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- PDB-4rgi: Crystal Structure of KTSC Domain Protein YPO2434 from Yersinia pestis -

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Basic information

Entry
Database: PDB / ID: 4rgi
TitleCrystal Structure of KTSC Domain Protein YPO2434 from Yersinia pestis
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Chicago Center for Functional Annotation / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta sandwich
Function / homologyKTSC domain / KTSC domain / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.732 Å
AuthorsKim, Y. / Chhor, G. / Endres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of KTSC Domain Protein YPO2434 from Yersinia pestis
Authors: Kim, Y. / Chhor, G. / Endres, M. / Babnigg, G. / Joachimiak, A.
History
DepositionSep 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8825
Polymers8,5091
Non-polymers3724
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.166, 70.908, 55.846
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-222-

HOH

21A-244-

HOH

31A-257-

HOH

41A-261-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 8509.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: y1902, YPO2434, YP_2222 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 gold / References: UniProt: Q7CIU6, UniProt: A0A5P8YFX5*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 289 K / pH: 6
Details: 0.1 M MES pH 6.0, 1.26 M ammonium sulfate, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2013 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. all: 7880 / Num. obs: 7880 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 18.52 Å2 / Rsym value: 0.09 / Net I/σ(I): 14.36
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 1.58 / Num. unique all: 328 / Rsym value: 0.653 / % possible all: 83.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
DMmodel building
PHENIX(phenix.refine: dev_1745)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.732→29.932 Å / SU ML: 0.18 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.201 353 4.69 %random
Rwork0.174 ---
all0.176 7533 --
obs0.176 7533 92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.8 Å2
Refinement stepCycle: LAST / Resolution: 1.732→29.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms572 0 23 66 661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008627
X-RAY DIFFRACTIONf_angle_d1.111836
X-RAY DIFFRACTIONf_dihedral_angle_d15.311246
X-RAY DIFFRACTIONf_chiral_restr0.04781
X-RAY DIFFRACTIONf_plane_restr0.004109
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.732-1.98250.24711030.19422071217481
1.9825-2.49760.22621190.18942544266399
2.4976-29.93610.18121310.16292565269696
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9202-1.40130.5033.9227-0.75351.83650.17880.1961-0.62340.1654-0.19110.23670.31720.3730.05460.28890.0128-0.10840.1660.00560.28415.92586.46431.2488
23.5664-0.15580.7751.6838-0.44735.41470.2933-0.0195-0.5887-0.0449-0.09420.0640.7060.3809-0.02180.14410.0096-0.03370.08390.00480.151210.96986.39726.731
32.8338-0.9220.10731.84510.9531.40830.0714-0.0178-0.2091-0.0584-0.06330.0707-0.0263-0.0857-0.01070.1115-0.0072-0.0040.10420.01250.09559.887311.50755.6937
43.0048-0.46270.00281.47770.12871.65410.09010.08170.2016-0.1556-0.0636-0.158-0.04350.0531-0.00790.105-0.00460.00460.10410.02240.123212.928115.80343.9192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 27 )
3X-RAY DIFFRACTION3chain 'A' and (resid 28 through 48 )
4X-RAY DIFFRACTION4chain 'A' and (resid 49 through 70 )

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