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- PDB-3s6k: Crystal structure of xcNAGS -

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Basic information

Entry
Database: PDB / ID: 3s6k
TitleCrystal structure of xcNAGS
ComponentsAcetylglutamate kinase
KeywordsTRANSFERASE / synthase / kinase
Function / homology
Function and homology information


acetylglutamate kinase / acetylglutamate kinase activity / L-arginine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Acetylglutamate kinase ArgB, GNAT domain-containing / N-Acetyl-L-glutamate kinase, fungal-type / Vertebrate-like NAGS Gcn5-related N-acetyltransferase (GNAT) domain / NAT, N-acetyltransferase, of N-acetylglutamate synthase / Vertebrate-like NAGS Gcn5-related N-acetyltransferase (GNAT) domain profile. / Acetylglutamate kinase family / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily ...Acetylglutamate kinase ArgB, GNAT domain-containing / N-Acetyl-L-glutamate kinase, fungal-type / Vertebrate-like NAGS Gcn5-related N-acetyltransferase (GNAT) domain / NAT, N-acetyltransferase, of N-acetylglutamate synthase / Vertebrate-like NAGS Gcn5-related N-acetyltransferase (GNAT) domain profile. / Acetylglutamate kinase family / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetylglutamate kinase / Acetylglutamate kinase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8018 Å
AuthorsShi, D. / Li, Y. / Cabrera-Luque, J. / Jin, Z. / Yu, X. / Allewell, N.M. / Tuchman, M.
CitationJournal: Plos One / Year: 2011
Title: A Novel N-acetylglutamate synthase architecture revealed by the crystal structure of the bifunctional enzyme from Maricaulis maris.
Authors: Shi, D. / Li, Y. / Cabrera-Luque, J. / Jin, Z. / Yu, X. / Zhao, G. / Haskins, N. / Allewell, N.M. / Tuchman, M.
History
DepositionMay 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylglutamate kinase


Theoretical massNumber of molelcules
Total (without water)51,8791
Polymers51,8791
Non-polymers00
Water00
1
A: Acetylglutamate kinase

A: Acetylglutamate kinase

A: Acetylglutamate kinase

A: Acetylglutamate kinase


Theoretical massNumber of molelcules
Total (without water)207,5154
Polymers207,5154
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+2/31
crystal symmetry operation10_665-y+1,-x+1,-z+2/31
Buried area10270 Å2
ΔGint-52 kcal/mol
Surface area77140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.228, 133.228, 191.364
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Acetylglutamate kinase


Mass: 51878.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Strain: 8004 / Gene: XC_1873 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q4UVI7, UniProt: A0A0H2X8L7*PLUS, amino-acid N-acetyltransferase, acetylglutamate kinase

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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: 4.74 Å3/Da / Density % sol: 74.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4 M Sodium malonate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9734 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9734 Å / Relative weight: 1
ReflectionRedundancy: 17.2 % / Number: 362784 / Rmerge(I) obs: 0.065 / Χ2: 1.7 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 21146 / % possible obs: 83.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.035099.410.0453.36319.5
4.796.0310010.0622.19221.1
4.184.7999.810.0541.44521.5
3.84.1810010.1041.34221.7
3.533.810010.1591.24818.7
3.323.5393.810.1931.10913.7
3.153.3274.310.2150.97113
3.023.1559.510.2341.04212.2
2.93.0248.810.2880.93110.7
2.82.95410.3341.0138
ReflectionResolution: 2.8→46.072 Å / Num. obs: 33401 / % possible obs: 83.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.2 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 55.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 8 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1336 / % possible all: 54

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Processing

Software
NameVersionClassificationNB
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
ISIRphasing
RefinementResolution: 2.8018→46.072 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.4901 / SU ML: 0.56 / σ(F): 0 / Phase error: 52.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3878 1690 5.06 %
Rwork0.3211 31711 -
obs0.3244 33401 71.49 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 161.528 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 687.33 Å2 / Biso mean: 190.1302 Å2 / Biso min: 60.18 Å2
Baniso -1Baniso -2Baniso -3
1-32.309 Å20 Å2-0 Å2
2--32.309 Å20 Å2
3----64.618 Å2
Refinement stepCycle: LAST / Resolution: 2.8018→46.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3407 0 0 0 3407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013466
X-RAY DIFFRACTIONf_angle_d1.6474699
X-RAY DIFFRACTIONf_chiral_restr0.121543
X-RAY DIFFRACTIONf_plane_restr0.006607
X-RAY DIFFRACTIONf_dihedral_angle_d20.0291276
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8018-2.90190.4695700.41161360143031
2.9019-3.01810.4462800.3991437151732
3.0181-3.15540.4611960.37921837193341
3.1554-3.32170.4941240.3632340246453
3.3217-3.52970.39211730.35823264343773
3.5297-3.80220.39622160.34923992420890
3.8022-4.18450.44382230.31684298452197
4.1845-4.78950.36642370.28964331456898
4.7895-6.03220.41252330.33784424465799
6.0322-46.07780.34982380.303144284666100
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)
17.72054.9181-0.08325.2422-0.81121.53191.9089-3.8348-0.39013.3131-3.00211.15351.04950.87281.1796-1.43971.7513-1.37190.3893-0.18121.937740.391763.262190.362
2-1.16264.3641-3.4993-1.99470.11055.37660.717-0.95380.5859-0.2466-0.527-0.0736-0.2502-0.2786-0.04120.3927-0.1919-0.2861.2843-0.15291.140856.453640.669274.5591
310.53525.0499-3.66258.40030.16838.48061.0468-0.35871.62260.4542-0.17492.53590.2093-0.7947-0.71810.45370.1555-0.19111.1386-0.31.027653.014445.497495.4749
48.6371-2.1749-1.35451.64562.07644.18580.5415-0.6747-0.24930.2213-0.3632-0.3068-0.32151.2487-0.16191.3720.0975-0.17291.2701-0.31751.123755.045866.1085113.1535
55.9733.2330.95975.49940.58186.7456-1.2178-2.85410.05090.1451.3715-1.8295-2.8354-1.9927-0.21660.98830.65580.12722.141-0.16821.05239.821261.9348120.4085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 10:38)A10 - 38
2X-RAY DIFFRACTION2(chain A and resid 39:207)A39 - 207
3X-RAY DIFFRACTION3(chain A and resid 208:294)A208 - 294
4X-RAY DIFFRACTION4(chain A and resid 295:388)A295 - 388
5X-RAY DIFFRACTION5(chain A and resid 389:447)A389 - 447

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