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- PDB-5h3k: Crystal structure of a hypothetical protein from Synechocystis -

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Basic information

Entry
Database: PDB / ID: 5h3k
TitleCrystal structure of a hypothetical protein from Synechocystis
ComponentsSlr0280 protein
KeywordsUNKNOWN FUNCTION / hypothetical protein / Synechocystis
Function / homologyPhosphodiester glycosidase / Phosphodiester glycosidase / Slr0280 protein
Function and homology information
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.702 Å
AuthorsDong, L.-L. / Wu, D.
CitationJournal: To Be Published
Title: Crystal structure of a hypothetical protein from Synechocystis
Authors: Dong, L.-L. / Wu, D. / Gao, X.-Q. / Zhou, M. / Liu, Z.-J. / Zhao, K.-H.
History
DepositionOct 25, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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: Slr0280 protein


Theoretical massNumber of molelcules
Total (without water)65,4511
Polymers65,4511
Non-polymers00
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.152, 83.924, 96.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Slr0280 protein


Mass: 65451.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: slr0280 / Production host: Escherichia coli (E. coli) / References: UniProt: P74396
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.04 Å3/Da / Density % sol: 39.62 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG 8000, 0.1M Tris-HCl pH8.3,

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Data collection

DiffractionMean temperature: 77.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 48042 / % possible obs: 81 % / Redundancy: 5.7 % / Rsym value: 0.043 / Net I/σ(I): 2.36
Reflection shellResolution: 1.7→1.76 Å / % possible all: 30.9

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.702→38.454 Å / SU ML: 0.13 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 21.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2093 2354 5.06 %
Rwork0.1715 --
obs0.1734 46491 78.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.702→38.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4063 0 0 462 4525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074146
X-RAY DIFFRACTIONf_angle_d1.1525650
X-RAY DIFFRACTIONf_dihedral_angle_d14.691503
X-RAY DIFFRACTIONf_chiral_restr0.083629
X-RAY DIFFRACTIONf_plane_restr0.005759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7022-1.7370.1949220.1908395X-RAY DIFFRACTION12
1.737-1.77470.225480.2036803X-RAY DIFFRACTION25
1.7747-1.8160.2304590.19721346X-RAY DIFFRACTION41
1.816-1.86140.2582980.18981681X-RAY DIFFRACTION52
1.8614-1.91170.2541130.18182062X-RAY DIFFRACTION63
1.9117-1.9680.25121280.17942340X-RAY DIFFRACTION72
1.968-2.03150.18731330.17352613X-RAY DIFFRACTION80
2.0315-2.10410.20741530.18032917X-RAY DIFFRACTION89
2.1041-2.18840.2261440.17373216X-RAY DIFFRACTION97
2.1884-2.28790.22841590.17813313X-RAY DIFFRACTION100
2.2879-2.40850.20991790.17823299X-RAY DIFFRACTION100
2.4085-2.55940.23362000.18073286X-RAY DIFFRACTION100
2.5594-2.7570.23421910.18053306X-RAY DIFFRACTION100
2.757-3.03430.20391810.18383316X-RAY DIFFRACTION100
3.0343-3.47320.20541540.17233376X-RAY DIFFRACTION100
3.4732-4.37480.21131920.15193375X-RAY DIFFRACTION100
4.3748-38.46360.16042000.15423493X-RAY DIFFRACTION99

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