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- PDB-7rsf: Acetylornithine deacetylase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 7rsf
TitleAcetylornithine deacetylase from Escherichia coli
ComponentsAcetylornithine deacetylase
KeywordsHYDROLASE / acetylornithine deacetylase / ArgE / M20 peptidase / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


acetylornithine deacetylase / acetylornithine deacetylase activity / L-arginine biosynthetic process / zinc ion binding / cytoplasm
Similarity search - Function
Acetylornithine deacetylase ArgE / ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / : / Bacterial exopeptidase dimerisation domain / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40
Similarity search - Domain/homology
Acetylornithine deacetylase
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.13 Å
AuthorsOsipiuk, J. / Endres, M. / Becker, D.P. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Acetylornithine deacetylase from Escherichia coli
Authors: Osipiuk, J. / Endres, M. / Becker, D.P. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetylornithine deacetylase
B: Acetylornithine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8297
Polymers85,4792
Non-polymers3505
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-100 kcal/mol
Surface area30800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.700, 70.994, 289.884
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein Acetylornithine deacetylase / AO / Acetylornithinase / N-acetylornithinase / NAO


Mass: 42739.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 3 N-terminal residues (SNA) are cloning artifacts
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Strain: K-12 substr. MG1655 / Gene: argE, Z5515, ECs4886 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8X742, acetylornithine deacetylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.81 Å3/Da / Density % sol: 56.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Bis-Tris Propane, 1 M ammonium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.13→46.15 Å / Num. obs: 54637 / % possible obs: 98.8 % / Redundancy: 4.9 % / CC1/2: 0.986 / CC star: 0.996 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.057 / Rrim(I) all: 0.133 / Χ2: 1.349 / Net I/av σ(I): 15.7 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.13-2.183.11.0131.0223960.5130.8230.6041.1870.9490.5
2.18-2.224.10.99926480.5960.5211.1340.93897.4
2.22-2.264.60.91326820.680.4511.0240.94598.8
2.26-2.314.80.81327230.7590.3930.9070.95399.6
2.31-2.3650.70727230.7970.3410.7880.9899.4
2.36-2.4150.59226560.8380.2850.661.02899.1
2.41-2.475.10.54127390.8680.2570.6021.05699.3
2.47-2.544.80.47826840.8770.2340.5351.08599.4
2.54-2.6150.37927560.9290.1810.4211.15499.6
2.61-2.75.40.32426820.9450.1490.3581.18899.6
2.7-2.795.30.27427460.9540.1280.3031.2999.6
2.79-2.95.30.2227350.9720.1020.2431.50299.6
2.9-3.045.10.18127550.9770.0860.2011.60399.7
3.04-3.24.80.14527480.9840.0710.1621.78399.5
3.2-3.45.30.1327750.9860.060.1441.86499.5
3.4-3.665.30.11127620.9840.0510.1231.86199.6
3.66-4.035.10.09627820.9890.0450.1071.76599.6
4.03-4.615.10.08228130.9920.0380.0911.60499.8
4.61-5.815.20.06728290.9950.0310.0741.51698.3
5.81-46.154.80.04430030.9980.0220.051.39398.4

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.13→46.15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 14.135 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 2776 5.1 %RANDOM
Rwork0.1875 ---
obs0.1899 51807 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.29 Å2 / Biso mean: 46.425 Å2 / Biso min: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.07 Å2-0 Å20 Å2
2--2.45 Å2-0 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 2.13→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5917 0 15 155 6087
Biso mean--67.64 46.32 -
Num. residues----759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136155
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175754
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.6458407
X-RAY DIFFRACTIONr_angle_other_deg1.3131.57213289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5385773
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23422.288319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2115979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7731538
X-RAY DIFFRACTIONr_chiral_restr0.0760.2813
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026995
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021369
LS refinement shellResolution: 2.13→2.18 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.345 191 -
Rwork0.337 3134 -
obs--82.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8275-0.10970.94740.3244-0.13572.26320.0483-0.1372-0.00590.01850.0730.0318-0.10080.0088-0.12130.04040.00310.0270.24830.0110.020645.232650.810743.4693
20.7372-0.101-0.01460.4474-0.07822.37420.07430.13710.02410.00810.0870.0244-0.2289-0.1824-0.16130.0350.01810.01060.1050.04360.023927.045657.0175-13.8497
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 502
2X-RAY DIFFRACTION2B4 - 503

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