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- PDB-8v8r: Crystal Structure of Reactive Enamine Deaminase A (RidA) Homolog ... -

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Basic information

Entry
Database: PDB / ID: 8v8r
TitleCrystal Structure of Reactive Enamine Deaminase A (RidA) Homolog from an Opportunistic Pathogen, Streptococcus sanguinis.
ComponentsEnamine/imine deaminase
KeywordsHYDROLASE / YjgF_YER057c_UK117 family protein / Reactive intermediate deaminase / metabolic damage repair / enamine deaminase
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / deaminase activity / cytosol
Similarity search - Function
RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily
Similarity search - Domain/homology
Enamine/imine deaminase
Similarity search - Component
Biological speciesStreptococcus sanguinis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsThomas, L.M. / Rajan, R. / Somalinga, V. / Benedict, A. / Aquino, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM145423 United States
CitationJournal: To Be Published
Title: Crystal Structure of Reactive Enamine Deaminase A (RidA) Homolog from an Opportunistic Pathogen, Streptococcus sanguinis.
Authors: Thomas, L.M. / Rajan, R. / Somalinga, V.
History
DepositionDec 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enamine/imine deaminase
B: Enamine/imine deaminase
C: Enamine/imine deaminase
D: Enamine/imine deaminase
E: Enamine/imine deaminase
F: Enamine/imine deaminase


Theoretical massNumber of molelcules
Total (without water)81,4356
Polymers81,4356
Non-polymers00
Water7,764431
1
A: Enamine/imine deaminase
B: Enamine/imine deaminase
D: Enamine/imine deaminase


Theoretical massNumber of molelcules
Total (without water)40,7173
Polymers40,7173
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-34 kcal/mol
Surface area14750 Å2
MethodPISA
2
C: Enamine/imine deaminase
E: Enamine/imine deaminase
F: Enamine/imine deaminase


Theoretical massNumber of molelcules
Total (without water)40,7173
Polymers40,7173
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-33 kcal/mol
Surface area14730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.509, 61.759, 75.725
Angle α, β, γ (deg.)90.000, 113.407, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-290-

HOH

21A-291-

HOH

31C-258-

HOH

41C-266-

HOH

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Components

#1: Protein
Enamine/imine deaminase


Mass: 13572.479 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sanguinis (bacteria) / Gene: tdcF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2X3YM18
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5 10% v/v 2-Propanol 20% w/v Polyethylene Glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 29, 2023 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. obs: 47778 / % possible obs: 99.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 31.39 Å2 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.046 / Rrim(I) all: 0.125 / Rsym value: 0.115 / Net I/σ(I): 10.6
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.869 / Num. unique obs: 2349 / CC1/2: 0.493 / Rpim(I) all: 0.619

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5144refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→34.75 Å / SU ML: 0.2664 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8801
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2603 1990 4.18 %
Rwork0.2014 45662 -
obs0.2038 47652 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.78 Å2
Refinement stepCycle: LAST / Resolution: 2→34.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5683 0 0 431 6114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025779
X-RAY DIFFRACTIONf_angle_d0.46357871
X-RAY DIFFRACTIONf_chiral_restr0.0447965
X-RAY DIFFRACTIONf_plane_restr0.00341019
X-RAY DIFFRACTIONf_dihedral_angle_d16.03372081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.33591220.30832967X-RAY DIFFRACTION90.03
2.05-2.110.3791480.29513202X-RAY DIFFRACTION98.3
2.11-2.170.30091440.26793272X-RAY DIFFRACTION99.16
2.17-2.240.29411280.253245X-RAY DIFFRACTION99.15
2.24-2.320.28721540.23283253X-RAY DIFFRACTION99.59
2.32-2.410.27071460.22833266X-RAY DIFFRACTION99.77
2.41-2.520.29551380.23443274X-RAY DIFFRACTION99.82
2.52-2.660.30831450.2343273X-RAY DIFFRACTION99.53
2.66-2.820.32521460.24963294X-RAY DIFFRACTION99.83
2.82-3.040.30891430.23263281X-RAY DIFFRACTION99.8
3.04-3.350.23971390.19733315X-RAY DIFFRACTION99.97
3.35-3.830.20191470.15873302X-RAY DIFFRACTION99.97
3.83-4.830.22151440.15333309X-RAY DIFFRACTION99.42
4.83-34.750.24851460.18093409X-RAY DIFFRACTION99.72

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