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- PDB-4uav: Crystal structure of CbbY (AT3G48420) from Arabidobsis thaliana -

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Basic information

Entry
Database: PDB / ID: 4uav
TitleCrystal structure of CbbY (AT3G48420) from Arabidobsis thaliana
ComponentsHaloacid dehalogenase-like hydrolase domain-containing protein At3g48420
KeywordsHYDROLASE / haloacid dehalogenase (HAD) hydrolase superfamily / phosphatase
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / chloroplast envelope / chloroplast stroma / chloroplast / hydrolase activity / metal ion binding / cytosol
Similarity search - Function
Protein CbbY-like / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold ...Protein CbbY-like / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsBracher, A. / Sharma, A. / Starling-Windhof, A. / Hartl, F.U. / Hayer-Hartl, M.
CitationJournal: Nat.Plants / Year: 2015
Title: Degradation of potent Rubisco inhibitor by selective sugar phosphatase.
Authors: Bracher, A. / Sharma, A. / Starling-Windhof, A. / Hartl, F.U. / Hayer-Hartl, M.
History
DepositionAug 11, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Haloacid dehalogenase-like hydrolase domain-containing protein At3g48420
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8032
Polymers26,7791
Non-polymers241
Water6,792377
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-8 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.725, 140.041, 87.107
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-518-

HOH

21A-553-

HOH

31A-585-

HOH

41A-599-

HOH

Detailsbiological unit is a monomer

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Components

#1: Protein Haloacid dehalogenase-like hydrolase domain-containing protein At3g48420


Mass: 26778.793 Da / Num. of mol.: 1 / Fragment: UNP residues 74-319
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g48420, T29H11.60 / Plasmid: pHue / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q94K71, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25 % (wt/vol) PEG-6000 and 0.1 M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→70.021 Å / Num. all: 70347 / Num. obs: 70347 / % possible obs: 97.9 % / Redundancy: 3.7 % / Rpim(I) all: 0.029 / Rrim(I) all: 0.058 / Rsym value: 0.049 / Net I/av σ(I): 9.566 / Net I/σ(I): 13.2 / Num. measured all: 257575
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.3-1.373.60.6241.23588598770.370.6242.195.3
1.37-1.453.60.4061.93450796030.2420.4063.197.6
1.45-1.553.70.25833394990860.150.2584.998.3
1.55-1.683.60.1624.73037285140.0970.1627.198.3
1.68-1.843.80.10872997578660.0620.10810.498.7
1.84-2.053.60.067112559470920.040.06716.298.2
2.05-2.373.80.04714.52377962950.0280.04723.898.2
2.37-2.913.60.03717.61929953780.0230.03728.998.8
2.91-4.113.70.02721.61575142210.0160.02739.998.5
4.11-45.1743.50.02320.9846424150.0140.02341.298.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å45.17 Å
Translation3 Å45.17 Å

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
MOLREP10.2.35phasing
PDB_EXTRACT3.14data extraction
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4UAR

4uar


Resolution: 1.3→30 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.1673 / WRfactor Rwork: 0.1331 / FOM work R set: 0.9146 / SU B: 1.431 / SU ML: 0.027 / SU R Cruickshank DPI: 0.0406 / SU Rfree: 0.0426 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.172 3530 5 %RANDOM
Rwork0.1363 66619 --
obs0.1381 70149 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.61 Å2 / Biso mean: 17.581 Å2 / Biso min: 7.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å2-0 Å2
2---0.54 Å2-0 Å2
3---1.1 Å2
Refinement stepCycle: final / Resolution: 1.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 1 377 2244
Biso mean--9.57 32.76 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191952
X-RAY DIFFRACTIONr_bond_other_d0.0010.021902
X-RAY DIFFRACTIONr_angle_refined_deg2.0861.9862651
X-RAY DIFFRACTIONr_angle_other_deg0.97434408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5445257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17825.06577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15715344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.351159
X-RAY DIFFRACTIONr_chiral_restr0.1450.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212220
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02397
X-RAY DIFFRACTIONr_rigid_bond_restr6.64533854
X-RAY DIFFRACTIONr_sphericity_free30.4125100
X-RAY DIFFRACTIONr_sphericity_bonded10.9754093
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 246 -
Rwork0.248 4693 -
all-4939 -
obs--94.6 %

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