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- PDB-4yi7: Anthranilate bound at active site of anthranilate phosphoribosyl ... -

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Basic information

Entry
Database: PDB / ID: 4yi7
TitleAnthranilate bound at active site of anthranilate phosphoribosyl transferase from Acinetobacter (AnPRT; TrpD)
ComponentsAnthranilate phosphoribosyltransferase
KeywordsTRANSFERASE / phosphoribosyl binding / anthranilate bound
Function / homology
Function and homology information


anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / tryptophan biosynthetic process / magnesium ion binding
Similarity search - Function
Anthranilate phosphoribosyl transferase / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C / Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / Glycosyl transferase family 3, N-terminal domain / Glycosyl transferase family 3, N-terminal domain superfamily / Glycosyl transferase family, helical bundle domain / Glycosyl transferase, family 3 / Glycosyl transferase family, a/b domain ...Anthranilate phosphoribosyl transferase / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C / Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / Glycosyl transferase family 3, N-terminal domain / Glycosyl transferase family 3, N-terminal domain superfamily / Glycosyl transferase family, helical bundle domain / Glycosyl transferase, family 3 / Glycosyl transferase family, a/b domain / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-AMINOBENZOIC ACID / Anthranilate phosphoribosyltransferase
Similarity search - Component
Biological speciesAcinetobacter baylyi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.853 Å
AuthorsEvans, G.L. / Newton, M.S. / Norris, G.E. / Patrick, W.M.
CitationJournal: To Be Published
Title: Substrate inhibition of protein in tryptophan biosynthesis pathway redirects flux to aromatic catabolism in Acinetobacter baylyi ADP1.
Authors: Evans, G.E. / Nigon, L.V. / Ponniah, K. / Burr, N. / Anderson, B.F. / Norris, G.E. / Patrick, W.M.
History
DepositionFeb 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anthranilate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5902
Polymers39,4531
Non-polymers1371
Water2,144119
1
A: Anthranilate phosphoribosyltransferase
hetero molecules

A: Anthranilate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1804
Polymers78,9062
Non-polymers2742
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area2450 Å2
ΔGint-8 kcal/mol
Surface area24330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.997, 70.830, 169.156
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 Anthranilate phosphoribosyltransferase /


Mass: 39453.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1) (bacteria)
Strain: ATCC 33305 / BD413 / ADP1 / Gene: trpD, ACIAD2462 / Plasmid: pCA24N-ACTRPD / Production host: Escherichia coli (E. coli) / Strain (production host): JMP19 (DELTA -TRPF)
References: UniProt: P00500, anthranilate phosphoribosyltransferase
#2: Chemical ChemComp-BE2 / 2-AMINOBENZOIC ACID / Anthranilic acid


Type: L-peptide linking / Mass: 137.136 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C7H7NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.92 % / Description: Very rough-surfaced rectangular
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.96 / Details: PEG 8000, sodium cacodylate, magnesium acetate

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 8, 2014
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.85→45 Å / Num. obs: 31276 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.025 / Net I/σ(I): 28.7
Reflection shellResolution: 1.85→1.91 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.7 / % possible all: 99

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
Aimless(aimless: 0.3.11)data scaling
PHASER(phaser_mr: 2.5.6)phasing
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GTN

4gtn


Resolution: 1.853→42.289 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2577 1545 4.94 %Random selection
Rwork0.223 ---
obs0.2247 31276 99.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.853→42.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 10 119 2464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072368
X-RAY DIFFRACTIONf_angle_d0.9363215
X-RAY DIFFRACTIONf_dihedral_angle_d12.516811
X-RAY DIFFRACTIONf_chiral_restr0.038399
X-RAY DIFFRACTIONf_plane_restr0.004417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8533-1.91310.38681390.36572593X-RAY DIFFRACTION97
1.9131-1.98150.38961570.32622611X-RAY DIFFRACTION98
1.9815-2.06090.30141510.26782695X-RAY DIFFRACTION100
2.0609-2.15460.32781230.26892694X-RAY DIFFRACTION100
2.1546-2.26820.30571410.28172626X-RAY DIFFRACTION97
2.2682-2.41030.28151480.2342658X-RAY DIFFRACTION99
2.4103-2.59640.29621290.22762751X-RAY DIFFRACTION100
2.5964-2.85770.26781120.22722735X-RAY DIFFRACTION100
2.8577-3.2710.26041530.22452742X-RAY DIFFRACTION100
3.271-4.12060.21211390.19012755X-RAY DIFFRACTION100
4.1206-42.30.20761530.18382871X-RAY DIFFRACTION99

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