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- PDB-1ylx: Crystal Structure of a Protein of Unknown Function from Bacillus ... -

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Basic information

Entry
Database: PDB / ID: 1ylx
TitleCrystal Structure of a Protein of Unknown Function from Bacillus stearothermophilus
Componentshypothetical protein APC35702
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / Bacillus stearothermophilus / dimer / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyGK1464-like / GK1464-like / GK1464-like domain / Family of unknown function (DUF5634) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / GK1464-like domain-containing protein
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsMidwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of APC35702, a hypothetical protein from Bacillus stearothermophilus
Authors: Duke, N.E.C. / Moy, S. / Li, H. / Collart, F. / Joachimiak, A.
History
DepositionJan 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 999SEQUENCE THERE IS NO SUITABLE SEQUENCE DATABASE REFERENCE AT THE TIME OF PROCESSING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein APC35702
B: hypothetical protein APC35702


Theoretical massNumber of molelcules
Total (without water)24,5882
Polymers24,5882
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.189, 70.156, 81.361
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 APC35702


Mass: 12293.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5KZY7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.08 Å3/Da / Density % sol: 38.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, calcium chloride, bis-tris pH 6.5, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 2004 / Details: double crystal monochromator (Si 111) plus mirror
RadiationMonochromator: double crystal monochromator (Si 111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 49668 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.079
Reflection shellResolution: 1.6→1.66 Å / % possible all: 94.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
Omodel building
Cootmodel building
CCP4phasing
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→40.68 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2126460.88 / 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
Rfree0.247 4613 9.7 %RANDOM
Rwork0.229 ---
obs0.229 47316 94.7 %-
all-49964 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.6896 Å2 / ksol: 0.369162 e/Å3
Displacement parametersBiso mean: 19.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å20 Å2
2--3.06 Å20 Å2
3----4.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.6→40.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 0 89 1735
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.432
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_scangle_it3.682.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 623 9 %
Rwork0.288 6288 -
obs--82.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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