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- PDB-1ryl: The Crystal Structure of a Protein of Unknown Function YfbM from ... -

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Basic information

Entry
Database: PDB / ID: 1ryl
TitleThe Crystal Structure of a Protein of Unknown Function YfbM from Escherichia coli
ComponentsHypothetical protein yfbM
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyYfbM-like super family / Protein of unknown function DUF1877 / YfbM-like super family / Domain of unknown function (DUF1877) / Hypothetical protein yfbM fold / 3-Layer(aba) Sandwich / Alpha Beta / Protein YfbM
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsZhang, R. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 1.6A crystal structure of a hypothetical protein yfbM from E. coli
Authors: Zhang, R. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionDec 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein yfbM
B: Hypothetical protein yfbM


Theoretical massNumber of molelcules
Total (without water)38,0812
Polymers38,0812
Non-polymers00
Water4,666259
1
A: Hypothetical protein yfbM


Theoretical massNumber of molelcules
Total (without water)19,0411
Polymers19,0411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein yfbM


Theoretical massNumber of molelcules
Total (without water)19,0411
Polymers19,0411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.848, 60.455, 57.931
Angle α, β, γ (deg.)90.00, 114.62, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a monomer. MolA and MolB represent two molecules in asymmetric unit.

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Components

#1: Protein Hypothetical protein yfbM


Mass: 19040.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YFBM, B2272 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P76483
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M MgCl2, 0.1 M HEPES, 30%PEG3350, 8% Ethanol, pH 7, 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: 0.9795,0.9797,0.94656
DetectorType: SBC-2 / Detector: CCD / Date: Dec 12, 2003 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97971
30.946561
ReflectionResolution: 1.6→50 Å / Num. all: 84444 / Num. obs: 78702 / % possible obs: 93.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 2.37 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.85
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 1.223 / Num. unique all: 4690 / % possible all: 55.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→30.23 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 441847.86 / 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
Rfree0.259 3615 4.9 %RANDOM
Rwork0.212 ---
all0.22 84644 --
obs0.212 74487 88 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.6538 Å2 / ksol: 0.410761 e/Å3
Displacement parametersBiso mean: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å2-1.15 Å2
2--1.6 Å20 Å2
3----0.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.6→30.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 0 0 259 2731
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d0.66
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 355 4.7 %
Rwork0.335 7195 -
obs--53.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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