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- PDB-2qzu: Crystal structure of the putative sulfatase yidJ from Bacteroides... -

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Basic information

Entry
Database: PDB / ID: 2qzu
TitleCrystal structure of the putative sulfatase yidJ from Bacteroides fragilis. Northeast Structural Genomics Consortium target BfR123
ComponentsPutative sulfatase yidJ
KeywordsHYDROLASE / Q64XZ4_BACFR / Sulfatase / Arylsulfatase / yidJ / BfR123 / NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


sulfuric ester hydrolase activity
Similarity search - Function
Arylsulfatase, C-terminal domain - #10 / Sulfatases signature 1. / Sulfatase, conserved site / Arylsulfatase, C-terminal domain / Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 2-Layer Sandwich ...Arylsulfatase, C-terminal domain - #10 / Sulfatases signature 1. / Sulfatase, conserved site / Arylsulfatase, C-terminal domain / Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative sulfatase yidJ
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsVorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Wang, D. / Cunningham, K. / Maglaqui, M. / Owens, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Wang, D. / Cunningham, K. / Maglaqui, M. / Owens, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-ray crystal structure of the putative sulfatase yidJ from Bacteroides fragilis.
Authors: Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Wang, D. / Cunningham, K. / Maglaqui, M. / Owens, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionAug 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Remark 300 BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ... BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS A DIMER ACCORDING TO THE AGGREGATION SCREEN. THE ASSEMBLY SHOWN IN REMARK 350 IS PROPOSED BY AUTHORS BASED ON MOST CLOSE INTERMOLECULAR CONTACTS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative sulfatase yidJ


Theoretical massNumber of molelcules
Total (without water)57,2281
Polymers57,2281
Non-polymers00
Water8,233457
1
A: Putative sulfatase yidJ

A: Putative sulfatase yidJ


Theoretical massNumber of molelcules
Total (without water)114,4562
Polymers114,4562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_564-x+1/2,-y+1,z-1/21
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.894, 82.336, 89.359
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsDimer according to aggregation screen. Most close crystallographic contacts are with symmetry mate generated by -x+1/2,-y+1,z-1/2 operator.

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Components

#1: Protein Putative sulfatase yidJ


Mass: 57227.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: YCH46 / Gene: BF0881 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q64XZ4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.12 Å3/Da / Density % sol: 41.92 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 3350, 0.1M HEPES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 97617 / Num. obs: 97617 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 8.5 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 17.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 3.4 / Num. unique all: 10259 / % possible all: 96

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→37.39 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 137820.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used for phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.217 4185 4.9 %RANDOM
Rwork0.195 ---
obs0.195 84760 82.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.2331 Å2 / ksol: 0.31804 e/Å3
Displacement parametersBiso mean: 13.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å20 Å20 Å2
2---0.3 Å20 Å2
3----1.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.7→37.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3727 0 0 457 4184
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.221 638 5.3 %
Rwork0.208 11329 -
obs--69.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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