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- PDB-1g2r: Structure of Cytosolic Protein of Unknown Function Coded by Gene ... -

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Basic information

Entry
Database: PDB / ID: 1g2r
TitleStructure of Cytosolic Protein of Unknown Function Coded by Gene from NUSA/INFB Region, a YlxR Homologue
ComponentsHYPOTHETICAL CYTOSOLIC PROTEIN
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical / NusA-InfB operon / Streptococcus pneumoniae / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


YlxR-like / YlxR domain / YlxR-like superfamily / YlxR / Protein of unknown function (DUF448) / Hypothetical Cytosolic Protein; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
YlxR domain-containing protein / YlxR domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.35 Å
AuthorsOsipiuk, J. / Gornicki, P. / Maj, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Streptococcus pneumonia YlxR at 1.35 A shows a putative new fold.
Authors: Osipiuk, J. / Gornicki, P. / Maj, L. / Dementieva, I. / Laskowski, R. / Joachimiak, A.
History
DepositionOct 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

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Assembly

Deposited unit
A: HYPOTHETICAL CYTOSOLIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8344
Polymers11,5451
Non-polymers2883
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.050, 48.750, 73.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HYPOTHETICAL CYTOSOLIC PROTEIN


Mass: 11545.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q97S59, UniProt: A0A0H2UNW2*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M potassium sodium tartrate, 0.1 M tri-sodium citrate, 2.0 M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mMprotein1drop
210 mMTris-HCl1drop
320 mM1dropNaCl
41 mMdithiothreitol1drop
50.2 Mpotassium sodium tartrate1reservoir
6100 mMsodium acetate1reservoir
72 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0332 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 15, 2000
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. all: 21402 / Num. obs: 101345 / % possible obs: 93.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 11.2
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 2.7 / Num. unique all: 684 / % possible all: 61.3
Reflection
*PLUS
Num. obs: 21402 / Num. measured all: 101345
Reflection shell
*PLUS
% possible obs: 61.3 %

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
CNSrefinement
REFMACrefinement
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.35→29.4 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 780502.53 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1846 1573 7.3 %RANDOM
Rwork0.1568 ---
all0.1564 21218 --
obs0.1564 21402 93.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.17 Å2 / ksol: 0.398 e/Å3
Displacement parametersBiso mean: 20.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.35→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms835 0 15 131 981
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_planar_d0.0340.05
LS refinement shellResolution: 1.35→1.42 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.229 169 8.2 %
Rwork0.185 2392 -
obs-1904 68 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 7.3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.4 Å2

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