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- PDB-2e7p: Crystal structure of the holo form of glutaredoxin C1 from populu... -

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Basic information

Entry
Database: PDB / ID: 2e7p
TitleCrystal structure of the holo form of glutaredoxin C1 from populus tremula x tremuloides
ComponentsGlutaredoxin
KeywordsELECTRON TRANSPORT / THIOREDOXIN FOLD / GLUTAREDOXIN / POPLAR
Function / homology
Function and homology information


glutathione disulfide oxidoreductase activity / 2 iron, 2 sulfur cluster binding / cellular response to oxidative stress / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
Glutaredoxin subgroup / Glutaredoxin, eukaryotic/virial / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / GLUTATHIONE / Glutaredoxin
Similarity search - Component
Biological speciesPopulus tremula x Populus tremuloides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsUnno, H. / Takahashi, T. / Kawakami, T. / Aimoto, S. / Hase, T. / Kusunoki, M. / Rouhier, N. / Jacquot, J.P.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Functional, structural, and spectroscopic characterization of a glutathione-ligated [2Fe-2S] cluster in poplar glutaredoxin C1
Authors: Rouhier, N. / Unno, H. / Bandyopadhyay, S. / Masip, L. / Kim, S.K. / Hirasawa, M. / Gualberto, J.M. / Lattard, V. / Kusunoki, M. / Knaff, D.B. / Georgiou, G. / Hase, T. / Johnson, M.K. / Jacquot, J.P.
History
DepositionJan 12, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Dec 7, 2011Group: Non-polymer description
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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: Glutaredoxin
B: Glutaredoxin
C: Glutaredoxin
D: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1469
Polymers49,7414
Non-polymers1,4055
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-55 kcal/mol
Surface area21400 Å2
MethodPISA
2
A: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9183
Polymers12,4351
Non-polymers4832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7432
Polymers12,4351
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
C: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7432
Polymers12,4351
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
D: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7432
Polymers12,4351
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)97.774, 97.774, 91.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Glutaredoxin


Mass: 12435.191 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-116
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus tremula x Populus tremuloides (plant)
Plasmid: PET-3D / Production host: Escherichia coli (E. coli) / References: UniProt: Q5PSJ1
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% PEG6000, 0.1M CITRIC ACID, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
2951
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44XU10.9
SYNCHROTRONPhoton Factory BL-5A21.7399, 1.7415, 1.6000
Detector
TypeIDDetectorDate
BRUKER DIP-6040B1IMAGE PLATEOct 29, 2004
ADSC QUANTUM 3152CCDNov 6, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
21.73991
31.74151
41.61
ReflectionResolution: 2.1→50 Å / Num. obs: 28968 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.062
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.345 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→24.75 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.558 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22039 1469 5.1 %RANDOM
Rwork0.18406 ---
obs0.18591 27449 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.617 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 0 84 293 3639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223394
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9924565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0565430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16925.725131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97415590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1871512
X-RAY DIFFRACTIONr_chiral_restr0.0950.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022488
X-RAY DIFFRACTIONr_nbd_refined0.1980.21579
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22287
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2301
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.225
X-RAY DIFFRACTIONr_mcbond_it0.8991.52211
X-RAY DIFFRACTIONr_mcangle_it1.43823418
X-RAY DIFFRACTIONr_scbond_it3.1431330
X-RAY DIFFRACTIONr_scangle_it3.5554.51147
LS refinement shellResolution: 2.102→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 120 -
Rwork0.209 1992 -
obs--98.51 %

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