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- PDB-3bb4: Crystal structure of Toc33 from Arabidopsis thaliana in complex w... -

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Basic information

Entry
Database: PDB / ID: 3bb4
TitleCrystal structure of Toc33 from Arabidopsis thaliana in complex with Mg2+ and GMPPNP
ComponentsT7I23.11 protein
KeywordsHYDROLASE / Rossmann fold / GTPase domain / chloroplast import
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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Translocase of chloroplast 33, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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.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
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 650DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700DETERMINATION 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)29,8043
Polymers29,2581
Non-polymers5472
Water48627
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.567, 121.567, 42.879
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: 29257.521 Da / Num. of mol.: 1 / Fragment: UNP residues 1-251 / Mutation: S181E
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-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*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: 54.57 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 22% PEG1500, 15% glycerol, pH7.4, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9746 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9746 Å / Relative weight: 1
ReflectionResolution: 2.84→25 Å / Num. all: 7834 / Num. obs: 7827 / % possible obs: 99.6 % / Observed criterion σ(F): -4 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 69.8 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 15.39
Reflection shellResolution: 2.84→2.94 Å / Redundancy: 6 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.2 / Num. unique all: 748 / % possible all: 100

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Processing

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

1h65


Resolution: 2.85→25 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.896 / SU B: 33.329 / SU ML: 0.285 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27663 366 4.7 %RANDOM
Rwork0.21802 ---
obs0.22082 7461 98.53 %-
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: 69.779 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---0.29 Å20 Å2
3---0.58 Å2
Refine analyzeLuzzati coordinate error obs: 0.398 Å
Refinement stepCycle: LAST / Resolution: 2.85→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 33 27 1945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221955
X-RAY DIFFRACTIONr_bond_other_d0.0020.021318
X-RAY DIFFRACTIONr_angle_refined_deg2.0731.9892654
X-RAY DIFFRACTIONr_angle_other_deg1.35933230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6265238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.20224.69983
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.69815354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.1221511
X-RAY DIFFRACTIONr_chiral_restr0.1030.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022106
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02372
X-RAY DIFFRACTIONr_nbd_refined0.2410.2443
X-RAY DIFFRACTIONr_nbd_other0.2190.21282
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2894
X-RAY DIFFRACTIONr_nbtor_other0.0860.2994
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1930.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1441.51539
X-RAY DIFFRACTIONr_mcbond_other0.0891.5487
X-RAY DIFFRACTIONr_mcangle_it1.32521930
X-RAY DIFFRACTIONr_scbond_it1.9163886
X-RAY DIFFRACTIONr_scangle_it2.9614.5722
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.848→2.921 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 19 -
Rwork0.315 474 -
obs--86.49 %
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)
12.6704-0.76730.70593.1954-0.3721.4361-0.079-0.00260.14020.03770.09690.0622-0.1674-0.1274-0.018-0.11730.06230.0217-0.0923-0.0082-0.158447.657319.98165.615
272.1643-10.81426.9813.681-1.83735.8315-1.2005-2.1073-0.22281.18140.71180.3702-0.7458-1.02520.48870.010.11580.12140.01310.0235-0.195945.697716.052217.9229
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 2507 - 250
2X-RAY DIFFRACTION2AC2641

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