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- PDB-3ds8: The crystal structure of the gene lin2722 products from Listeria ... -

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Basic information

Entry
Database: PDB / ID: 3ds8
TitleThe crystal structure of the gene lin2722 products from Listeria innocua
ComponentsLin2722 protein
Keywordsstructural genomics / unknown function / Unkonwn function / lin2722 / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homologyProtein of unknown function DUF915, hydrolase-like / Alpha/beta hydrolase of unknown function (DUF915) / Alpha/Beta hydrolase fold, catalytic domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Lin2722 protein
Function and homology information
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsZhang, R. / Wu, R. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crysatl structure of the gene lin2722 products from Listeria innocua
Authors: Zhang, R. / Wu, R. / Freeman, L. / Joachimiak, A.
History
DepositionJul 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jun 22, 2022Group: Database references / Derived calculations / Structure summary
Category: database_2 / struct ...database_2 / struct / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lin2722 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1986
Polymers28,7181
Non-polymers4805
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.211, 63.211, 163.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Detailsauthors state that the protein does not complexate in solution

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Components

#1: Protein Lin2722 protein


Mass: 28718.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Strain: Clip11262 / Gene: lin2722 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q927R6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 10% Glycerol, 20.5% PEK4000, 0.065M tris_Na Citrate, 0.1M NH4 acetate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2008 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.8→49.94 Å / Num. all: 29987 / Num. obs: 29792 / % possible obs: 99.35 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 17 % / Biso Wilson estimate: 15.02 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 31.68
Reflection shellResolution: 1.8→1.847 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2270 / % possible all: 95.29

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→49.94 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.532 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.106 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20373 1591 5.1 %RANDOM
Rwork0.16793 ---
obs0.16973 29792 99.35 %-
all-29987 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.844 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 25 321 2328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222057
X-RAY DIFFRACTIONr_bond_other_d0.0010.021372
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.9812789
X-RAY DIFFRACTIONr_angle_other_deg1.00833382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0565254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29426.02293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28215362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.504155
X-RAY DIFFRACTIONr_chiral_restr0.110.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022264
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02374
X-RAY DIFFRACTIONr_nbd_refined0.2240.2441
X-RAY DIFFRACTIONr_nbd_other0.20.21481
X-RAY DIFFRACTIONr_nbtor_refined0.180.21005
X-RAY DIFFRACTIONr_nbtor_other0.0890.2997
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2285
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3260.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2990.224
X-RAY DIFFRACTIONr_mcbond_it1.7211.51534
X-RAY DIFFRACTIONr_mcbond_other0.3171.5512
X-RAY DIFFRACTIONr_mcangle_it1.69322046
X-RAY DIFFRACTIONr_scbond_it3.5583904
X-RAY DIFFRACTIONr_scangle_it4.7694.5743
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 106 -
Rwork0.187 2057 -
obs-2163 95.29 %
Refinement TLS params.Method: refined / Origin x: 23.4573 Å / Origin y: 2.6299 Å / Origin z: 55.6975 Å
111213212223313233
T-0.0296 Å2-0.0053 Å2-0.0111 Å2--0.0524 Å2-0.0097 Å2---0.038 Å2
L0.7002 °2-0.123 °20.214 °2-0.9344 °20.0704 °2--0.9524 °2
S-0.0297 Å °0.0183 Å °0.0053 Å °0.0184 Å °0.009 Å °-0.0261 Å °-0.0394 Å °0.0694 Å °0.0207 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 503 - 50
2X-RAY DIFFRACTION1AA51 - 10051 - 100
3X-RAY DIFFRACTION1AA101 - 150101 - 150
4X-RAY DIFFRACTION1AA151 - 200151 - 200
5X-RAY DIFFRACTION1AA201 - 254201 - 254

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