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- PDB-2odm: Crystal structure of S. aureus YlaN, an essential leucine rich pr... -

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Basic information

Entry
Database: PDB / ID: 2odm
TitleCrystal structure of S. aureus YlaN, an essential leucine rich protein involved in the control of cell shape
ComponentsUPF0358 protein MW0995
KeywordsUNKNOWN FUNCTION / triple helix
Function / homologyUncharacterised protein family UPF0358 / Protein of unknown function (DUF1507) / SO2669-like / UPF0358 superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / UPF0358 protein MW0995
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.24 Å
AuthorsXu, L. / Sedelnikova, S.E. / Baker, P.J. / Errington, J. / Hunt, A. / Rice, D.W.
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of S. aureus YlaN, an essential leucine rich protein involved in the control of cell shape.
Authors: Xu, L. / Sedelnikova, S.E. / Baker, P.J. / Hunt, A. / Errington, J. / Rice, D.W.
History
DepositionDec 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0358 protein MW0995
B: UPF0358 protein MW0995


Theoretical massNumber of molelcules
Total (without water)21,1132
Polymers21,1132
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-17 kcal/mol
Surface area10060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.425, 42.771, 62.593
Angle α, β, γ (deg.)90.00, 92.42, 90.00
Int Tables number4
Space group name H-MP1211
Detailsbiological dimer

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Components

#1: Protein UPF0358 protein MW0995 / YlaN


Mass: 10556.743 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: MW2 / Gene: ylaN / Plasmid: pETBLUE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7A161

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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: 1.99 Å3/Da / Density % sol: 38.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M Sodium acetate, 0.1M Tris-HCl pH 8.5, 20% PEG4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSRS PX10.110.98
SYNCHROTRONSRS PX9.621.5
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 26, 2005
RadiationMonochromator: double crystal Si(III) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
21.51
ReflectionResolution: 2.24→25 Å / Num. all: 7464 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 10.5
Reflection shellHighest resolution: 2.24 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1072 / Rsym value: 0.429 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SOLVEphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.24→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.566 / SU ML: 0.214 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.369 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28317 365 4.5 %RANDOM
Rwork0.22373 ---
obs0.22659 7464 99.16 %-
all-7464 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.86 Å2
Baniso -1Baniso -2Baniso -3
1--2.13 Å20 Å2-0.05 Å2
2---2.32 Å20 Å2
3---4.44 Å2
Refinement stepCycle: LAST / Resolution: 2.24→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1297 0 0 0 1297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221306
X-RAY DIFFRACTIONr_angle_refined_deg1.0312.0081748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.115158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.66526.83360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.89815279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.064154
X-RAY DIFFRACTIONr_chiral_restr0.0540.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02919
X-RAY DIFFRACTIONr_nbd_refined0.1860.2563
X-RAY DIFFRACTIONr_nbtor_refined0.2780.2912
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0670.220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.21
X-RAY DIFFRACTIONr_mcbond_it7.14110831
X-RAY DIFFRACTIONr_mcangle_it8.774101286
X-RAY DIFFRACTIONr_scbond_it8.94510514
X-RAY DIFFRACTIONr_scangle_it10.9710462
LS refinement shellResolution: 2.24→2.296 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 23 -
Rwork0.292 510 -
obs-1072 92.06 %

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