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- PDB-3ipz: Crystal structure of Arabidopsis monothiol glutaredoxin AtGRXcp -

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Basic information

Entry
Database: PDB / ID: 3ipz
TitleCrystal structure of Arabidopsis monothiol glutaredoxin AtGRXcp
ComponentsMonothiol glutaredoxin-S14, chloroplastic
KeywordsELECTRON TRANSPORT / OXIDOREDUCTASE / glutaredoxin / monothiol / Chloroplast / Plastid / Redox-active center / Transit peptide / Transport
Function / homology
Function and homology information


chloroplast envelope / antiporter activity / chloroplast stroma / monoatomic cation transport / chloroplast / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
Monothiol glutaredoxin-related / Glutaredoxin, PICOT-like / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Monothiol glutaredoxin-S14, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLi, L. / Cheng, N. / Wang, X.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structure of Arabidopsis chloroplastic monothiol glutaredoxin AtGRXcp.
Authors: Li, L. / Cheng, N. / Hirschi, K.D. / Wang, X.
History
DepositionAug 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Monothiol glutaredoxin-S14, chloroplastic


Theoretical massNumber of molelcules
Total (without water)12,3541
Polymers12,3541
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Monothiol glutaredoxin-S14, chloroplastic

A: Monothiol glutaredoxin-S14, chloroplastic

A: Monothiol glutaredoxin-S14, chloroplastic


Theoretical massNumber of molelcules
Total (without water)37,0623
Polymers37,0623
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area2700 Å2
ΔGint-22 kcal/mol
Surface area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.404, 81.404, 55.438
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Monothiol glutaredoxin-S14, chloroplastic / AtGrxS14 / AtGRXcp / CAX-interacting protein 1 / CXIP1


Mass: 12354.149 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GRXS14, CXIP1, At3g54900, F28P10.120 / Plasmid: pET41a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q84Y95
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
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: 4.29 Å3/Da / Density % sol: 71.34 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.5
Details: 10% MPD, 1.0M PBS, pH 8.5, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 22, 2007 / Details: Blue Max-Flux Confocal Optical
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. all: 8608 / Num. obs: 8608 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 21.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.9 / Num. unique all: 833 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YKA

1yka


Resolution: 2.4→24.02 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 163876.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.226 893 10.7 %RANDOM
Rwork0.191 ---
obs0.191 8345 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.4796 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 46 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20 Å2
2--1.21 Å20 Å2
3----2.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.4→24.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms865 0 0 84 949
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.84
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 136 10.4 %
Rwork0.249 1171 -
obs--94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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