrane / cytoplasm
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPlasmodium yoelii yoelii str. 17XNL (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDong, A. / Gao, M. / Choe, J. / Zhao, Y. / Lew, J. / Wasney, G. / Alam, Z. / Melone, M. / Kozieradzki, I. / Vedadi, M. ...Dong, A. / Gao, M. / Choe, J. / Zhao, Y. / Lew, J. / Wasney, G. / Alam, Z. / Melone, M. / Kozieradzki, I. / Vedadi, M. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Artz, J.D. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2007
Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R.
History
DepositionMar 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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: transport protein
B: transport protein
C: transport protein
D: transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,63415
Polymers116,5784
Non-polymers1,05711
Water6,377354
1
A: transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5295
Polymers29,1441
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4334
Polymers29,1441
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4334
Polymers29,1441
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2402
Polymers29,1441
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.015, 70.689, 74.384
Angle α, β, γ (deg.)69.81, 76.69, 82.29
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
transport protein


Mass: 29144.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium yoelii yoelii str. 17XNL (eukaryote)
Species: Plasmodium yoelii / Strain: yoelii str. 17XNL / Plasmid: P28-LIC-THROMBIN DERIVED FROM PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon plus Ril / References: UniProt: Q7RBT4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 50.97 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 29%Peg 3350, 0.2M Li2SO4, 4% Glycerol, and 0.1M BisTris pH 5.5 , VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 9, 2006 / Details: VariMax HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 56948 / Num. obs: 56948 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 43.6 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.77 / Num. unique all: 2824 / Rsym value: 0.67 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data scaling
PHASERV. 1.3.1phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MV5

1mv5


Resolution: 2.2→32.67 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.905 / SU B: 8.121 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.26 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28834 857 1.5 %RANDOM
Rwork0.20448 ---
all0.20568 56088 --
obs0.20568 56087 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20.62 Å20.1 Å2
2--0.55 Å2-0.42 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7551 0 55 354 7960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227709
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8811.9710399
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1615961
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.13724.494316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.327151397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6321537
X-RAY DIFFRACTIONr_chiral_restr0.130.21212
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025558
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.23381
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.25229
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2434
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.289
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9691.54977
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.627738
X-RAY DIFFRACTIONr_scbond_it2.57333108
X-RAY DIFFRACTIONr_scangle_it3.8494.52661
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 54 -
Rwork0.288 3712 -
obs--88.53 %

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