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- PDB-2wxb: Acetylglutamate kinase from Escherichia coli free of substrates -

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Basic information

Entry
Database: PDB / ID: 2wxb
TitleAcetylglutamate kinase from Escherichia coli free of substrates
ComponentsACETYLGLUTAMATE KINASE
KeywordsTRANSFERASE / ACETYLGLUTAMATE KINASE / AMINOACID KINASE FAMILY / KINASE / ARGININE BIOSYNTHESIS
Function / homology
Function and homology information


acetylglutamate kinase / acetylglutamate kinase activity / arginine biosynthetic process via ornithine / arginine biosynthetic process / phosphorylation / cellular response to DNA damage stimulus / ATP binding / cytoplasm
Similarity search - Function
N-Acetyl-L-glutamate kinase, noncyclic / Acetylglutamate kinase ArgB / Acetylglutamate kinase family / Carbamate kinase / Acetylglutamate kinase-like / Amino acid kinase family / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetylglutamate kinase / ACETATE ION / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Acetylglutamate kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRamon-Maiques, S. / Gil-Ortiz, F. / Rubio, V.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Two Crystal Structures of Escherichia Coli N-Acetyl-L-Glutamate Kinase Demonstrate the Cycling between Open and Closed Conformations.
Authors: Gil-Ortiz, F. / Ramon-Maiques, S. / Fernandez-Murga, M.L. / Fita, I. / Rubio, V.
History
DepositionNov 6, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYLGLUTAMATE KINASE
B: ACETYLGLUTAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8036
Polymers54,3732
Non-polymers4304
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-21.2 kcal/mol
Surface area20970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.696, 78.696, 277.743
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 54
2115B1 - 54
1215A73 - 178
2215B73 - 178

NCS oper: (Code: given
Matrix: (0.2369, 0.8983, 0.3702), (0.8866, -0.3557, 0.2956), (0.3972, 0.2581, -0.8807)
Vector: -74.11, 31.1, 165.6)

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Components

#1: Protein ACETYLGLUTAMATE KINASE / / NAG KINASE / AGK / N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE / N-ACETYL-L-GLUTAMATE KINASE


Mass: 27186.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) / Plasmid: PET15-B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A6C8, UniProt: A0A140NEG9*PLUS, acetylglutamate kinase
#2: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Dithioerythritol


