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- PDB-2x2w: Acetylglutamate kinase from Escherichia coli bound to N-acetyl-L-... -

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Basic information

Entry
Database: PDB / ID: 2x2w
TitleAcetylglutamate kinase from Escherichia coli bound to N-acetyl-L-glutamyl-5-phosphate
ComponentsACETYLGLUTAMATE KINASE
KeywordsTRANSFERASE / ARGININE BIOSYNTHESIS / ATP-BINDING / NUCLEOTIDE-BINDING / AMINO-ACID BIOSYNTHESIS / AMINO ACID KINASE FAMILY
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
N-ACETYL-L-GLUTAMYL 5-PHOSPHATE / Acetylglutamate kinase / Acetylglutamate kinase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGil-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
DepositionJan 18, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Refinement description
Revision 1.2Mar 6, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / reflns_shell / struct_biol
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _reflns_shell.pdbx_Rsym_value
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)55,1036
Polymers54,3732
Non-polymers7304
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-50.7 kcal/mol
Surface area20760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.652, 78.652, 283.054
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: (0.236, 0.8912, 0.3873), (0.8841, -0.3623, 0.2951), (0.4033, 0.2728, -0.8734)
Vector: -75.6, 30.51, 167.6)

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Components

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


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-X2W / N-ACETYL-L-GLUTAMYL 5-PHOSPHATE / N-ACETYL-5-OXO-5-(PHOSPHONOOXY)-L-NORVALINE


