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- PDB-1h3d: STRUCTURE OF THE E.COLI ATP-PHOSPHORIBOSYLTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1h3d
TitleSTRUCTURE OF THE E.COLI ATP-PHOSPHORIBOSYLTRANSFERASE
ComponentsATP-PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE / PHOSPHORIBOSYLTRANSFERASE / HISITIDINE BIOSYNTHESIS / GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / magnesium ion binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
ATP phosphoribosyltransferase HisG, long form / Histidine biosynthesis HisG, C-terminal / HisG, C-terminal domain / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature. / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta ...ATP phosphoribosyltransferase HisG, long form / Histidine biosynthesis HisG, C-terminal / HisG, C-terminal domain / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature. / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / L(+)-TARTARIC ACID / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsLohkamp, B. / McDermott, G. / Coggins, J.R. / Lapthorn, A.J.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The Structure of Escherichia Coli ATP-Phosphoribosyltransferase: Identification of Substrate Binding Sites and Mode of AMP Inhibition
Authors: Lohkamp, B. / Mcdermott, G. / Campbell, S. / Coggins, J.R. / Lapthorn, A.J.
History
DepositionAug 27, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 285 TEXT TO EXPLAIN UNUSUAL UNIT-CELL DATA: HEXAGONAL SETTING USED

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: ATP-PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0564
Polymers33,4091
Non-polymers6473
Water00
1
A: ATP-PHOSPHORIBOSYLTRANSFERASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)204,33724
Polymers200,4526
Non-polymers3,88418
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
MethodPQS
Unit cell
Length a, b, c (Å)133.645, 133.645, 114.118
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein ATP-PHOSPHORIBOSYLTRANSFERASE


Mass: 33408.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PTB361 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)PLYSS
References: UniProt: P10366, UniProt: P60757*PLUS, ATP phosphoribosyltransferase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
Compound detailsCATALYTIC ACTIVITY: 1-(5-PHOSPHO-D-RIBOSYL)-ATP + DIPHOSPHATE = ATP + 5-PHOSPHO-ALPHA-D-RIBOSE 1- ...CATALYTIC ACTIVITY: 1-(5-PHOSPHO-D-RIBOSYL)-ATP + DIPHOSPHATE = ATP + 5-PHOSPHO-ALPHA-D-RIBOSE 1-DIPHOSPHATE. FIRST STEP IN HISTIDINE BIOSYNTHESIS. CRITICAL FOR REGULATION OF HISTIDINE METABOLISM. EXISTS AS A HOMOHEXAMER.

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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: 2.95 Å3/Da / Density % sol: 58 %
Crystal growpH: 5.6
Details: PROTEIN WAS CRYSTALLIZED FROM 1.3M SODIUM TARTRATE, 50-200MM MGCL2, 100MM CITRATE BUFFER, PH 5.6, IN PRESENCE OF 2MM AMP
Crystal grow
*PLUS
Temperature: 293 K / pH: 5.6 / Method: vapor diffusion, sitting drop / Details: Lohkamp, B., (2000) Acta Crystallogr., D56, 1488.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.3 Msodium tartrate1reservoir
250-200 mM1reservoirMgCl2
3100 mMcitrate1reservoirpH5.6
42 mMAMP1reservoir
510 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.7→81.65 Å / Num. obs: 10860 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 83.842 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 18
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 3.1 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.7 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→81.65 Å / SU B: 13.292 / SU ML: 0.2812 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.89567 / ESU R Free: 0.36452
RfactorNum. reflection% reflectionSelection details
Rfree0.27715 883 8.1 %RANDOM
Rwork0.22189 ---
obs0.2263 9975 99.5 %-
Displacement parametersBiso mean: 46.118 Å2
Baniso -1Baniso -2Baniso -3
1-2.15 Å21.08 Å20 Å2
2--2.15 Å20 Å2
3----3.23 Å2
Refinement stepCycle: LAST / Resolution: 2.7→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2187 0 43 0 2230
Refinement
*PLUS
Highest resolution: 2.7 Å / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.017
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.9

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