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- PDB-4puh: Oxidized BolA2 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 4puh
TitleOxidized BolA2 from Arabidopsis thaliana
ComponentsAt5g09830
KeywordsPROTEIN BINDING / stress-responsive protein / transcriptional regulator / morphogen
Function / homology
Function and homology information


response to iron ion / protein maturation / 2 iron, 2 sulfur cluster binding / response to oxidative stress / intracellular iron ion homeostasis / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
BolA-like protein 2 / BolA-like / BolA protein / BolA-like superfamily / BolA-like protein / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 Å
AuthorsRoret, T. / Didierjean, C.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural and spectroscopic insights into BolA-glutaredoxin complexes.
Authors: Roret, T. / Tsan, P. / Couturier, J. / Zhang, B. / Johnson, M.K. / Rouhier, N. / Didierjean, C.
History
DepositionMar 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 20, 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 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED THROUGH ELECTRON DENSITY AND D2O EXCHANGE EXPERIMENTS. ...SHEET DETERMINATION METHOD: AUTHOR DETERMINED THROUGH ELECTRON DENSITY AND D2O EXCHANGE EXPERIMENTS.THE SHEET STRUCTURE OF THIS MOLECULE IS NOT A 3 STRANDS BETA-SHEET BUT A 4 STRANDS BETA-SHEET IN WHICH STRAND 3 IS SPLITTED INTO STRANDS 3 AND 4. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORD BELOW, TWO SHEETS ARE DEFINED. STRANDS 1, 2, 3 AND 4 OF SHEET *A* AND *B* ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: At5g09830
B: At5g09830


Theoretical massNumber of molelcules
Total (without water)20,7802
Polymers20,7802
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-5 kcal/mol
Surface area9730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.640, 81.419, 33.112
Angle α, β, γ (deg.)90.00, 108.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein At5g09830 / BolA-like family protein / Putative uncharacterized protein At5g09830


Mass: 10389.839 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT5G09830, At5g09830 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FIC3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 1.82 Å3/Da / Density % sol: 32.49 %
Crystal growTemperature: 278 K / Method: oil microbatch method / pH: 8.5
Details: 30% PEG1000, pH 8.5, Oil microbatch method, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979733 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2013
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979733 Å / Relative weight: 1
ReflectionResolution: 1.898→40.71 Å / Num. all: 11470 / Num. obs: 11470 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.2
Reflection shellResolution: 1.898→2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 4 / Num. unique all: 1395 / % possible all: 80.8

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Processing

Software
NameVersionClassification
Xnemodata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4PUG

