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- PDB-3k7x: Crystal structure of the Lin0763 protein from Listeria innocua. N... -

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Basic information

Entry
Database: PDB / ID: 3k7x
TitleCrystal structure of the Lin0763 protein from Listeria innocua. Northeast Structural Genomics Consortium Target LkR23.
ComponentsLin0763 protein
Keywordsstructural genomics / unknown function / Lin0763 / Q92DQ0 / LkR23 / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Predicted O-glycosyl hydrolase / Glycoside hydrolase, family 76 / Glycosyl hydrolase family 76 / Glycosyltransferase - #20 / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Lin0763 protein
Similarity search - Component
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.889 Å
AuthorsVorobiev, S. / Su, M. / Seetharaman, J. / Maglaqui, M. / Ciccosanti, C. / Buchwald, W.A. / Sahdev, S. / Xiao, R. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S. / Su, M. / Seetharaman, J. / Maglaqui, M. / Ciccosanti, C. / Buchwald, W.A. / Sahdev, S. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the Lin0763 protein from Listeria innocua.
Authors: Vorobiev, S. / Su, M. / Seetharaman, J. / Maglaqui, M. / Ciccosanti, C. / Buchwald, W.A. / Sahdev, S. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionOct 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Lin0763 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5252
Polymers41,4301
Non-polymers951
Water8,125451
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.194, 75.333, 53.756
Angle α, β, γ (deg.)90.00, 95.28, 90.00
Int Tables number4
Space group name H-MP1211
Detailsmonomer according to aggregation screening

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Components

#1: Protein Lin0763 protein


Mass: 41430.105 Da / Num. of mol.: 1 / Mutation: K233I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Gene: lin0763 / Plasmid: pET 21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) +Magic / References: UniProt: Q92DQ0
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 291 K / Method: microbatch under paraffin oil / pH: 10
Details: 40% PEG 8000, 0.1M KH2PO4, 0.1M CAPS, pH 10.0, MICROBATCH UNDER PARAFFIN OIL, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97879 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97879 Å / Relative weight: 1
ReflectionResolution: 1.889→50 Å / Num. all: 57664 / Num. obs: 56453 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 13.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5773 / % possible all: 84.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SnBphasing
RESOLVEmodel building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.889→33.4 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1843 2874 5.1 %RANDOM
Rwork0.1674 ---
obs0.1683 56348 97.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.43 Å2 / ksol: 0.333 e/Å3
Refinement stepCycle: LAST / Resolution: 1.889→33.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2876 0 5 451 3332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062958
X-RAY DIFFRACTIONf_angle_d1.1744011
X-RAY DIFFRACTIONf_dihedral_angle_d19.1061039
X-RAY DIFFRACTIONf_chiral_restr0.087415
X-RAY DIFFRACTIONf_plane_restr0.007510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8886-1.91960.2171150.26461891X-RAY DIFFRACTION72
1.9196-1.95270.26951220.23852223X-RAY DIFFRACTION87
1.9527-1.98820.22891300.21752463X-RAY DIFFRACTION93
1.9882-2.02640.26361160.20412505X-RAY DIFFRACTION97
2.0264-2.06780.27481270.21192644X-RAY DIFFRACTION100
2.0678-2.11270.20951250.19092640X-RAY DIFFRACTION100
2.1127-2.16190.17041440.16622598X-RAY DIFFRACTION100
2.1619-2.21590.18641540.16652610X-RAY DIFFRACTION100
2.2159-2.27580.18261400.17142585X-RAY DIFFRACTION100
2.2758-2.34280.20251310.16242630X-RAY DIFFRACTION100
2.3428-2.41840.17731390.16222638X-RAY DIFFRACTION100
2.4184-2.50480.18821170.1542637X-RAY DIFFRACTION100
2.5048-2.6050.15291230.15372606X-RAY DIFFRACTION100
2.605-2.72350.18691440.17262645X-RAY DIFFRACTION100
2.7235-2.86710.18451550.17312568X-RAY DIFFRACTION100
2.8671-3.04660.18241670.16352598X-RAY DIFFRACTION100
3.0466-3.28160.18291370.16342639X-RAY DIFFRACTION100
3.2816-3.61150.16071470.15342583X-RAY DIFFRACTION100
3.6115-4.13330.13331530.13532616X-RAY DIFFRACTION100
4.1333-5.20430.14571340.12892602X-RAY DIFFRACTION99
5.2043-33.40520.15691540.14672553X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 3.9187 Å / Origin y: 51.9978 Å / Origin z: 41.2935 Å
111213212223313233
T0.0187 Å20.0046 Å20.0005 Å2-0.0155 Å20.0065 Å2--0.0214 Å2
L0.2009 °2-0.0582 °20.0179 °2-0.197 °2-0.0407 °2--0.2028 °2
S0.014 Å °-0.0043 Å °-0.0001 Å °-0.0141 Å °-0.014 Å °-0.0087 Å °0.0039 Å °-0 Å °-0 Å °
Refinement TLS groupSelection details: chain A

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