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- PDB-4uar: Crystal structure of apo-CbbY from Rhodobacter sphaeroides -

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Basic information

Entry
Database: PDB / ID: 4uar
TitleCrystal structure of apo-CbbY from Rhodobacter sphaeroides
ComponentsProtein CbbY
KeywordsHYDROLASE / haloacid dehalogenase (HAD) hydrolase superfamily / phosphatase
Function / homology
Function and homology information


xylulose catabolic process / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / hydrolase activity / magnesium ion binding
Similarity search - Function
Protein CbbY-like / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 ...Protein CbbY-like / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / 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 speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / SIRAS / Resolution: 1.9 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein CbbY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2442
Polymers25,1521
Non-polymers921
Water2,630146
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint0 kcal/mol
Surface area10100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.685, 117.685, 43.994
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Detailsbiological unit is the same as asym.

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Components

#1: Protein Protein CbbY


Mass: 25151.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: cbbY / Plasmid: pHue / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P95649
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 16-20 % PEG-6000 and 0.1 M Hepes-NaOH pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97138 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97141
20.971381
ReflectionRedundancy: 13.4 % / Number: 101392 / Rsym value: 0.151 / D res high: 2.796 Å / D res low: 41.734 Å / Num. obs: 7592 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
8.8441.7310.0590.05912.2
6.258.8410.0840.08412.9
5.16.2510.1090.10913.7
4.425.110.0970.09713.2
3.954.4210.1130.11313.6
3.613.9510.1450.14513.9
3.343.6110.1940.19413
3.133.3410.2760.27613.7
2.953.1310.3870.38714
2.82.9510.4830.48312.7
ReflectionResolution: 1.9→41.608 Å / Num. all: 24048 / Num. obs: 24048 / % possible obs: 99.8 % / Redundancy: 6.5 % / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Rsym value: 0.05 / Net I/av σ(I): 10.75 / Net I/σ(I): 19.5 / Num. measured all: 156631
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-25.20.37621813734580.2020.3763.499
2-2.126.90.2393.22259432870.1070.2396.3100
2.12-2.276.60.164.72069231120.0740.169.1100
2.27-2.456.80.1136.51981129100.0510.11312.6100
2.45-2.686.80.0828.81812226620.0370.08217.2100
2.68-36.60.05712.21601524100.0260.05723.9100
3-3.476.80.04116.11471821600.0180.04134.7100
3.47-4.246.70.03119.41206218080.0140.03145.8100
4.24-66.50.0319.5924314280.0140.0348.399.9
6-41.6086.40.02819.452378130.0130.02850.699.8

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Phasing

PhasingMethod: SIRAS
Phasing dmFOM : 0.52 / FOM acentric: 0.51 / FOM centric: 0.85 / Reflection: 22898 / Reflection acentric: 22221 / Reflection centric: 677
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.4-41.6080.930.940.891098913185
3.4-5.40.930.930.9132452959286
2.7-3.40.790.80.7139623756206
2.4-2.70.560.5637903790
2-2.40.310.3167606760
1.9-20.110.1140434043

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
RESOLVE2.13model building
PDB_EXTRACT3.14data extraction
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
XSCALEdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2215 / WRfactor Rwork: 0.1963 / FOM work R set: 0.8583 / SU B: 2.899 / SU ML: 0.086 / SU R Cruickshank DPI: 0.1347 / SU Rfree: 0.1241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 1199 5 %RANDOM
Rwork0.1989 22783 --
obs0.2001 23982 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 75.07 Å2 / Biso mean: 28.125 Å2 / Biso min: 16.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20 Å2
2---0.99 Å20 Å2
3---1.97 Å2
Refinement stepCycle: final / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1724 0 6 146 1876
Biso mean--30.63 35.37 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221762
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.9792385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3955224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75222.37580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84215287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2071520
X-RAY DIFFRACTIONr_chiral_restr0.0730.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211347
X-RAY DIFFRACTIONr_mcbond_it0.6191.51117
X-RAY DIFFRACTIONr_mcangle_it1.19421773
X-RAY DIFFRACTIONr_scbond_it2.0633645
X-RAY DIFFRACTIONr_scangle_it3.5464.5612
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 87 -
Rwork0.246 1641 -
all-1728 -
obs--100 %

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