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- PDB-3t7b: Crystal Structure of N-acetyl-L-glutamate kinase from Yersinia pestis -

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Basic information

Entry
Database: PDB / ID: 3t7b
TitleCrystal Structure of N-acetyl-L-glutamate kinase from Yersinia pestis
ComponentsAcetylglutamate kinase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / AMINO ACID KINASE / ACETYLGLUTAMATE KINASE
Function / homology
Function and homology information


acetylglutamate kinase / acetylglutamate kinase activity / arginine biosynthetic process via ornithine / arginine biosynthetic process / arginine binding / ATP binding / cytoplasm
Similarity search - Function
N-Acetyl-L-glutamate kinase, noncyclic / Acetylglutamate kinase ArgB / Acetylglutamate kinase family / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / S,R MESO-TARTARIC ACID / Acetylglutamate kinase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsDemas, M.W. / Solberg, R.G. / Cooper, D.R. / Chruszcz, M. / Porebski, P.J. / Zheng, H. / Onopriyenko, O. / Skarina, T. / Savchenko, A. / Anderson, W.F. ...Demas, M.W. / Solberg, R.G. / Cooper, D.R. / Chruszcz, M. / Porebski, P.J. / Zheng, H. / Onopriyenko, O. / Skarina, T. / Savchenko, A. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of N-acetyl-L-glutamate kinase from Yersinia pestis
Authors: Demas, M.W. / Solberg, R.G. / Cooper, D.R. / Chruszcz, M. / Porebski, P.J. / Zheng, H. / Onopriyenko, O. / Skarina, T. / Savchenko, A. / Anderson, W.F. / Minor, W. / Center for Structural ...Authors: Demas, M.W. / Solberg, R.G. / Cooper, D.R. / Chruszcz, M. / Porebski, P.J. / Zheng, H. / Onopriyenko, O. / Skarina, T. / Savchenko, A. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)55,4085
Polymers54,9642
Non-polymers4443
Water1,838102
1
A: Acetylglutamate kinase
B: Acetylglutamate kinase
hetero molecules

A: Acetylglutamate kinase
B: Acetylglutamate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,81610
Polymers109,9274
Non-polymers8896
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area9760 Å2
ΔGint-58 kcal/mol
Surface area37720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.456, 134.688, 98.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Acetylglutamate kinase / / N-acetyl-L-glutamate 5-phosphotransferase / NAG kinase / AGK