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 5.6
Details: 0.1 M SODIUM CITRATE PH 5.6, 26-32% PEG 4000 AND 0.1-0.3 M AMMONIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8468
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 24, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8468 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 35514 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GS5
Resolution: 2→19.95 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.213 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1761 5 %RANDOM
Rwork0.214 ---
obs0.216 33717 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.98 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å2-0.72 Å20 Å2
2---1.44 Å20 Å2
3---2.16 Å2
Refinement stepCycle: LAST / Resolution: 2→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 24 176 3996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223862
X-RAY DIFFRACTIONr_bond_other_d0.0010.022535
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.9965233
X-RAY DIFFRACTIONr_angle_other_deg0.83836280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7865513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01125.775142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82315679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8091518
X-RAY DIFFRACTIONr_chiral_restr0.0680.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214287
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02651
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_it0.4821.52544
X-RAY DIFFRACTIONr_mcbond_other0.1351.51062
X-RAY DIFFRACTIONr_mcangle_it0.83624057
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.47731318
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.334.51176
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A930medium positional0.350.5
2B930medium positional0.350.5
1A972loose positional0.725
2B972loose positional0.725
1A930medium thermal0.532
2B930medium thermal0.532
1A972loose thermal0.6210
2B972loose thermal0.6210
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 130 -
Rwork0.237 2401 -
obs--100 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.48351.04542.04514.6468-0.05644.90170.2603-0.5605-0.32860.5472-0.17630.0660.20060.0128-0.08390.2011-0.00620.06490.2370.04590.07189.37857.86116.153
211.59063.78311.12291.90191.00040.72360.3321-0.91430.68730.133-0.0717-0.097-0.00660.1368-0.26030.2974-0.03390.02420.3408-0.06860.254525.30969.665109.007
313.2958-7.10761.14273.8703-0.76550.5636-0.2182-0.45730.8650.05930.1798-0.4691-0.051-0.00670.03850.4043-0.0218-0.01460.3523-0.06030.370125.16982.578103.935
43.08780.47610.59974.5769-0.96732.6463-0.0536-0.1935-0.08790.1012-0.0335-0.168-0.10840.14720.08710.05740.01790.01630.09290.00180.023319.1762.298103.484
54.22870.7001-0.73743.628-0.11121.6483-0.05880.07260.1149-0.24960.07670.3188-0.1469-0.0361-0.0180.06580.0097-0.02320.07150.00310.02910.48466.70699.013
65.9972-6.6158-1.00947.84592.28996.6611-0.7563-1.31270.59070.86370.9483-0.4613-0.2456-0.0319-0.1920.31490.00440.04720.8896-0.25660.31282.11174.441123.609
710.51171.4513-2.73231.00851.976713.2277-0.7365-0.52051.09880.00740.5372-0.0824-0.97580.60420.19930.9920.2178-0.38060.8147-0.35030.6284.49584.08120.888
82.6321-1.8191.08666.0505-1.96975.4267-0.0917-0.4766-0.02650.5083-0.0069-0.01960.20380.11340.09870.22390.00880.03980.2732-0.02760.12882.17268.578117.368
92.4613-0.26710.38435.604-0.75123.0086-0.12820.216-0.0173-0.45160.0562-0.2071-0.36290.15370.0720.2454-0.01610.06350.1447-0.02420.068723.36952.67382.745
108.724710.92715.969213.73417.51274.1202-0.3110.3507-0.2641-0.30810.5061-0.3677-0.16680.3376-0.19520.20570.01970.040.32960.00990.290234.10460.23396.993
116.1945-4.58511.299614.2565-6.25952.9315-0.24450.0434-0.1389-0.9243-0.0272-1.16380.53710.07090.27160.38180.0535-0.0210.5464-0.18071.151143.47154.726105.61
122.79070.48780.56713.25640.28061.9959-0.0432-0.2314-0.35580.11310.0948-0.32790.07560.164-0.05150.08180.01760.05520.1040.01070.117124.89552.38199.887
131.6215-0.5179-0.06692.28440.71632.583-0.019-0.1497-0.25160.09770.1198-0.08790.14460.1846-0.10080.09330.00780.03940.08650.03420.147725.00546.96897.286
144.0687-4.5838-2.0168.282.5081.31570.2257-0.01930.1172-0.22940.0145-0.4256-0.0640.3351-0.24020.4619-0.07210.13050.4569-0.08830.368941.96641.19177.208
159.53984.0713-2.01632.98742.868211.6819-0.1066-0.2203-0.4788-0.23310.4968-0.4661-0.43811.956-0.39020.52070.05220.05570.69050.05360.900847.24639.74285.637
164.9345-0.16020.19516.3289-0.35163.8388-0.05820.18150.2925-0.48350.079-0.5503-0.20810.2564-0.02070.2023-0.02220.10860.1881-0.06580.241132.50243.07181.966
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 39
2X-RAY DIFFRACTION2A40 - 55
3X-RAY DIFFRACTION3A56 - 66
4X-RAY DIFFRACTION4A67 - 113
5X-RAY DIFFRACTION5A114 - 176
6X-RAY DIFFRACTION6A177 - 199
7X-RAY DIFFRACTION7A200 - 217
8X-RAY DIFFRACTION8A218 - 258
9X-RAY DIFFRACTION9B1 - 38
10X-RAY DIFFRACTION10B39 - 55
11X-RAY DIFFRACTION11B56 - 69
12X-RAY DIFFRACTION12B70 - 137
13X-RAY DIFFRACTION13B138 - 179
14X-RAY DIFFRACTION14B180 - 199
15X-RAY DIFFRACTION15B200 - 217
16X-RAY DIFFRACTION16B218 - 258

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