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- PDB-2w21: Crystal structure of the aminoacid kinase domain of the glutamate... -

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Basic information

Entry
Database: PDB / ID: 2w21
TitleCrystal structure of the aminoacid kinase domain of the glutamate 5 kinase of Escherichia coli.
ComponentsGLUTAMATE 5-KINASE
KeywordsTRANSFERASE / AMINO ACID KINASE FAMILY / PROLINE BIOSYNTHESIS / AMINO-ACID BIOSYNTHESIS / KINASE / CYTOPLASM / GLUTAMATE KINASEAMINO ACID KINASE FAMILY / GLUTAMATE KINASE
Function / homology
Function and homology information


proline binding / glutamate 5-kinase / glutamate 5-kinase activity / proline biosynthetic process / L-proline biosynthetic process / phosphorylation / magnesium ion binding / protein homodimerization activity / RNA binding / ATP binding ...proline binding / glutamate 5-kinase / glutamate 5-kinase activity / proline biosynthetic process / L-proline biosynthetic process / phosphorylation / magnesium ion binding / protein homodimerization activity / RNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
Glutamate 5-kinase / Glutamate-5-kinase domain / Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase / Glutamate 5-kinase, conserved site / Glutamate 5-kinase signature. / PUA domain / Glutamate/acetylglutamate kinase / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. ...Glutamate 5-kinase / Glutamate-5-kinase domain / Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase / Glutamate 5-kinase, conserved site / Glutamate 5-kinase signature. / PUA domain / Glutamate/acetylglutamate kinase / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. / PUA domain superfamily / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / PUA-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsPerez-Arellano, I. / Gil-Ortiz, F. / Marco-Marin, C. / Cervera, J. / Rubio, V.
CitationJournal: To be Published
Title: The Structure of Glutamate 5 Kinase of Escherichia Coli without Substrates
Authors: Perez-Arellano, I. / Gil-Ortiz, F. / Marco-Marin, C. / Cervera, J. / Rubio, V.
History
DepositionOct 21, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: GLUTAMATE 5-KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6645
Polymers27,2801
Non-polymers3844
Water724
1
A: GLUTAMATE 5-KINASE
hetero molecules

A: GLUTAMATE 5-KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,32910
Polymers54,5602
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area5250 Å2
ΔGint-159.85 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.358, 141.358, 78.373
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 GLUTAMATE 5-KINASE / / GAMMA-GLUTAMYL KINASE


Mass: 27280.154 Da / Num. of mol.: 1 / Fragment: AMINO ACID KINASE DOMAIN, RESIDUES 1-259 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P0A7B5, glutamate 5-kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ILE 129 TO VAL

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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: 4.15 Å3/Da / Density % sol: 70.35 % / Description: NONE
Crystal growpH: 5.6
Details: LITHIUM SULFATE 1M, AMMONIUM SULFATE 0.5M, SODIUM SITRATE 0.1M PH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9796
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.95→122.17 Å / Num. obs: 10173 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 15.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.6
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 15.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J5T

2j5t


Resolution: 2.95→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.88 / SU B: 13.905 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.546 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 490 4.8 %RANDOM
Rwork0.206 ---
obs0.209 9677 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.95 Å2-0.97 Å20 Å2
2---1.95 Å20 Å2
3---2.92 Å2
Refinement stepCycle: LAST / Resolution: 2.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 20 4 1812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221843
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.9792506
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4015245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.0824.72272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.43715302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1171512
X-RAY DIFFRACTIONr_chiral_restr0.1340.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021347
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2510.2861
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21256
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.257
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4910.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9151.51234
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70421933
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2323653
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8734.5573
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
LS refinement shellResolution: 2.95→3.03 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.375 38
Rwork0.283 691

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