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- PDB-6l8p: Crystal structure of RidA from Antarctic bacterium Psychrobacter ... -

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Basic information

Entry
Database: PDB / ID: 6l8p
TitleCrystal structure of RidA from Antarctic bacterium Psychrobacter sp. PAMC 21119
ComponentsRidA family protein
KeywordsHYDROLASE / RidA / Deamination / Psychrophile / Antarctic bacterium / Cold-adaptability
Function / homology
Function and homology information


RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / RidA family protein
Similarity search - Component
Biological speciesPsychrobacter sp. MES7-P7E (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsKwon, S. / Lee, C.W. / Koh, H.Y. / Lee, J.H. / Park, H.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of the reactive intermediate/imine deaminase A homolog from the Antarctic bacterium Psychrobacter sp. PAMC 21119.
Authors: Kwon, S. / Lee, C.W. / Koh, H.Y. / Park, H. / Lee, J.H. / Park, H.H.
History
DepositionNov 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 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: RidA family protein
B: RidA family protein
C: RidA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3036
Polymers46,9973
Non-polymers3063
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-21 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.284, 71.141, 108.479
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RidA family protein


Mass: 15665.569 Da / Num. of mol.: 3 / Mutation: D39E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter sp. MES7-P7E (bacteria) / Gene: CXF62_02540 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2N5LLK3
#2: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris Propane/HCl (pH 7), 1.1 M malonic acid, 0.15 M ammonium citrate tribasic, 0.072 M succinic acid, 0.18 M DL-malic acid, 0.24 M sodium acetate, 0.3 M sodium formate, and 0.1 M ...Details: 0.1 M Bis-Tris Propane/HCl (pH 7), 1.1 M malonic acid, 0.15 M ammonium citrate tribasic, 0.072 M succinic acid, 0.18 M DL-malic acid, 0.24 M sodium acetate, 0.3 M sodium formate, and 0.1 M ammonium tartrate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 69280 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.044 / Rrim(I) all: 0.115 / Χ2: 2.494 / Net I/σ(I): 10.6 / Num. measured all: 479686
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.637.40.48633850.9240.1930.5230.936100
1.63-1.667.30.4434680.930.1750.4751.021100
1.66-1.697.30.3933910.9440.1550.421.094100
1.69-1.727.20.33634290.9550.1340.3621.25100
1.72-1.767.20.30834260.9620.1230.3321.305100
1.76-1.87.20.27534310.9650.110.2971.478100
1.8-1.857.10.2434180.9740.0970.2591.631100
1.85-1.970.20634080.9770.0840.2231.946100
1.9-1.956.90.18634290.9790.0770.2022.2100
1.95-2.026.60.1634480.9850.0680.1752.527100
2.02-2.096.20.14434730.9860.0630.1582.813100
2.09-2.176.50.13434510.9870.0580.1463.08100
2.17-2.277.20.12134140.990.0490.133.17499.9
2.27-2.397.20.11134720.9910.0450.123.28199.9
2.39-2.547.10.10234700.9910.0420.113.385100
2.54-2.7470.09234710.9930.0380.13.60999.9
2.74-3.016.90.08334930.9940.0340.093.682100
3.01-3.456.60.07435150.9950.0320.0813.791100
3.45-4.345.90.06735610.9950.030.0733.99999.8
4.34-506.90.06937270.9950.0290.0754.22899.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K0T

3k0t


Resolution: 1.601→42.227 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 14.6
RfactorNum. reflection% reflection
Rfree0.164 2011 2.91 %
Rwork0.1482 --
obs0.1487 69200 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.17 Å2 / Biso mean: 17.355 Å2 / Biso min: 5.2 Å2
Refinement stepCycle: final / Resolution: 1.601→42.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2786 0 21 460 3267
Biso mean--21.63 31.29 -
Num. residues----371
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.601-1.64060.1891380.1629468499
1.6406-1.68490.18781450.15494745100
1.6849-1.73450.17861330.14984732100
1.7345-1.79050.17991520.15154753100
1.7905-1.85450.17671370.15894751100
1.8545-1.92870.17791430.1434781100
1.9287-2.01650.16111380.13864759100
2.0165-2.12280.18011430.1384791100
2.1228-2.25580.16431470.14174748100
2.2558-2.430.15341450.15224822100
2.43-2.67450.16991450.15714812100
2.6745-3.06140.16461440.15974851100
3.0614-3.85660.14621480.13634872100
3.8566-42.2270.15531530.14915088100

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