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- PDB-1pug: Structure of E. coli Ybab -

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Basic information

Entry
Database: PDB / ID: 1pug
TitleStructure of E. coli Ybab
ComponentsHypothetical UPF0133 protein ybaB
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NYSGXRC T5 / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


bacterial nucleoid / response to radiation / DNA binding / cytosol
Similarity search - Function
Nucleoid-associated protein YbaB-like domain / Nucleoid-associated protein YbaB/EbfC family / YbaB/EbfC DNA-binding family / Ybab; Chain: A; / Nucleoid-associated protein YbaB-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoid-associated protein YbaB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.2 Å
AuthorsKniewel, R. / Buglino, J. / Chadna, T. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Structure of E. coli Ybab
Authors: Kniewel, R. / Buglino, J. / Chadna, T. / Lima, C.D.
History
DepositionJun 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 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 UPF0133 protein ybaB
B: Hypothetical UPF0133 protein ybaB
C: Hypothetical UPF0133 protein ybaB
D: Hypothetical UPF0133 protein ybaB


Theoretical massNumber of molelcules
Total (without water)48,1154
Polymers48,1154
Non-polymers00
Water2,936163
1
A: Hypothetical UPF0133 protein ybaB
B: Hypothetical UPF0133 protein ybaB


Theoretical massNumber of molelcules
Total (without water)24,0582
Polymers24,0582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-13 kcal/mol
Surface area10440 Å2
MethodPISA
2
C: Hypothetical UPF0133 protein ybaB
D: Hypothetical UPF0133 protein ybaB


Theoretical massNumber of molelcules
Total (without water)24,0582
Polymers24,0582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-12 kcal/mol
Surface area9310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.866, 84.236, 86.636
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
DetailsAPPARENT DIMER (A,B) AND (C,D) ALSO BY GEL FILTRATION

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Components

#1: Protein
Hypothetical UPF0133 protein ybaB / Ybab / hypothetical protein ybaB


Mass: 12028.819 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YBAB / Plasmid: PET T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 DE3 / References: UniProt: P0A8B5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 1.9M Ammonium Sulfate 0.1MSodium HEPES pH 7.5 5% Ethylene Glycol, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9798 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 28, 2003
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 37158 / Num. obs: 36898 / % possible obs: 99.3 % / Observed criterion σ(I): -0.5 / Rmerge(I) obs: 0.073
Reflection shellResolution: 1.9→1.97 Å / % possible all: 94.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5.1.24refinement
RESOLVEphasing
RefinementMethod to determine structure: SIR / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.202 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.217 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28412 1177 4.9 %RANDOM
Rwork0.21211 ---
obs0.21584 22865 99.64 %-
all-22948 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 63.383 Å2
Baniso -1Baniso -2Baniso -3
1-2.41 Å20 Å20 Å2
2---3.67 Å20 Å2
3---1.26 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 0 163 2655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0212502
X-RAY DIFFRACTIONr_bond_other_d0.0020.022303
X-RAY DIFFRACTIONr_angle_refined_deg2.4071.9753345
X-RAY DIFFRACTIONr_angle_other_deg1.18735413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2225319
X-RAY DIFFRACTIONr_chiral_restr0.1420.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022783
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02405
X-RAY DIFFRACTIONr_nbd_refined0.270.2624
X-RAY DIFFRACTIONr_nbd_other0.2670.22754
X-RAY DIFFRACTIONr_nbtor_other0.1040.21644
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.2125
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3240.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3690.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4140.224
X-RAY DIFFRACTIONr_mcbond_it1.7761.51599
X-RAY DIFFRACTIONr_mcangle_it3.13422551
X-RAY DIFFRACTIONr_scbond_it3.9663903
X-RAY DIFFRACTIONr_scangle_it6.8454.5794
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 92 5.7 %
Rwork0.237 1605 -

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