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- PDB-1yav: Crystal structure of CBS domain-containing protein ykuL from Baci... -

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Basic information

Entry
Database: PDB / ID: 1yav
TitleCrystal structure of CBS domain-containing protein ykuL from Bacillus subtilis
Componentshypothetical protein BSU14130
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Cystathionine beta synthase (CBS) domain / Protein Structure Initiative / PSI / New York SGX Research Center for Structural Genomics / NYSGXRC / T1655 / Sulfur SAD Technique
Function / homology: / : / CBS-domain / CBS-domain / CBS domain superfamily / Roll / Alpha Beta / Cyclic di-AMP receptor B
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Sulfur SAD / Resolution: 2.1 Å
AuthorsKumaran, D. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of a hypothetical protein (ykul) containing CBS domains from Bacillus subtilis.
Authors: Kumaran, D. / Swaminathan, S.
History
DepositionDec 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details ..._audit_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein BSU14130
B: hypothetical protein BSU14130
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1223
Polymers36,0262
Non-polymers961
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-37 kcal/mol
Surface area13480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.564, 69.592, 70.903
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 protein BSU14130


Mass: 18012.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ykuL / Production host: Escherichia coli (E. coli) / References: UniProt: O31698
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.1 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium sulfate, Hepes, Xylitol, KCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.7 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jun 12, 2004 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 17293 / Num. obs: 17293 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 41.7 % / Biso Wilson estimate: 25.1 Å2 / Rsym value: 0.063 / Net I/σ(I): 16.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 17.2 % / Num. unique all: 1207 / Rsym value: 0.457 / % possible all: 67.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data scaling
SOLVEphasing
SHARPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: Sulfur SAD / Resolution: 2.1→38.41 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 400881.13 / 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
Rfree0.262 1173 6.9 %RANDOM
Rwork0.228 ---
obs0.228 17062 94.4 %-
all-17062 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.6304 Å2 / ksol: 0.391109 e/Å3
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2--1.52 Å20 Å2
3----2.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.1→38.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2131 0 5 72 2208
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 141 6.6 %
Rwork0.268 1988 -
obs--71.8 %

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