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- PDB-3bb1: Crystal structure of Toc34 from Pisum sativum in complex with Mg2... -

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Basic information

Entry
Database: PDB / ID: 3bb1
TitleCrystal structure of Toc34 from Pisum sativum in complex with Mg2+ and GMPPNP
ComponentsTranslocase of chloroplast 34
KeywordsHYDROLASE / Rossmann fold / GTPase domain / chloroplast import / GTP-binding / Membrane / Nucleotide-binding / Outer membrane / Protein transport / Transmembrane / Transport
Function / homology
Function and homology information


chloroplast outer membrane / protein-transporting ATPase activity / intracellular protein transport / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / hydrolase activity / GTP binding / identical protein binding
Similarity search - Function
Chloroplast protein import component Toc34 / AIG1-type guanine nucleotide-binding (G) domain / GTPase GIMA/IAN/Toc / AIG1 family / AIG1-type G domain profile. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / TRIETHYLENE GLYCOL / Translocase of chloroplast 34
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 / Refinement description / 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.ptnr1_auth_asym_id / _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_asym_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
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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: Translocase of chloroplast 34
B: Translocase of chloroplast 34
C: Translocase of chloroplast 34
D: Translocase of chloroplast 34
E: Translocase of chloroplast 34
F: Translocase of chloroplast 34
G: Translocase of chloroplast 34
H: Translocase of chloroplast 34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,28232
Polymers240,0578
Non-polymers5,22524
Water5,891327
1
A: Translocase of chloroplast 34
B: Translocase of chloroplast 34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3508
Polymers60,0142
Non-polymers1,3356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Translocase of chloroplast 34
D: Translocase of chloroplast 34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1997
Polymers60,0142
Non-polymers1,1855
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Translocase of chloroplast 34
F: Translocase of chloroplast 34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4429
Polymers60,0142
Non-polymers1,4277
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Translocase of chloroplast 34
H: Translocase of chloroplast 34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2918
Polymers60,0142
Non-polymers1,2776
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)178.776, 180.061, 90.948
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Translocase of chloroplast 34 / psToc34 / 34 kDa chloroplast outer envelope protein / GTP-binding protein OEP34 / GTP-binding protein IAP34


Mass: 30007.146 Da / Num. of mol.: 8 / Fragment: UNP residues 1-266 / Mutation: E10G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: TOC34 / Plasmid: pET21d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q41009, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement

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Non-polymers , 5 types, 351 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 3.05 Å3/Da / Density % sol: 59.66 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2M di-potassiumphosphate 20% PEG3350, pH7.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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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: Jul 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 73060 / Num. obs: 72688 / % possible obs: 99.5 % / Observed criterion σ(F): -4 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 65.4 Å2 / Rsym value: 0.077 / Net I/σ(I): 15.5
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 3462 / Rsym value: 0.471 / % possible all: 95.9

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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: 2.8→49.88 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.868 / SU B: 29.167 / SU ML: 0.276 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 1.066 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28231 3668 5 %RANDOM
Rwork0.2242 ---
obs0.22714 69019 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: 60.756 Å2
Baniso -1Baniso -2Baniso -3
1-2.83 Å20 Å20 Å2
2--2.75 Å20 Å2
3----5.58 Å2
Refine analyzeLuzzati coordinate error obs: 0.371 Å
Refinement stepCycle: LAST / Resolution: 2.8→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15155 0 320 327 15802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02215752
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210486
X-RAY DIFFRACTIONr_angle_refined_deg2.0552.00421442
X-RAY DIFFRACTIONr_angle_other_deg1.457325808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.52451961
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.42825.065616
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.443152733
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8871580
X-RAY DIFFRACTIONr_chiral_restr0.2720.22526
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216975
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022849
X-RAY DIFFRACTIONr_nbd_refined0.2570.24309
X-RAY DIFFRACTIONr_nbd_other0.2310.211687
X-RAY DIFFRACTIONr_nbtor_refined0.1960.27755
X-RAY DIFFRACTIONr_nbtor_other0.0960.28620
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2668
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0140.23
X-RAY DIFFRACTIONr_metal_ion_refined0.1230.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3350.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.214
X-RAY DIFFRACTIONr_mcbond_it0.8521.510631
X-RAY DIFFRACTIONr_mcbond_other0.1121.54017
X-RAY DIFFRACTIONr_mcangle_it1.308215916
X-RAY DIFFRACTIONr_scbond_it1.76136552
X-RAY DIFFRACTIONr_scangle_it2.774.55510
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 274 -
Rwork0.282 4881 -
obs--97.14 %
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)
11.6696-0.9184-0.40241.00050.22921.2894-0.02580.10650.09210.0174-0.0425-0.0219-0.06740.22010.0683-0.1993-0.06530.0036-0.02680.0369-0.04231.353259.290152.9363
22.7432-0.5218-0.70421.5353-0.10752.09270.11360.3611-0.0502-0.1327-0.0791-0.00080.0503-0.076-0.0345-0.17820.0520.01370.06290.0016-0.154720.350539.516629.6199
31.4125-0.4024-0.47130.87540.35122.0624-0.0936-0.0802-0.110.06-0.0065-0.01270.1286-0.05710.1001-0.1855-0.00790.0144-0.0929-0.0334-0.049555.851321.094946.8681
42.4652-0.9980.33682.0245-0.12732.0054-0.084-0.226-0.22860.12860.20340.1385-0.0135-0.2628-0.1195-0.20960.03830.04250.01790.0139-0.140729.214928.557768.3028
50.8942-0.36110.25291.4755-0.54822.1227-0.03690.0605-0.0002-0.0319-0.1056-0.0676-0.03150.1490.1425-0.1227-0.0111-0.0216-0.16240.0105-0.047567.847833.881390.0315
61.5782-0.6357-0.02991.92940.11271.84820.21720.13010.1366-0.1783-0.1389-0.2729-0.2255-0.0449-0.0783-0.01430.05160.0192-0.17940.0341-0.101960.351160.411568.7375
70.8392-0.65210.20481.9822-0.11560.9337-0.04130.03350.01090.2192-0.05410.10440.2384-0.05040.0954-0.0255-0.04210.0626-0.18870.0079-0.052129.779988.890683.0392
81.5258-0.88960.1812.9056-0.46391.5033-0.1635-0.1820.09720.50220.2589-0.1613-0.0822-0.0864-0.09540.17530.1296-0.0188-0.1855-0.0218-0.227748.391669.7268106.7256
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 258
2X-RAY DIFFRACTION2B8 - 259
3X-RAY DIFFRACTION3C8 - 258
4X-RAY DIFFRACTION4D7 - 258
5X-RAY DIFFRACTION5E8 - 258
6X-RAY DIFFRACTION6F8 - 257
7X-RAY DIFFRACTION7G2 - 258
8X-RAY DIFFRACTION8H8 - 258

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