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- PDB-3bb3: Crystal structure of Toc33 from Arabidopsis thaliana in complex w... -

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Basic information

Entry
Database: PDB / ID: 3bb3
TitleCrystal structure of Toc33 from Arabidopsis thaliana in complex with GDP and Mg2+
ComponentsT7I23.11 protein
KeywordsHYDROLASE / Rossmann fold / GTPase domain / Chloroplast import / GTP-binding / Membrane / Nucleotide-binding / Outer membrane / Protein transport / Transmembrane / Transport
Function / homology
Function and homology information


protein targeting to chloroplast / chloroplast outer membrane / protein-transporting ATPase activity / chloroplast envelope / chloroplast / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / intracellular protein transport / GTPase activity / GTP binding / protein homodimerization activity ...protein targeting to chloroplast / chloroplast outer membrane / protein-transporting ATPase activity / chloroplast envelope / chloroplast / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / intracellular protein transport / GTPase activity / GTP binding / protein homodimerization activity / extracellular region / identical protein binding / metal ion binding
Similarity search - Function
Chloroplast protein import component Toc34 / GTPase GIMA/IAN/Toc / AIG1-type guanine nucleotide-binding (G) domain / AIG1 family / AIG1-type G domain profile. / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Translocase of chloroplast 33, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsKoenig, P. / Sinning, I. / Schleiff, E. / Tews, I.
CitationJournal: Structure / Year: 2008
Title: The GTPase cycle of the chloroplast import receptors Toc33/Toc34: implications from monomeric and dimeric structures.
Authors: Koenig, P. / Oreb, M. / Hofle, A. / Kaltofen, S. / Rippe, K. / Sinning, I. / Schleiff, E. / Tews, I.
History
DepositionNov 9, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Nov 1, 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 / struct_conn / 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 / _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.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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T7I23.11 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6833
Polymers29,2151
Non-polymers4682
Water48627
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.617, 121.617, 42.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein T7I23.11 protein / At1g02280 / At1g02280/T7I23.11 / AtToc33 protein


Mass: 29215.486 Da / Num. of mol.: 1 / Fragment: UNP residues 1-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Columbia / Gene: T7I23.11 / Plasmid: pET21d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O23680
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 24% PEG1500, 20% Glycerol, pH7.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.9→29 Å / Num. all: 7288 / Num. obs: 7234 / % possible obs: 99.3 % / Observed criterion σ(F): -4 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 82 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.4
Reflection shellResolution: 2.94→3.04 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 1.9 / Num. unique all: 702 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.3.0008refinement
DNAdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H65

1h65


Resolution: 2.94→25 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.911 / SU B: 32.695 / SU ML: 0.284 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26196 335 4.7 %RANDOM
Rwork0.218 ---
obs0.22006 6866 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 104.928 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å20 Å20 Å2
2---2.14 Å20 Å2
3---4.27 Å2
Refine analyzeLuzzati coordinate error obs: 0.453 Å
Refinement stepCycle: LAST / Resolution: 2.94→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 29 27 1950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221960
X-RAY DIFFRACTIONr_angle_refined_deg2.0571.9862658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5615240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32924.69983
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.59315354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7931511
X-RAY DIFFRACTIONr_chiral_restr0.1210.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021424
X-RAY DIFFRACTIONr_nbd_refined0.2490.2766
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21260
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.239
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.25
X-RAY DIFFRACTIONr_mcbond_it0.851.51261
X-RAY DIFFRACTIONr_mcangle_it1.37921943
X-RAY DIFFRACTIONr_scbond_it1.993833
X-RAY DIFFRACTIONr_scangle_it3.1184.5713
LS refinement shellResolution: 2.941→3.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 25 -
Rwork0.317 477 -
obs--97.29 %
Refinement TLS params.Method: refined / Origin x: 13.1466 Å / Origin y: 40.5473 Å / Origin z: 5.7409 Å
111213212223313233
T-0.1328 Å20.0572 Å20.01 Å2--0.154 Å20.0255 Å2---0.2256 Å2
L3.3841 °2-1.1046 °2-0.2004 °2-3.8899 °20.5869 °2--1.6294 °2
S-0.0719 Å °0.0056 Å °-0.1229 Å °0.1685 Å °0.0936 Å °-0.1008 Å °0.2693 Å °0.1185 Å °-0.0217 Å °

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