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- PDB-8uw6: Acetylornithine deacetylase from Escherichia coli, di-zinc form. -

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Basic information

Entry
Database: PDB / ID: 8uw6
TitleAcetylornithine deacetylase from Escherichia coli, di-zinc form.
ComponentsAcetylornithine deacetylase
KeywordsHYDROLASE / Acetylornithine deacetylase / ArgE / M20 peptidase / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOsipiuk, J. / Endres, M. / Kelley, E. / Becker, D.P. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00035 United States
CitationJournal: Front Chem / Year: 2024
Title: N alpha-acetyl-L-ornithine deacetylase from Escherichia coli and a ninhydrin-based assay to enable inhibitor identification.
Authors: Kelley, E.H. / Osipiuk, J. / Korbas, M. / Endres, M. / Bland, A. / Ehrman, V. / Joachimiak, A. / Olsen, K.W. / Becker, D.P.
History
DepositionNov 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)172,94927
Polymers170,9584
Non-polymers1,99123
Water21,7981210
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B: Acetylornithine deacetylase
hetero molecules

A: Acetylornithine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,52314
Polymers85,4792
Non-polymers1,04412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area2670 Å2
ΔGint-221 kcal/mol
Surface area33550 Å2
MethodPISA
2
D: Acetylornithine deacetylase
hetero molecules

C: Acetylornithine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,42713
Polymers85,4792
Non-polymers94811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area2490 Å2
ΔGint-207 kcal/mol
Surface area33430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.399, 126.323, 123.408
Angle α, β, γ (deg.)90.00, 90.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 42739.465 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Three N-terminal residues, SNA, are cloning artifacts
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: argE, Z5515, ECs4886 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8X742, acetylornithine deacetylase

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Non-polymers , 5 types, 1233 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1210 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M lithium sulfate, 0.1 M Tris buffer, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→48.54 Å / Num. obs: 144787 / % possible obs: 97.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 19.6 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.057 / Rrim(I) all: 0.132 / Χ2: 0.996 / Net I/av σ(I): 14.8 / Net I/σ(I): 5.4
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
1.8-1.835.31.0011.2470890.4620.7950.4781.1110.59496.5
1.83-1.865.50.86771540.570.8520.4020.9560.62596.4
1.86-1.95.60.76171320.6520.8890.3510.8380.64996.3
1.9-1.945.60.65871760.7340.920.3030.7250.67696.9
1.94-1.985.60.56271320.7860.9380.260.620.70896.7
1.98-2.035.50.48571810.840.9560.2250.5350.74696.8
2.03-2.085.50.41371940.8790.9670.1930.4560.78397.1
2.08-2.135.40.3671710.8960.9720.1690.3980.79997.1
2.13-2.25.40.30272090.9260.9810.1430.3340.84997.3
2.2-2.275.20.25572370.940.9840.1240.2840.88797.5
2.27-2.355.20.22672100.9530.9880.110.2520.9197.6
2.35-2.445.50.19772250.9660.9910.0930.2180.94797.8
2.44-2.555.20.16472810.9730.9930.080.1830.99598
2.55-2.695.60.14272760.9840.9960.0650.1561.07398
2.69-2.865.70.11872860.9890.9970.0540.131.19398.3
2.86-3.085.60.09673470.9930.9980.0450.1061.28498.5
3.08-3.395.50.07472850.9950.9990.0350.0821.41998.6
3.39-3.885.10.05773680.9960.9990.0280.0631.58798.7
3.88-4.884.70.04673610.9970.9990.0240.0521.67598.5
4.88-48.5450.04374730.9980.9990.0220.0491.6898.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
HKL-3000data scaling
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.54 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.074 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 7260 5 %RANDOM
Rwork0.16288 ---
obs0.16493 137493 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.676 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0.28 Å2
2---0.86 Å20 Å2
3---0.83 Å2
Refinement stepCycle: 1 / Resolution: 1.8→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11872 0 91 1210 13173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01212545
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611744
X-RAY DIFFRACTIONr_angle_refined_deg1.481.66517174
X-RAY DIFFRACTIONr_angle_other_deg0.5061.57927160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70951604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.403579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.841102015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0710.21921
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214896
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022780
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_it1.9121.8916176
X-RAY DIFFRACTIONr_mcbond_other1.9111.8916174
X-RAY DIFFRACTIONr_mcangle_it2.8433.397727
X-RAY DIFFRACTIONr_mcangle_other2.8433.397728
X-RAY DIFFRACTIONr_scbond_it2.6592.2656369
X-RAY DIFFRACTIONr_scbond_other2.6592.2656370
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1663.9999405
X-RAY DIFFRACTIONr_long_range_B_refined6.19127.0314309
X-RAY DIFFRACTIONr_long_range_B_other6.07924.7714003
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.845 Å
RfactorNum. reflection% reflection
Rfree0.304 527 -
Rwork0.289 9839 -
obs--95.08 %
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)
10.1271-0.0390.23790.1073-0.13530.49220.0315-0.0247-0.0069-0.0109-0.0070.02210.0724-0.0456-0.02450.04590.00460.01790.07790.00350.019748.075159.0885-16.0612
20.1748-0.0333-0.32940.19740.05160.64120.0216-0.01810.02070.01360.02760.0164-0.0160.0571-0.04920.07170.0003-0.01940.063-0.00060.013150.794362.972142.7748
30.136-0.0297-0.25540.18490.05980.59580.0178-0.02150.03350.02820.017-0.0621-0.07180.0889-0.03490.0233-0.0122-0.01710.0771-0.01690.0430.233530.291743.7426
40.1185-0.00050.22350.22970.27310.87930.00190.0125-0.01050.02560.0387-0.012-0.08120.0551-0.04060.1171-0.0020.01330.0328-0.01340.007124.559527.7553102.6465
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 506
2X-RAY DIFFRACTION2B3 - 506
3X-RAY DIFFRACTION3C4 - 506
4X-RAY DIFFRACTION4D3 - 506

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