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- PDB-1q1k: Structure of ATP-phosphoribosyltransferase from E. coli complexed... -

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Basic information

Entry
Database: PDB / ID: 1q1k
TitleStructure of ATP-phosphoribosyltransferase from E. coli complexed with PR-ATP
ComponentsATP phosphoribosyltransferase
KeywordsTRANSFERASE / histidine biosynthesis / PRPP binding / PR-ATP inhibition
Function / homology
Function and homology information


ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / histidine biosynthetic process / magnesium ion binding / ATP binding / 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
PHOSPHORIBOSYL ATP / L(+)-TARTARIC ACID / ATP phosphoribosyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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.A. / Coggins, J.R. / Lapthorn, A.J.
History
DepositionJul 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 3, 2017Group: Non-polymer description
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN The ligand PRT is a fragment of Phosphoribosyl ATP with the ribose and triphosphate ...HETEROGEN The ligand PRT is a fragment of Phosphoribosyl ATP with the ribose and triphosphate either disordered or cleaved within the crystal. The authors modelled the ribose and triphosphate with zero occupancy.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4284
Polymers33,4091
Non-polymers1,0193
Water0
1
A: ATP phosphoribosyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)206,56924
Polymers200,4526
Non-polymers6,11718
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 operation17_555x-y+1/3,-y+2/3,-z+2/31
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area28510 Å2
ΔGint-165 kcal/mol
Surface area72260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)132.100, 132.100, 113.379
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe biological assembly is a hexamer generated from the monomer in the asymmetric unit by the operations: -y, x-y, z; -x+y, -x, z; 1/3+y, 2/3+x, 2/3-z; 1/3+x-y, 2/3-y, 2/3-z and 1/3-x, 2/3-x+y, 2/3-z.

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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) / Gene: HISG / Plasmid: pTB361 / Production host: Escherichia coli (E. coli) / Strain (production host): B824(DE3)pLysS / References: UniProt: P60757, ATP phosphoribosyltransferase
#2: Chemical ChemComp-PRT / PHOSPHORIBOSYL ATP / [[(2~{R},3~{S},4~{R},5~{R})-5-[6-azanylidene-1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 719.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H25N5O20P4
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6

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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: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: sodium tartrate, magnesium chloride, sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.86 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 5, 2002
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.86 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 8521 / Num. obs: 8521 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.9
Reflection shellResolution: 2.9→3.02 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H3D

1h3d


Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.898 / SU B: 17.014 / SU ML: 0.317 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.435 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27243 687 8.1 %RANDOM
Rwork0.20967 ---
all0.21454 8521 --
obs0.21454 7834 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.098 Å2
Baniso -1Baniso -2Baniso -3
1-3.04 Å21.52 Å20 Å2
2--3.04 Å20 Å2
3----4.56 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2187 0 64 0 2251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212255
X-RAY DIFFRACTIONr_angle_refined_deg2.0182.013049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8075286
X-RAY DIFFRACTIONr_chiral_restr0.1260.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021639
X-RAY DIFFRACTIONr_nbd_refined0.2640.21000
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.26
X-RAY DIFFRACTIONr_mcbond_it0.7361.51429
X-RAY DIFFRACTIONr_mcangle_it1.42422282
X-RAY DIFFRACTIONr_scbond_it2.2553826
X-RAY DIFFRACTIONr_scangle_it3.8424.5767
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.556 60
Rwork0.342 555
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)
15.8823-1.17622.31025.2731-0.02445.98590.1142-0.4007-0.59760.60060.27390.2980.81430.3694-0.38810.15720.1577-0.00520.3670.01870.275341.561928.942955.2993
22.6445-1.0763-2.22612.80611.3148.20260.1089-0.01510.4922-0.23910.4939-0.3377-1.01380.3868-0.60280.1483-0.07960.11120.2518-0.06910.396736.687155.423544.9857
39.7782-3.41110.148917.1269-1.22785.69360.57-0.89530.87371.2122-0.07790.9288-0.37290.0358-0.49210.5444-0.19030.260.8776-0.04480.126857.971847.634579.145
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 1025 - 102
2X-RAY DIFFRACTION1AA192 - 225192 - 225
3X-RAY DIFFRACTION1AC - D410 - 4111
4X-RAY DIFFRACTION2AA103 - 191103 - 191
5X-RAY DIFFRACTION2AB5001
6X-RAY DIFFRACTION3AA226 - 299226 - 299

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