Type: L-peptide linking / Mass: 269.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H12NO8P
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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 growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30-35 % PEG MONOMETHYL ETHER 5K, 0.1 M MES PH 6.5, 0.1-0.2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→29.24 Å / Num. obs: 35550 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Rsym value: 0.071 / Net I/σ(I): 44
Reflection shellResolution: 2→2.07 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 6.3 / Rsym value: 0.406 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000Kdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WXB
Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.35 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1802 5 %RANDOM
Rwork0.199 ---
obs0.2 34319 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: 39.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å2-0.25 Å20 Å2
2---0.51 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 0 44 157 4009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223894
X-RAY DIFFRACTIONr_bond_other_d0.0010.022544
X-RAY DIFFRACTIONr_angle_refined_deg1.1682.0015282
X-RAY DIFFRACTIONr_angle_other_deg0.8383.0016286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7365514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.54625.775142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94915686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4381518
X-RAY DIFFRACTIONr_chiral_restr0.0630.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214316
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02654
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_it0.4111.52556
X-RAY DIFFRACTIONr_mcbond_other0.1081.51066
X-RAY DIFFRACTIONr_mcangle_it0.76424078
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.35931338
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2354.51204
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
1A936medium positional0.40.5
2B936medium positional0.40.5
1A992loose positional0.755
2B992loose positional0.755
1A936medium thermal0.552
2B936medium thermal0.552
1A992loose thermal0.5510
2B992loose thermal0.5510
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 121 -
Rwork0.216 2442 -
obs--99.81 %
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)
112.93412.87875.05367.07392.23397.77760.3096-0.5117-0.08040.555-0.16880.08360.1038-0.0057-0.14080.14360.06330.05050.11720.02120.03255.62261.796113.433
210.83894.2611-0.15699.71260.26164.58740.1174-0.71780.24610.6946-0.0851-0.2837-0.43240.325-0.03220.28650.00640.00720.31270.0090.144415.74158.362122.174
39.1844-1.4634-4.85710.92430.2124.0190.1113-1.2221-0.10830.4407-0.04550.115-0.13960.6135-0.06580.4034-0.20460.0540.42720.0130.025812.16259.698113.938
40.6402-2.92010.766713.4487-3.56241.10720.0928-0.07330.0943-0.58890.144-0.10620.0033-0.2807-0.23670.67960.13670.07140.9029-0.18661.018727.68779.95107.049
53.2315-0.4708-0.22082.7085-0.40182.2002-0.0027-0.07310.2193-0.0170.0317-0.0475-0.14140.1128-0.02910.0204-0.00380.01290.0552-0.02060.036414.07564.758103.675
66.3762-6.4415-9.68886.738210.595417.5993-0.6599-0.4245-0.20450.35530.25840.2323-0.16080.22860.40140.6114-0.0015-0.01060.6538-0.0750.6263.04776.65130.157
74.0813-0.2390.0748.0215-8.06211.4697-0.2584-0.6911-0.02250.6954-0.0178-0.2502-0.3312-0.01130.27610.33120.0470.03980.368-0.05040.2717-3.12276.273124.914
813.80415.4064-1.13327.0692.095810.5085-0.4433-0.38170.83830.62770.3139-0.1892-0.8522-0.00590.12930.940.143-0.27870.5341-0.22280.40194.92984.169122.92
98.5865-1.13735.11570.45510.502912.1054-0.1016-0.1130.4680.05950.0242-0.0622-0.21070.33150.07730.1637-0.01190.01150.1146-0.00540.13040.90575.709111.38
101.897-2.94631.674310.8175-1.64433.823-0.2605-0.5457-0.20521.23640.3218-0.07280.2350.1379-0.06120.31920.07590.07070.48250.0610.19992.81165.721122.667
112.2117-0.82030.30485.58510.34513.71250.0209-0.05450.3833-0.07970.0095-0.3448-0.48640.2962-0.03050.1137-0.00790.05550.05120.01140.110727.32451.93688.363
122.2376-0.24520.75044.7124-0.22122.7584-0.03310.26760.134-0.69890.06510.014-0.17410.0093-0.0320.1598-0.0080.05360.0730.02550.083321.97252.82683.262
138.0585.49423.443911.92467.50185.6832-0.27890.4852-0.1514-0.1410.1228-0.24040.28860.51340.1560.23850.08440.0730.37430.05980.299238.04863.365101.242
141.60193.34110.72412.2167-0.53371.1280.07940.3115-0.4199-0.30960.0371-1.15460.24690.3881-0.11660.39880.02920.06330.5909-0.01020.490843.91755.945105.975
152.2570.28160.38733.56840.17812.49320.0225-0.2805-0.08820.20080.0361-0.39920.12270.2456-0.05850.040.0190.00970.13010.01030.094926.59352.524102.615
161.89530.03790.49612.25270.90223.6021-0.0687-0.2517-0.16580.14070.1659-0.01390.19010.0751-0.09730.03860.02490.0340.0610.03050.069423.35446.48599.186
173.491-0.9336-2.22182.79671.76873.58130.15070.10230.0168-0.39730.0171-0.76090.19340.1562-0.16780.2792-0.03520.13660.1742-0.01740.318241.70641.37678.942
1810.5605-3.83990.23647.41122.94547.48810.27430.6532-0.15210.2433-0.031-0.97020.41220.9399-0.24320.2812-0.0092-0.00270.3854-0.06920.454747.76839.15286.721
195.2551.9331-0.53698.1323-0.19412.6683-0.0511-0.09840.0277-0.16840.1848-0.454-0.06420.1346-0.13380.05080.00670.08110.1147-0.05330.168534.68642.20887.569
207.5697-5.27555.15769.2922-0.27558.5582-0.00870.25280.1228-1.14770.0129-0.1509-0.4459-0.0152-0.00420.3191-0.05610.11980.08910.00270.201130.17244.0578.654
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 12
2X-RAY DIFFRACTION2A13 - 29
3X-RAY DIFFRACTION3A30 - 51
4X-RAY DIFFRACTION4A52 - 66
5X-RAY DIFFRACTION5A67 - 181
6X-RAY DIFFRACTION6A182 - 190
7X-RAY DIFFRACTION7A191 - 200
8X-RAY DIFFRACTION8A201 - 217
9X-RAY DIFFRACTION9A218 - 230
10X-RAY DIFFRACTION10A231 - 258
11X-RAY DIFFRACTION11B1 - 18
12X-RAY DIFFRACTION12B19 - 43
13X-RAY DIFFRACTION13B44 - 55
14X-RAY DIFFRACTION14B56 - 66
15X-RAY DIFFRACTION15B67 - 132
16X-RAY DIFFRACTION16B133 - 177
17X-RAY DIFFRACTION17B178 - 199
18X-RAY DIFFRACTION18B200 - 217
19X-RAY DIFFRACTION19B218 - 240
20X-RAY DIFFRACTION20B241 - 258

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