4pug


Resolution: 1.898→31.378 Å / SU ML: 0.19 / σ(F): 0 / σ(I): 0 / Phase error: 21.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2042 539 4.7 %RANDOM
Rwork0.1775 ---
all0.1788 11470 --
obs0.1788 11470 96.95 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.067 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.5749 Å20 Å2-10.5735 Å2
2---0.5416 Å20 Å2
3----3.0334 Å2
Refinement stepCycle: LAST / Resolution: 1.898→31.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1278 0 0 194 1472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071299
X-RAY DIFFRACTIONf_angle_d1.0411744
X-RAY DIFFRACTIONf_dihedral_angle_d14.248508
X-RAY DIFFRACTIONf_chiral_restr0.067198
X-RAY DIFFRACTIONf_plane_restr0.004224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8981-2.08910.24171260.2152477X-RAY DIFFRACTION88
2.0891-2.39130.23541470.19912791X-RAY DIFFRACTION100
2.3913-3.01230.2181280.18952835X-RAY DIFFRACTION100
3.0123-31.38250.17881380.15582814X-RAY DIFFRACTION100
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)
13.80590.88263.93143.80032.99885.69050.5975-0.23490.17750.8059-0.4258-0.29620.90950.1393-0.02620.37240.0095-0.05660.2420.03460.28918.4386-3.550611.8561
22.37211.74071.80523.41972.65063.8950.04650.1709-0.1329-0.01310.3088-0.4090.01850.4997-0.32610.21170.01840.00390.2427-0.03490.227521.39661.35735.4724
37.3395-2.3474-1.06447.26130.31195.27240.05650.6468-0.3644-0.2115-0.2481.36360.3342-0.39730.29440.1588-0.06140.00950.2342-0.03290.35274.4852-3.4801-0.6073
41.1397-0.57630.41072.3221-0.37983.40030.1648-0.06480.1390.2438-0.29820.3760.0621-0.3824-0.02170.1445-0.03570.06660.2138-0.02660.22666.47982.9045.9641
51.014-0.0827-1.72447.8933-1.83443.55150.4636-0.8769-0.08691.4275-0.6063-0.1219-0.0567-0.71370.0730.3578-0.1351-0.01070.38480.03390.196715.54865.794716.8049
62.27912.30452.18694.0652.90983.0932-0.3090.33240.2605-0.30280.11190.0746-0.36650.2713-0.16780.11960.00190.02270.1731-0.00350.240115.50435.05711.4108
72.6623-0.0621-0.46682.7904-0.17224.0096-0.16770.7487-0.4816-1.0305-0.02370.38570.4918-0.36260.09120.32580.03090.03070.294-0.02240.239812.2168-5.337-8.9907
81.72530.28721.35623.99451.94786.2952-0.3868-0.1240.3242-0.363-0.2760.0681-0.703-0.70630.44390.31730.0872-0.05050.2615-0.00940.301626.316622.298828.8607
91.94830.76330.40024.19043.32294.3402-0.23640.29250.04610.06430.00920.0268-0.14030.02580.13660.2741-0.0488-0.00360.20780.02820.202733.482818.974227.7556
101.8982.29123.0064.06354.94187.0902-0.15530.25110.11320.2027-0.1058-0.10450.08890.40020.09040.23890.00480.00530.180.01460.187234.432416.91331.4843
112.8494-0.0852-0.32433.34280.10713.40540.1695-0.24730.25640.4413-0.35760.4677-0.2432-0.46630.05480.2148-0.0050.06690.2233-0.04280.206728.87417.497543.9717
122.8808-0.54010.93584.80920.49950.39840.37290.347-0.2207-0.6468-1.00191.5661-0.3267-0.97930.42860.2470.0046-0.05710.4089-0.07760.43421.867312.323228.5897
130.4550.67561.062.71572.93743.6372-0.12860.19160.0235-0.25620.3324-0.3298-0.39130.3853-0.14820.2186-0.02350.05320.1984-0.01390.179635.408614.60135.5437
145.30810.91390.30912.07890.62410.18770.09620.02040.15270.7342-0.0357-0.6931-0.89251.01650.07570.4232-0.1651-0.07350.34570.03050.298541.880225.235244.0857
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and ( resseq 2:15 )A2 - 15
2X-RAY DIFFRACTION2chain A and ( resseq 16:38 )A16 - 38
3X-RAY DIFFRACTION3chain A and ( resseq 39:46 )A39 - 46
4X-RAY DIFFRACTION4chain A and ( resseq 47:57 )A47 - 57
5X-RAY DIFFRACTION5chain A and ( resseq 58:66 )A58 - 66
6X-RAY DIFFRACTION6chain A and ( resseq 67:74 )A67 - 74
7X-RAY DIFFRACTION7chain A and ( resseq 75:82 )A75 - 82
8X-RAY DIFFRACTION8chain B and ( resseq 2:15 )B2 - 15
9X-RAY DIFFRACTION9chain B and ( resseq 16:31 )B16 - 31
10X-RAY DIFFRACTION10chain B and ( resseq 32:38 )B32 - 38
11X-RAY DIFFRACTION11chain B and ( resseq 39:57 )B39 - 57
12X-RAY DIFFRACTION12chain B and ( resseq 58:66 )B58 - 66
13X-RAY DIFFRACTION13chain B and ( resseq 67:74 )B67 - 74
14X-RAY DIFFRACTION14chain B and ( resseq 75:82 )B75 - 82

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