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- PDB-1z7m: ATP Phosphoribosyl transferase (HisZG ATP-PRTase) from Lactococcu... -

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Basic information

Entry
Database: PDB / ID: 1z7m
TitleATP Phosphoribosyl transferase (HisZG ATP-PRTase) from Lactococcus lactis
Components
  • ATP phosphoribosyltransferase
  • ATP phosphoribosyltransferase regulatory subunit
KeywordsTRANSFERASE / ATP-PRT / histidine biosynthesis / HisZG / allosteric / evolution
Function / homology
Function and homology information


ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / histidyl-tRNA aminoacylation / histidine-tRNA ligase activity / L-histidine biosynthetic process / transferase activity / ATP binding / cytoplasm
Similarity search - Function
ATP phosphoribosyltransferase regulatory subunit / ATP phosphoribosyltransferase HisG, short form / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature. / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase ...ATP phosphoribosyltransferase regulatory subunit / ATP phosphoribosyltransferase HisG, short form / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature. / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / TUNGSTATE(VI)ION / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase regulatory subunit
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsChampagne, K.S. / Sissler, M. / Larrabee, Y. / Doublie, S. / Francklyn, C.S.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Activation of the hetero-octameric ATP phosphoribosyl transferase through subunit interface rearrangement by a tRNA synthetase paralog.
Authors: Champagne, K.S. / Sissler, M. / Larrabee, Y. / Doublie, S. / Francklyn, C.S.
History
DepositionMar 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: ATP phosphoribosyltransferase regulatory subunit
B: ATP phosphoribosyltransferase regulatory subunit
C: ATP phosphoribosyltransferase regulatory subunit
D: ATP phosphoribosyltransferase regulatory subunit
E: ATP phosphoribosyltransferase
F: ATP phosphoribosyltransferase
G: ATP phosphoribosyltransferase
H: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,29216
Polymers254,2278
Non-polymers1,0668
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: ATP phosphoribosyltransferase regulatory subunit
B: ATP phosphoribosyltransferase regulatory subunit
G: ATP phosphoribosyltransferase
H: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,6468
Polymers127,1134
Non-polymers5334
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-57 kcal/mol
Surface area46980 Å2
MethodPISA
3
C: ATP phosphoribosyltransferase regulatory subunit
D: ATP phosphoribosyltransferase regulatory subunit
E: ATP phosphoribosyltransferase
F: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,6468
Polymers127,1134
Non-polymers5334
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10280 Å2
ΔGint-62 kcal/mol
Surface area45940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.684, 222.936, 86.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
ATP phosphoribosyltransferase regulatory subunit


Mass: 39848.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Gene: hisZ / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: Q02147
#2: Protein
ATP phosphoribosyltransferase / ATP-PRTase / ATP-PRT


Mass: 23708.254 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Gene: hisG / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: Q02129, ATP phosphoribosyltransferase
#3: Chemical ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: WO4
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4

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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: 3.12 Å3/Da / Density % sol: 60.32 % / Description: File contains Friedel Pairs
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, Tris-HCL, MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X26C11.2124
SYNCHROTRONNSLS X26C20.97939, 0.95, 0.95
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 10, 2003
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.21241
20.979391
30.951
ReflectionResolution: 2.9→40 Å / Num. obs: 110115 / % possible obs: 96.7 % / Redundancy: 4 % / Biso Wilson estimate: 79 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.052 / Net I/σ(I): 15.72
Reflection shellResolution: 2.9→3.08 Å / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.09 / Num. unique all: 8903 / Rsym value: 0.391 / % possible all: 82.7

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.9→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: File contains Friedel Pairs
RfactorNum. reflectionSelection details
Rfree0.2855 5020 random
Rwork0.2447 --
all0.305 125404 -
obs0.298 110115 -
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.81 Å0.73 Å
Refinement stepCycle: LAST / Resolution: 2.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16569 0 40 0 16609
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0095
X-RAY DIFFRACTIONc_angle_deg1.41

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