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- PDB-6lrg: Crystal Structure of the Ternary Complex of AgrE with Ornithine a... -

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Basic information

Entry
Database: PDB / ID: 6lrg
TitleCrystal Structure of the Ternary Complex of AgrE with Ornithine and NAD+
ComponentsAlr4995 protein
KeywordsHYDROLASE / arginine dihydrolase / bifunctional enzyme / GME family
Function / homology
Function and homology information


LOR/SDH bifunctional enzyme, conserved domain superfamily / : / : / Arginine dihydrolase ArgZ-like, C-terminal, Rossmann fold / Arginine dihydrolase ArgZ-like, C-terminal, first region / Conserved hypothetical protein CHP00300 / LOR/SDH bifunctional enzyme, conserved domain / LOR/SDH bifunctional enzyme conserved region / N,N dimethylarginine dimethylhydrolase, eukaryotic / Arginine deiminase
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-ornithine / Alr4995 protein
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4121811586 Å
AuthorsLee, H. / Rhee, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Rural Development AdministrationPJ01325801 Korea, Republic Of
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural and mutational analyses of the bifunctional arginine dihydrolase and ornithine cyclodeaminase AgrE from the cyanobacteriumAnabaena.
Authors: Lee, H. / Rhee, S.
History
DepositionJan 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_gen.gene_src_strain ..._entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.2May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: Alr4995 protein
B: Alr4995 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,0625
Polymers156,1342
Non-polymers9283
Water2,378132
1
A: Alr4995 protein
B: Alr4995 protein
hetero molecules

A: Alr4995 protein
B: Alr4995 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,12410
Polymers312,2694
Non-polymers1,8556
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area20460 Å2
ΔGint-97 kcal/mol
Surface area97240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.895, 201.141, 99.436
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Alr4995 protein / arginine-guanidine removing enzyme


Mass: 78067.219 Da / Num. of mol.: 2
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: alr4995 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YMD9
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-ORN / L-ornithine / Ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion
Details: sodium acetate, sodium citrate (pH5.5), PEG4000, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 71345 / % possible obs: 99 % / Redundancy: 5.8 % / Biso Wilson estimate: 28.6547168205 Å2 / CC1/2: 0.967 / Net I/σ(I): 9.77
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 7051 / CC1/2: 0.535

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LRF

6lrf


Resolution: 2.4121811586→46.7322103795 Å / SU ML: 0.300364896667 / Cross valid method: FREE R-VALUE / σ(F): 1.32630767749 / Phase error: 24.8930398103
RfactorNum. reflection% reflection
Rfree0.250967979569 2007 2.81518262919 %
Rwork0.19145144531 --
obs0.193120163194 71292 98.6289999032 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.2448740933 Å2
Refinement stepCycle: LAST / Resolution: 2.4121811586→46.7322103795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10605 0 62 132 10799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088407749956510865
X-RAY DIFFRACTIONf_angle_d1.1762313718114732
X-RAY DIFFRACTIONf_chiral_restr0.04581399406731677
X-RAY DIFFRACTIONf_plane_restr0.005244141161641907
X-RAY DIFFRACTIONf_dihedral_angle_d15.10889441424020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4122-2.47250.2777496328651390.2237245915784672X-RAY DIFFRACTION94.8728061526
2.4725-2.53930.3358152020621360.2225315019634981X-RAY DIFFRACTION99.5138078569
2.5393-2.61410.3065223438291570.2280889379664939X-RAY DIFFRACTION99.6480250293
2.6141-2.69840.2920516031871290.2264598764434944X-RAY DIFFRACTION99.4900960973
2.6984-2.79490.2993861392021370.22706701364716X-RAY DIFFRACTION94.9334898279
2.7949-2.90670.2845541848671370.2268477084084959X-RAY DIFFRACTION99.201868795
2.9067-3.0390.309358456321550.2234489304914954X-RAY DIFFRACTION99.687804878
3.039-3.19920.2705780503321450.2158095775544994X-RAY DIFFRACTION99.7670355271
3.1992-3.39960.3091995182391450.2129071418154991X-RAY DIFFRACTION99.8833138856
3.3996-3.6620.2386369583831380.1939572137815018X-RAY DIFFRACTION99.9806088811
3.662-4.03030.2387532610531480.1779225348344943X-RAY DIFFRACTION98.3198146002
4.0303-4.61310.2096601855111440.1589093931744933X-RAY DIFFRACTION97.8981874277
4.6131-5.81020.2232520286981430.1632030279025097X-RAY DIFFRACTION99.9237223494
5.8102-46.7320.1767498725431540.1505273672175144X-RAY DIFFRACTION97.695002766

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