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- PDB-3f5d: Crystal Structure of a protein of unknown function from Bacillus ... -

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Basic information

Entry
Database: PDB / ID: 3f5d
TitleCrystal Structure of a protein of unknown function from Bacillus subtilis
Componentsprotein YdeA
Keywordsstructural genomics / unknown function / Unknow protein / Bacillus subtilis / PSI-II / NYSGRC / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Hydrolases; Glycosylases / peptidase activity / proteolysis / cytoplasm
Similarity search - Function
DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protease YdeA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.06 Å
AuthorsSugadev, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of a protein of unknown function from Bacillus subtilis
Authors: Sugadev, R. / Burley, S.K. / Swaminathan, S.
History
DepositionNov 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: protein YdeA


Theoretical massNumber of molelcules
Total (without water)23,8581
Polymers23,8581
Non-polymers00
Water2,288127
1
A: protein YdeA

A: protein YdeA


Theoretical massNumber of molelcules
Total (without water)47,7162
Polymers47,7162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3050 Å2
ΔGint-20 kcal/mol
Surface area16650 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.597, 72.500, 47.560
Angle α, β, γ (deg.)90.00, 124.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein protein YdeA


Mass: 23858.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: BL21(DE3) / Gene: ydeA, BSU05110 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: P96658
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES 7.5, 20%PEG4000, 25% Iso-propanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 29, 2008 / Details: Mirror
RadiationMonochromator: Si(111)channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. all: 12920 / Num. obs: 12920 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 28.8
Reflection shellResolution: 2.06→2.13 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 2 / Num. unique all: 1120 / % possible all: 83.9

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXmodel building
SHARPphasing
ARPmodel building
WARPmodel building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.06→36.25 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 224649.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 517 4.2 %RANDOM
Rwork0.213 ---
all0.239 12920 --
obs0.213 12412 94.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.3499 Å2 / ksol: 0.341256 e/Å3
Displacement parametersBiso mean: 30.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å25.19 Å2
2---1.58 Å20 Å2
3---1.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.06→36.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 0 127 1679
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it2.862.5
LS refinement shellResolution: 2.06→2.19 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.287 65 3.4 %
Rwork0.26 1863 -
obs--88 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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