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- PDB-6omx: Crystal structure of alr5209, a pentapeptide repeat protein from ... -

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Basic information

Entry
Database: PDB / ID: 6omx
TitleCrystal structure of alr5209, a pentapeptide repeat protein from Nostoc Pcc 7120, determined at 1.7 Angstrom resolution
ComponentsAlr5209 protein
KeywordsUNKNOWN FUNCTION / pentapeptide repeat / protein repeat / five residue right-handed beta helix
Function / homology: / Pentapeptide repeats (8 copies) / Pentapeptide repeat / Alr5209 protein
Function and homology information
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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
DepositionApr 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: 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: Alr5209 protein


Theoretical massNumber of molelcules
Total (without water)16,3621
Polymers16,3621
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.001, 27.835, 60.837
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein Alr5209 protein


Mass: 16362.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: alr5209 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YLT7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.15 M Potassium sodium tartrate tetrahydrate, 0.075 M Sodium citrate tribasic dihydrate pH 5.6, 1.5 M Ammonium sulfate, 25% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.71→46.2 Å / Num. obs: 13612 / % possible obs: 98.8 % / Redundancy: 2 % / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.017 / Rrim(I) all: 0.042 / Χ2: 0.86 / Net I/σ(I): 22
Reflection shellResolution: 1.71→1.8 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.596 / Num. unique obs: 1946 / CC1/2: 0.925 / Rpim(I) all: 0.248 / Rrim(I) all: 0.647 / Χ2: 0.74 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDS1.1.7data reduction
Aimless0.7.1data scaling
BALBES1.1.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J8K

2j8k


Resolution: 1.71→35.501 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.98
RfactorNum. reflection% reflection
Rfree0.2488 1359 10.01 %
Rwork0.215 --
obs0.2184 13583 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.71→35.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms925 0 0 13 938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009933
X-RAY DIFFRACTIONf_angle_d1.1121258
X-RAY DIFFRACTIONf_dihedral_angle_d12.192576
X-RAY DIFFRACTIONf_chiral_restr0.053144
X-RAY DIFFRACTIONf_plane_restr0.007171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7064-1.76740.38381330.33151202X-RAY DIFFRACTION99
1.7674-1.83820.33111350.28571209X-RAY DIFFRACTION99
1.8382-1.92180.3241320.27711196X-RAY DIFFRACTION100
1.9218-2.02320.30791350.25191213X-RAY DIFFRACTION99
2.0232-2.14990.28351350.22741212X-RAY DIFFRACTION99
2.1499-2.31590.26431310.21761180X-RAY DIFFRACTION96
2.3159-2.54890.23781350.22071220X-RAY DIFFRACTION99
2.5489-2.91750.29271370.23311229X-RAY DIFFRACTION99
2.9175-3.67520.22171390.23081250X-RAY DIFFRACTION99
3.6752-35.50820.21831470.17551313X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -16.2417 Å / Origin y: -4.6011 Å / Origin z: -12.2669 Å
111213212223313233
T0.217 Å2-0.0295 Å2-0.0076 Å2-0.2107 Å20.0113 Å2--0.2838 Å2
L4.8676 °22.2481 °2-0.1025 °2-5.5351 °2-1.3927 °2--1.8702 °2
S0.2954 Å °-0.1385 Å °-0.187 Å °0.4556 Å °-0.2641 Å °0.0443 Å °-0.1669 Å °0.0766 Å °-0.0114 Å °
Refinement TLS groupSelection details: all

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