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- PDB-1s5a: Crystal Structure of Putative Isomerase from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 1s5a
TitleCrystal Structure of Putative Isomerase from Bacillus subtilis
ComponentsHypothetical protein yesE
KeywordsStructural Genomics / Unknown function / Hypothetical Protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologySnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / ACETATE ION / Uncharacterized protein YesE
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsKim, Y. / Lezondra, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The Crystal Structure of APC1116 from Bacillus subtilis
Authors: Kim, Y. / Lezondra, L. / Joachimiak, A.
History
DepositionJan 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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 / 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
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein yesE
B: Hypothetical protein yesE
C: Hypothetical protein yesE
D: Hypothetical protein yesE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,38914
Polymers70,6004
Non-polymers78910
Water9,728540
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.613, 55.725, 72.405
Angle α, β, γ (deg.)102.47, 99.98, 106.51
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Hypothetical protein yesE


Mass: 17650.088 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YESE, BSU06870 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: O31511
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: ammonium sulfate, PEG 4000, glycerol, sodium acetate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: SBC-3 / Detector: CCD / Date: Dec 14, 2003 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→34.08 Å / Num. all: 66676 / Num. obs: 64170 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 2.2 / % possible all: 71.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→34.08 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 385804.99 / 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
Rfree0.236 6392 10.2 %RANDOM
Rwork0.199 ---
all0.203 ---
obs0.199 62952 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.5508 Å2 / ksol: 0.389382 e/Å3
Displacement parametersBiso mean: 19.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å2-0.24 Å2-0.99 Å2
2--2.03 Å20.55 Å2
3----0.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.7→34.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4635 0 52 540 5227
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.741.5
X-RAY DIFFRACTIONc_mcangle_it2.442
X-RAY DIFFRACTIONc_scbond_it3.182
X-RAY DIFFRACTIONc_scangle_it4.662.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.361 854 10.2 %
Rwork0.31 7527 -
obs-8381 73.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4LIGAND.PARAMLIGAND.TOP

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