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- PDB-5guy: Structural and functional study of chuY from E. coli CFT073 strain -

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Basic information

Entry
Database: PDB / ID: 5guy
TitleStructural and functional study of chuY from E. coli CFT073 strain
ComponentsUncharacterized protein chuY
KeywordsOXIDOREDUCTASE / chuY / flavin reductase
Function / homologyNAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding domain superfamily / NAD(P)-binding domain-containing protein
Function and homology information
Biological speciesEscherichia coli strain CFT073 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.399 Å
AuthorsKim, H. / Choi, J. / HA, S.C. / Chaurasia, A.K. / Kim, D. / Kim, K.K.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural and functional study of ChuY from Escherichia coli strain CFT073
Authors: Kim, H. / Chaurasia, A.K. / Kim, T. / Choi, J. / Ha, S.C. / Kim, D. / Kim, K.K.
History
DepositionAug 31, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Uncharacterized protein chuY
B: Uncharacterized protein chuY


Theoretical massNumber of molelcules
Total (without water)46,0652
Polymers46,0652
Non-polymers00
Water84747
1
A: Uncharacterized protein chuY


Theoretical massNumber of molelcules
Total (without water)23,0331
Polymers23,0331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein chuY


Theoretical massNumber of molelcules
Total (without water)23,0331
Polymers23,0331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.686, 67.836, 64.381
Angle α, β, γ (deg.)90.00, 90.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein chuY / Flavin reductase


Mass: 23032.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli strain CFT073 (bacteria)
Strain: CFT073 / Gene: chuY, c4316 / Plasmid: pET21a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: A0A0H2VDD2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 1.99 Å3/Da / Density % sol: 34.62 % / Description: rectangular prism
Crystal growTemperature: 295 K / Method: microbatch / pH: 6.5 / Details: 0.1M Bis-Tris pH 6.5, 50mM CaCl2, 30% PEG MME 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97941, 0.97955, 0.97243
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 22, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979411
20.979551
30.972431
ReflectionResolution: 2.4→50 Å / Num. obs: 13433 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 27.1
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.399→34.254 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.7 / Phase error: 25.02 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.259 1283 10.07 %
Rwork0.2084 --
obs0.2135 12738 94.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.399→34.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2776 0 0 47 2823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092820
X-RAY DIFFRACTIONf_angle_d1.2673831
X-RAY DIFFRACTIONf_dihedral_angle_d15.575981
X-RAY DIFFRACTIONf_chiral_restr0.085456
X-RAY DIFFRACTIONf_plane_restr0.005493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3993-2.49540.26681530.19851269X-RAY DIFFRACTION95
2.4954-2.60890.27621510.22251300X-RAY DIFFRACTION96
2.6089-2.74640.29821380.23521281X-RAY DIFFRACTION96
2.7464-2.91840.25431490.2251288X-RAY DIFFRACTION96
2.9184-3.14360.24651300.23151285X-RAY DIFFRACTION96
3.1436-3.45960.30221450.2051269X-RAY DIFFRACTION95
3.4596-3.95960.23531420.20011289X-RAY DIFFRACTION95
3.9596-4.98630.21631390.1781270X-RAY DIFFRACTION93
4.9863-34.25760.28131360.22031204X-RAY DIFFRACTION87

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