Mass: 27481.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Selenomethionine supplemented media / Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: argB, y0311, YPO3925, YP_3124 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q8ZA87, acetylglutamate kinase
#2: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.8 Å3/Da / Density % sol: 67.6 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: PEG3350 20%, NaTartrate 0.2M, 10mM ADP, 5mM Glutamic Acid, pH 7, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97903 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 11, 2010 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 29446 / % possible obs: 100 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.084 / Χ2: 2.122 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.549.10.65614420.9121100
2.54-2.599.20.58114690.9431100
2.59-2.649.30.55114360.9511100
2.64-2.699.30.4814340.9691100
2.69-2.759.30.36414671.0031100
2.75-2.829.40.31814781.0411100
2.82-2.899.40.27814431.0751100
2.89-2.969.40.22114491.1161100
2.96-3.059.40.17914621.1811100
3.05-3.159.40.14514601.2811100
3.15-3.269.40.11914611.3451100
3.26-3.399.40.10414711.4921100
3.39-3.559.40.08114811.6711100
3.55-3.739.40.07114641.951100
3.73-3.979.30.06314722.1771100
3.97-4.279.30.05514672.611100
4.27-4.79.20.05414953.249199.9
4.7-5.389.30.05914953.7371100
5.38-6.789.20.07515145.2961100
6.78-508.30.06915868.632199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-3000data reduction
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1978 / WRfactor Rwork: 0.1673 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8502 / SU B: 13.741 / SU ML: 0.146 / SU R Cruickshank DPI: 0.2586 / SU Rfree: 0.2045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 1475 5.1 %RANDOM
Rwork0.1781 ---
obs0.1799 29001 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 146.48 Å2 / Biso mean: 62.2146 Å2 / Biso min: 36.82 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å20 Å2
2--1.17 Å20 Å2
3----3.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3749 0 30 102 3881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223818
X-RAY DIFFRACTIONr_bond_other_d0.0010.022452
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9915188
X-RAY DIFFRACTIONr_angle_other_deg0.96836081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8815510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39225.267131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.67915661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7581520
X-RAY DIFFRACTIONr_chiral_restr0.0850.2657
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214224
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02648
X-RAY DIFFRACTIONr_mcbond_it0.6521.52544
X-RAY DIFFRACTIONr_mcbond_other0.1231.51056
X-RAY DIFFRACTIONr_mcangle_it1.22124066
X-RAY DIFFRACTIONr_scbond_it2.23231274
X-RAY DIFFRACTIONr_scangle_it3.4414.51122
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 125 -
Rwork0.255 1985 -
all-2110 -
obs--99.06 %
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)
115.2797-6.7781-7.60333.13312.66258.11280.04970.18640.1663-0.1379-0.1354-0.14580.0861-0.03650.08570.5127-0.13440.13780.34690.04360.381644.121451.2876-14.1577
24.1172-1.03280.47675.63052.26045.881-0.21240.10130.0202-0.2263-0.0410.3029-0.1625-0.380.25340.1907-0.1611-0.00930.2077-0.0260.143635.704753.0832-11.2254
35.64223.9255-2.9195.8666-1.71231.55150.2890.23970.5157-0.1287-0.10370.6827-0.2129-0.1411-0.18530.31480.0203-0.03840.27910.00740.372654.313163.4454.5101
42.2580.5084-0.31822.1792-0.4622.6567-0.10140.0968-0.3163-0.222-0.0846-0.32220.3340.16970.1860.0982-0.01050.05620.059-0.00430.178752.513748.6269-2.3915
54.6032-0.8719-0.60968.2803-4.92324.1961-0.1720.59540.2514-0.3688-0.1128-0.18440.3024-0.06840.28480.2185-0.08820.00450.2749-0.05660.118848.794457.6959-20.1115
64.48073.3501-1.60654.3697-1.19371.195-0.55050.87-0.178-0.28860.46-0.33570.387-0.26530.09050.2293-0.07130.09510.3297-0.06950.149856.607461.568-25.532
74.06030.2979-2.13822.2342-2.04325.56540.17150.599-0.0231-0.4009-0.1080.1091-0.278-0.2228-0.06350.3759-0.13240.00630.3532-0.07340.265941.901957.1338-21.0732
810.0384-5.0624-0.78653.8153-2.26745.7913-0.4902-0.9530.30460.10420.2214-0.36510.57690.64650.26880.6801-0.0239-0.03570.55230.11240.741950.030734.744416.8761
97.9813-0.14480.15388.6189-1.64993.4129-0.0489-0.3126-0.9673-0.1611-0.1109-0.88470.46980.28310.15970.2137-0.02180.09060.18320.13890.374553.213230.772412.7666
1012.48612.24910.11735.48733.53583.01880.3359-1.6889-0.44291.0403-0.42940.23630.3174-0.23610.09360.4812-0.09030.08650.45160.10530.289644.284857.600120.994
112.73740.6077-0.6793.6654-0.79892.91220.0224-0.0949-0.2456-0.0102-0.12060.06680.2057-0.30120.09820.0931-0.08580.0220.11890.03140.172541.4941.528210.0357
1215.70897.6962-7.53568.9765-8.76458.5668-0.457-2.0026-0.37551.0041-0.2559-0.7784-0.9580.28710.71291.1024-0.1309-0.08861.17630.18820.809747.283527.978633.0509
137.32640.39530.14154.53710.40529.2056-0.0052-0.76760.3640.5893-0.3152-0.3469-0.13280.25190.32040.3949-0.24620.00520.35210.1350.402241.615333.065130.8732
148.60891.1442-3.71011.08-1.65653.1133-0.4227-0.8447-1.118-0.4309-0.167-0.26470.81120.41350.58970.6279-0.03160.04910.43570.25010.701748.993424.639622.8356
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B0 - 12
2X-RAY DIFFRACTION2B13 - 40
3X-RAY DIFFRACTION3B41 - 60
4X-RAY DIFFRACTION4B61 - 161
5X-RAY DIFFRACTION5B162 - 191
6X-RAY DIFFRACTION6B192 - 228
7X-RAY DIFFRACTION7B229 - 257
8X-RAY DIFFRACTION8A0 - 17
9X-RAY DIFFRACTION9A18 - 46
10X-RAY DIFFRACTION10A47 - 72
11X-RAY DIFFRACTION11A73 - 178
12X-RAY DIFFRACTION12A179 - 196
13X-RAY DIFFRACTION13A197 - 238
14X-RAY DIFFRACTION14A239 - 257

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