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- PDB-1h65: Crystal structure of pea Toc34 - a novel GTPase of the chloroplas... -

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Basic information

Entry
Database: PDB / ID: 1h65
TitleCrystal structure of pea Toc34 - a novel GTPase of the chloroplast protein translocon
ComponentsCHLOROPLAST OUTER ENVELOPE PROTEIN OEP34
KeywordsGTPASE / CHLOROPLAST / TRANSLOCON
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
GUANOSINE-5'-DIPHOSPHATE / Translocase of chloroplast 34
Similarity search - Component
Biological speciesPISUM SATIVUM (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsSun, Y.J. / Forouhar, F. / Li, H.M. / Tu, S.L. / Kao, S. / Shr, H.L. / Chou, C.C. / Hsiao, C.D.
Citation
Journal: Nat.Struct.Biol. / Year: 2002
Title: Crystal Structure of Pea Toc34 - a Novel Gtpase of the Chloroplast Protein Translocon
Authors: Sun, Y.J. / Forouhar, F. / Li, H.M. / Tu, S.L. / Yeh, Y.H. / Kao, S. / Shr, H.L. / Chou, C.C. / Chen, C. / Hsiao, C.D.
#1: Journal: Science / Year: 1994
Title: Identification of Two GTP-Binding Proteins in the Chloroplast Protein Import Machinery.
Authors: Kessler, F. / Blobel, G. / Patel, H. / Schnell, D.
History
DepositionJun 6, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 27, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jun 12, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_seq_map_depositor_info
Item: _audit_author.name / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.5Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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: CHLOROPLAST OUTER ENVELOPE PROTEIN OEP34
B: CHLOROPLAST OUTER ENVELOPE PROTEIN OEP34
C: CHLOROPLAST OUTER ENVELOPE PROTEIN OEP34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7229
Polymers89,3203
Non-polymers1,4036
Water12,070670
1
A: CHLOROPLAST OUTER ENVELOPE PROTEIN OEP34
hetero molecules

A: CHLOROPLAST OUTER ENVELOPE PROTEIN OEP34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4826
Polymers59,5472
Non-polymers9354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
2
B: CHLOROPLAST OUTER ENVELOPE PROTEIN OEP34
C: CHLOROPLAST OUTER ENVELOPE PROTEIN OEP34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4826
Polymers59,5472
Non-polymers9354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)143.160, 78.673, 67.279
Angle α, β, γ (deg.)90.00, 91.44, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-2116-

HOH

21C-2117-

HOH

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Components

#1: Protein CHLOROPLAST OUTER ENVELOPE PROTEIN OEP34 / TOC34 / GTP-BINDING PROTEIN IAP34


Mass: 29773.318 Da / Num. of mol.: 3 / Fragment: GTP-BINDING DOMAIN RESIDUES 1-258
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONINE-INCORPORATED / Source: (gene. exp.) PISUM SATIVUM (garden pea) / Organ: LEAF / Variant: LITTLE MARVEL / Plasmid: PET21D-IAP34 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q41009
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE LAST SIX RESIDUES AT THE C-TERMINUS ARE THE CLONING ARTEFACT
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: THE TOC34 CRYSTALS WERE GROWN AT 4 DEGREES CELSIUS BY HANGING DROP VAPOR DIFFUSION. A 2-MICROLITER SOLUTION (10 MG/ML IN 50 MM TRIS-HCL AT PH 8.0 AND 0.1 M NACL) WAS MIXED WITH A 2- ...Details: THE TOC34 CRYSTALS WERE GROWN AT 4 DEGREES CELSIUS BY HANGING DROP VAPOR DIFFUSION. A 2-MICROLITER SOLUTION (10 MG/ML IN 50 MM TRIS-HCL AT PH 8.0 AND 0.1 M NACL) WAS MIXED WITH A 2-MICROLITER RESERVOIR SOLUTION CONTAINING 22% PEGMME 5K AND 10% GLYCEROL IN 0.1 M HEPES AT PH 6.5.
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
250 mMTris-HCl1droppH8.0
30.1 M1dropNaCl
422 %(w/v)PEG5000 MME1reservoir
510 %(v/v)glycerol1reservoir
60.1 MHEPES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.9796, 0.9794, 0.9680, 0.9802
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97941
30.9681
40.98021
ReflectionResolution: 2→31 Å / Num. obs: 50147 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 6.5 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 8
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 1.9 / % possible all: 98.8
Reflection
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
CNS1refinement
DPSdata reduction
MOSFLMdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→22.42 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2669990.65 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.23 7786 9.7 %RANDOM
Rwork0.186 ---
obs0.186 79906 80.5 %-
Displacement parametersBiso mean: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1-7.11 Å20 Å2-1.7 Å2
2---3.1 Å20 Å2
3----4.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→22.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5890 0 87 670 6647
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.681.5
X-RAY DIFFRACTIONc_mcangle_it5.712
X-RAY DIFFRACTIONc_scbond_it11.542
X-RAY DIFFRACTIONc_scangle_it11.972.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 1010 10.1 %
Rwork0.229 8981 -
obs--60.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
X-RAY DIFFRACTION4GDP.PARGDP.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 31 Å / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.97
LS refinement shell
*PLUS
Rfactor Rfree: 0.254 / Rfactor obs: 0.23

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