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- PDB-3nx3: Crystal structure of acetylornithine aminotransferase (argD) from... -

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Basic information

Entry
Database: PDB / ID: 3nx3
TitleCrystal structure of acetylornithine aminotransferase (argD) from Campylobacter jejuni
ComponentsAcetylornithine aminotransferase
KeywordsTRANSFERASE / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases / 3-Layer(aba) Sandwich / acetylornithine aminotransferase
Function / homology
Function and homology information


acetylornithine transaminase / N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity / arginine biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Acetylornithine/Succinylornithine transaminase family / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...Acetylornithine/Succinylornithine transaminase family / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetylornithine aminotransferase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Skarina, T. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,4376
Polymers88,3402
Non-polymers974
Water14,484804
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-57 kcal/mol
Surface area27930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.11, 66.16, 214.34
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acetylornithine aminotransferase / ACOAT


Mass: 44169.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: argD, Cj0227 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9PIR7, acetylornithine transaminase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 804 / 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: 2.05 Å3/Da / Density % sol: 40.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG3350, 200mM magnesium chloride, 100mM Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 17, 2010 / Details: BERYLLIUM LENS
RadiationMonochromator: C(111) DIAMOND LAUE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.75→29.4 Å / Num. obs: 73891 / % possible obs: 99.3 % / Observed criterion σ(I): 4.3 / Redundancy: 8.74 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 21.34
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 4.62 / % possible all: 95.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→29.4 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.19 / σ(F): 0 / Phase error: 16.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1961 3406 5.01 %
Rwork0.1531 --
obs0.1552 68039 99.35 %
all-74252 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.349 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2978 Å2-0 Å20 Å2
2---2.1993 Å2-0 Å2
3---0.9015 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5959 0 4 804 6767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076144
X-RAY DIFFRACTIONf_angle_d1.048259
X-RAY DIFFRACTIONf_dihedral_angle_d11.822325
X-RAY DIFFRACTIONf_chiral_restr0.077911
X-RAY DIFFRACTIONf_plane_restr0.0041064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.86430.26233290.2056211X-RAY DIFFRACTION97
1.8643-1.9390.23563330.17746303X-RAY DIFFRACTION98
1.939-2.02720.22133350.1626386X-RAY DIFFRACTION99
2.0272-2.13410.20523390.15266410X-RAY DIFFRACTION99
2.1341-2.26770.19023380.14636405X-RAY DIFFRACTION100
2.2677-2.44270.2113400.15066484X-RAY DIFFRACTION100
2.4427-2.68840.2033410.15496483X-RAY DIFFRACTION100
2.6884-3.07710.19173420.15526488X-RAY DIFFRACTION100
3.0771-3.87540.16793470.13836602X-RAY DIFFRACTION100
3.8754-29.42280.18813620.15116861X-RAY DIFFRACTION100
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)
10.3108-0.0705-0.19740.69670.07020.43780.0104-0.034-0.0018-0.0608-0.005-0.0542-0.10170.0204-0.00210.0510.00120.01090.0616-0.00060.07071.7899-3.0799-40.8929
20.31450.21760.43970.58290.13910.6777-0.1068-0.1061-0.12890.13190.0583-0.12720.08770.10660.03320.13380.02240.01930.13510.02380.10911.1705-23.8423-23.9248
30.7575-0.1521-0.11171.0398-0.41461.0636-0.011-0.0182-0.02320.01850.03720.1210.0635-0.1028-0.01650.0602-0.00830.02740.0708-0.00630.084-6.1556-24.0897-35.3401
40.8143-0.0832-0.36850.91510.19930.6171-0.03410.0021-0.0886-0.1080.0084-0.12280.00410.06020.02530.06270.01360.04070.04420.00490.080211.9387-16.8889-51.588
50.6693-0.4305-0.13360.8457-0.00771.3229-0.0064-0.06620.06550.0528-0.0001-0.061-0.19630.00980.00740.0906-0.0102-0.00360.0767-0.01810.09341.52436.4349-29.0529
60.59970.46490.47140.52030.30720.49650.0256-0.2532-0.01810.2085-0.1098-0.01970.0935-0.07840.06060.13740.0065-0.010.19440.02790.08963.5647-14.6687-12.8458
70.8585-0.00470.23481.5035-0.77650.770.0929-0.19510.02390.2681-0.157-0.2136-0.09940.21060.0720.1705-0.0201-0.06540.2151-0.00650.091710.4715-3.1055-9.9715
81.3243-0.02450.87070.6970.00921.2399-0.0889-0.53960.20940.2284-0.00560.06-0.2756-0.28640.08530.20680.05980.03350.1971-0.09680.1092-8.51612.8828-12.6905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 16:102)
2X-RAY DIFFRACTION2(chain A and resid 103:161)
3X-RAY DIFFRACTION3(chain A and resid 162:280)
4X-RAY DIFFRACTION4(chain A and resid 281:395)
5X-RAY DIFFRACTION5(chain B and resid 16:102)
6X-RAY DIFFRACTION6(chain B and resid 103:161)
7X-RAY DIFFRACTION7(chain B and resid 162:280)
8X-RAY DIFFRACTION8(chain B and resid 281:395)

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