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- PDB-3tgh: GAP50 the anchor in the inner membrane complex of Plasmodium -

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Basic information

Entry
Database: PDB / ID: 3tgh
TitleGAP50 the anchor in the inner membrane complex of Plasmodium
ComponentsGlideosome-associated protein 50
KeywordsCELL INVASION / Phosphatase fold / not a phosphatase / MOTOR PROTEIN / STRUCTURAL PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


Vitamin B2 (riboflavin) metabolism / inner membrane pellicle complex / acid phosphatase / acid phosphatase activity / phosphoprotein phosphatase activity / protein-membrane adaptor activity / ferric iron binding / ferrous iron binding / membrane => GO:0016020 / endoplasmic reticulum / plasma membrane
Similarity search - Function
Purple acid phosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Acid phosphatase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBosch, J. / Paige, M.H. / Vaidya, A. / Bergman, L. / Hol, W.G.J.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Crystal structure of GAP50, the anchor of the invasion machinery in the inner membrane complex of Plasmodium falciparum.
Authors: Bosch, J. / Paige, M.H. / Vaidya, A.B. / Bergman, L.W. / Hol, W.G.
History
DepositionAug 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Glideosome-associated protein 50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9797
Polymers38,4951
Non-polymers4846
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.648, 57.648, 210.625
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-501-

SO4

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Components

#1: Protein Glideosome-associated protein 50


Mass: 38494.594 Da / Num. of mol.: 1 / Fragment: UNP residues 24-365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: 3D7 / Gene: GAP50, PFI0880c / Plasmid: pRSF1B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 De3 / References: UniProt: Q8I2X3, acid phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 6
Details: 0.2 M (NH4)2SO4, 0.1 M sodium acetate pH 6.0, 3% DMSO or 3 % ethanol, 40% PEG8000, EVAPORATION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 43472 / Num. obs: 43472 / % possible obs: 97.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -0.3 / Redundancy: 5.2 % / Rsym value: 0.089 / Net I/σ(I): 18.7
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 4.15 % / Rmerge(I) obs: 0.742 / Mean I/σ(I) obs: 2.08 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WAR

1war


Resolution: 1.7→19.44 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 4.784 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19874 2328 5.1 %RANDOM
Rwork0.17324 ---
obs0.17454 43471 100 %-
all-45825 --
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: 35.437 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 21 260 2793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222612
X-RAY DIFFRACTIONr_bond_other_d0.0010.021753
X-RAY DIFFRACTIONr_angle_refined_deg1.0221.9463534
X-RAY DIFFRACTIONr_angle_other_deg0.77334291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3045318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88825118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58115449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.221154
X-RAY DIFFRACTIONr_chiral_restr0.0670.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02531
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_refined0.1380.2182
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0190.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1870.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.270.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.55541569
X-RAY DIFFRACTIONr_mcbond_other0.4344645
X-RAY DIFFRACTIONr_mcangle_it2.68862527
X-RAY DIFFRACTIONr_scbond_it2.99461043
X-RAY DIFFRACTIONr_scangle_it4.731101004
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.791 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.391 357 -
Rwork0.346 6184 -
obs--100 %
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)
11.433-0.5826-0.10331.6030.34211.75490.06040.285-0.0202-0.1369-0.11780.005-0.1029-0.10590.05740.0745-0.02080.01330.09660.00380.04018.1405-13.8907-24.375
20.8122-0.5709-0.19331.01330.73772.72710.0110.1238-0.01840.018-0.08170.0235-0.0671-0.23830.07070.0687-0.04470.01020.0907-0.00770.09634.3673-13.042-12.8801
30.5261-0.1649-0.29840.41810.15291.432-0.05350.0636-0.11590.1094-0.03760.09270.1624-0.17180.0910.0916-0.07310.02880.0703-0.01850.13837.0919-23.0329-9.6203
40.5862-0.0486-0.15270.74980.01381.07-0.0324-0.0026-0.0050.04470.0051-0.1390.00250.22310.02740.07-0.05260.00480.0887-0.0030.113923.9986-18.7209-7.8071
54.9167-3.7274-0.69133.37050.11592.32660.02940.19230.4125-0.1185-0.0432-0.3824-0.27770.38610.01380.1215-0.12860.03040.17070.0220.144826.6017-9.3052-20.1632
60.3505-0.04340.03981.1157-0.48812.4137-0.01270.2058-0.0491-0.3157-0.0752-0.04890.10470.23740.08790.1238-0.01760.05170.1665-0.01890.098722.1617-21.2972-24.3788
70.598-1.8918-0.5879.2363.0261.215-0.0619-0.0893-0.10660.6227-0.05820.14740.2466-0.04450.120.1579-0.06710.03520.05940.01960.080313.7415-23.90324.0963
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 55
2X-RAY DIFFRACTION2A56 - 114
3X-RAY DIFFRACTION3A115 - 159
4X-RAY DIFFRACTION4A170 - 263
5X-RAY DIFFRACTION5A264 - 289
6X-RAY DIFFRACTION6A290 - 341
7X-RAY DIFFRACTION7A342 - 362

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