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- PDB-6uvi: Crystal structure of alr1298, a pentapeptide repeat protein from ... -

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Basic information

Entry
Database: PDB / ID: 6uvi
TitleCrystal structure of alr1298, a pentapeptide repeat protein from Nostoc Pcc 7120, determined at 2.3 Angstrom resolution
ComponentsAlr1298 protein
KeywordsUNKNOWN FUNCTION / pentapeptide repeat / protein repeat / five residue right-handed-beta helix
Function / homology: / Pentapeptide repeats (8 copies) / Pentapeptide repeat / Alr1298 protein
Function and homology information
Biological speciesNostoc sp. PCC 7120 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKennedy, M.A. / Zhang, R.
CitationJournal: Proteins / Year: 2020
Title: Crystal structure of Alr1298, a pentapeptide repeat protein from the cyanobacterium Nostoc sp. PCC 7120, determined at 2.1 angstrom resolution.
Authors: Zhang, R. / Ni, S. / Kennedy, M.A.
History
DepositionNov 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Alr1298 protein
B: Alr1298 protein


Theoretical massNumber of molelcules
Total (without water)41,9092
Polymers41,9092
Non-polymers00
Water1,22568
1
A: Alr1298 protein


Theoretical massNumber of molelcules
Total (without water)20,9551
Polymers20,9551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alr1298 protein


Theoretical massNumber of molelcules
Total (without water)20,9551
Polymers20,9551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.762, 85.922, 95.686
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Alr1298 protein


Mass: 20954.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: alr1298 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YXB7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.1→31.32 Å / Num. obs: 22287 / % possible obs: 98.03 % / Redundancy: 2 % / Biso Wilson estimate: 40.41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01859 / Rpim(I) all: 0.01859 / Rrim(I) all: 0.02629 / Net I/σ(I): 18.53
Reflection shellResolution: 2.1→2.21 Å / Rmerge(I) obs: 0.065 / Mean I/σ(I) obs: 17.7 / Num. unique obs: 22336 / Rpim(I) all: 0.028 / Rrim(I) all: 0.071

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDS1.1.7data reduction
Aimless0.7.1data scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UV7

6uv7


Resolution: 2.1→31.32 Å / SU ML: 0.3238 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.8294
RfactorNum. reflection% reflection
Rfree0.2744 1996 8.97 %
Rwork0.2085 --
obs0.2144 22261 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 60.16 Å2
Refinement stepCycle: LAST / Resolution: 2.1→31.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2413 0 0 68 2481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01182442
X-RAY DIFFRACTIONf_angle_d1.19573286
X-RAY DIFFRACTIONf_chiral_restr0.0547372
X-RAY DIFFRACTIONf_plane_restr0.0064438
X-RAY DIFFRACTIONf_dihedral_angle_d15.38331490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.35051380.31511404X-RAY DIFFRACTION98.09
2.15-2.210.34731410.31331427X-RAY DIFFRACTION98.25
2.21-2.280.40741390.30931408X-RAY DIFFRACTION96.81
2.28-2.350.36291380.28391404X-RAY DIFFRACTION97.29
2.35-2.430.3631420.26541443X-RAY DIFFRACTION98.33
2.43-2.530.32921420.26881441X-RAY DIFFRACTION98.51
2.53-2.650.3011410.25011426X-RAY DIFFRACTION99.18
2.65-2.790.33281430.25451460X-RAY DIFFRACTION98.89
2.79-2.960.34611370.25091392X-RAY DIFFRACTION95.32
2.96-3.190.30041440.24951463X-RAY DIFFRACTION99.08
3.19-3.510.27981450.22551479X-RAY DIFFRACTION99.33
3.51-4.010.25191460.17891484X-RAY DIFFRACTION99.45
4.01-5.050.17841470.14831487X-RAY DIFFRACTION97.49
5.05-31.320.26671530.16741547X-RAY DIFFRACTION97.31

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