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- PDB-1oq1: Crystal Structure of Protein of Unknown Function with Galectin-li... -

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Basic information

Entry
Database: PDB / ID: 1oq1
TitleCrystal Structure of Protein of Unknown Function with Galectin-like Fold from Bacillus subtilis
ComponentsProtein yesU
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Singleton / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyProtein of unknown function DUF1961 / Domain of unknown function (DUF1961) / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta / ACETIC ACID / Uncharacterized protein YesU
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: Crystal Structure of the Bacillus subtilis Hypothetical Protein APC1120
Authors: Kim, Y. / Lezondra, L. / Joachimiak, A.
History
DepositionMar 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 20, 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: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ...BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAINS. THE BIOLOGICAL MOLECULE MAY BE A DIMER OR TETRAMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein yesU
B: Protein yesU
C: Protein yesU
D: Protein yesU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,97710
Polymers103,5534
Non-polymers4246
Water17,997999
1
A: Protein yesU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0403
Polymers25,8881
Non-polymers1522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein yesU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9482
Polymers25,8881
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein yesU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9482
Polymers25,8881
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein yesU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0403
Polymers25,8881
Non-polymers1522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.839, 44.616, 139.391
Angle α, β, γ (deg.)90.00, 100.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein yesU / Hypothetical protein APC1120


Mass: 25888.197 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O31524
#2: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 999 / 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 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Ammonium Acetate, BisTris, PEG10000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945 Å
DetectorType: SBC-2 / Detector: CCD / Date: Feb 6, 2003 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.7→46.21 Å / Num. all: 88537 / Num. obs: 88537 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 8.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4.2 / % possible all: 51.4

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Processing

Software
NameVersionClassification
CNS1refinement
d*TREKdata reduction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→46.21 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 403841.08 / Data cutoff high rms absF: 403841.08 / 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
Rfree0.208 8765 10 %RANDOM
Rwork0.182 ---
all0.184 87402 --
obs0.184 87402 87.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.0314 Å2 / ksol: 0.385499 e/Å3
Displacement parametersBiso mean: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å20 Å2-0.79 Å2
2---0.41 Å20 Å2
3---1.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.7→46.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7151 0 28 999 8178
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it2.52
X-RAY DIFFRACTIONc_scangle_it3.812.5
LS refinement shellResolution: 1.7→1.78 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.261 1142 9.7 %
Rwork0.216 7483 -
obs-12178 0.499 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ACY.PARAMACY.TOP
X-RAY DIFFRACTION4GOL.PARAMGOL.TOP

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