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- PDB-5hp7: Crystal structures of RidA in the apo form -

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Basic information

Entry
Database: PDB / ID: 5hp7
TitleCrystal structures of RidA in the apo form
ComponentsReactive Intermediate Deaminase A, chloroplastic
KeywordsHYDROLASE / RidA / enamine/imine / deamination
Function / homology
Function and homology information


2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / deaminase activity / branched-chain amino acid biosynthetic process / thylakoid / chloroplast envelope / plant-type vacuole / isoleucine biosynthetic process / chloroplast stroma ...2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / deaminase activity / branched-chain amino acid biosynthetic process / thylakoid / chloroplast envelope / plant-type vacuole / isoleucine biosynthetic process / chloroplast stroma / plastid / chloroplast / response to toxic substance / cytosol
Similarity search - Function
RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / RutC-like / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Reactive Intermediate Deaminase A, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsXie, W. / Liu, X.
Funding support China, 3items
OrganizationGrant numberCountry
Science and Technology Program of Guangzhou201504010025 China
Guangdong Innovative Research Team2011Y038 China
Fundamental Research Funds for the Central Universities15lgjc15 China
CitationJournal: Sci Rep / Year: 2016
Title: Crystal structures of RidA, an important enzyme for the prevention of toxic side products
Authors: Liu, X. / Zeng, J. / Chen, X. / Xie, W.
History
DepositionJan 20, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Reactive Intermediate Deaminase A, chloroplastic


Theoretical massNumber of molelcules
Total (without water)13,2311
Polymers13,2311
Non-polymers00
Water1,53185
1
A: Reactive Intermediate Deaminase A, chloroplastic

A: Reactive Intermediate Deaminase A, chloroplastic

A: Reactive Intermediate Deaminase A, chloroplastic


Theoretical massNumber of molelcules
Total (without water)39,6933
Polymers39,6933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3950 Å2
ΔGint-26 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.907, 76.907, 40.298
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Reactive Intermediate Deaminase A, chloroplastic / 2-iminobutanoate/2-iminopropanoate deaminase


Mass: 13231.139 Da / Num. of mol.: 1 / Fragment: UNP residues 68-187
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RIDA, At3g20390, MQC12.15 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli)
References: UniProt: Q94JQ4, 2-iminobutanoate/2-iminopropanoate deaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 1.73 Å3/Da / Density % sol: 29.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 18% PEG 3350, 0.1 M MES pH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Agilent SuperNova / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Sep 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→25.7 Å / Num. obs: 6001 / % possible obs: 99.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 16.2
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 5.5 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
CrysalisProdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B33

2b33


Resolution: 2→25.67 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.068 / SU ML: 0.111 / Cross valid method: FREE R-VALUE / ESU R: 0.2 / ESU R Free: 0.17 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 273 4.6 %RANDOM
Rwork0.15261 ---
obs0.15534 5725 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.532 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.1 Å20 Å2
2---0.21 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 2→25.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms808 0 0 86 894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02820
X-RAY DIFFRACTIONr_bond_other_d0.0010.02798
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9891117
X-RAY DIFFRACTIONr_angle_other_deg2.62931842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7355107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.79626.66730
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3415138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg0.504151
X-RAY DIFFRACTIONr_chiral_restr0.1340.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021925
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02160
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.921.813431
X-RAY DIFFRACTIONr_mcbond_other1.881.808430
X-RAY DIFFRACTIONr_mcangle_it2.5592.705537
X-RAY DIFFRACTIONr_mcangle_other2.5722.708538
X-RAY DIFFRACTIONr_scbond_it2.862.035389
X-RAY DIFFRACTIONr_scbond_other2.862.033389
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9542.957580
X-RAY DIFFRACTIONr_long_range_B_refined5.34315.589943
X-RAY DIFFRACTIONr_long_range_B_other5.1215.155919
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 11 -
Rwork0.189 424 -
obs--98.64 %

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