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- PDB-1khd: Crystal Structure Analysis of the anthranilate phosphoribosyltran... -

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Basic information

Entry
Database: PDB / ID: 1khd
TitleCrystal Structure Analysis of the anthranilate phosphoribosyltransferase from Erwinia carotovora at 1.9 resolution (current name, Pectobacterium carotovorum)
ComponentsAnthranilate phosphoribosyltransferase
KeywordsTRANSFERASE / type 3 prt fold / nucleotide binding fold
Function / homology
Function and homology information


anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / L-tryptophan biosynthetic process / magnesium ion binding / cytosol
Similarity search - Function
Anthranilate phosphoribosyl transferase / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain / 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 / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain / 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
Anthranilate phosphoribosyltransferase
Similarity search - Component
Biological speciesPectobacterium carotovorum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsKim, C. / Xuong, N.-H. / Edwards, S. / Madhusudan / Yee, M.-C. / Spraggon, G. / Mills, S.E.
CitationJournal: FEBS Lett. / Year: 2002
Title: The Crystal Structure of Anthranilate Phosphoribosyltransferase from the Enterobacterium Pectobacterium carotovorum
Authors: Kim, C. / Xuong, N.-H. / Edwards, S. / Madhusudan / Yee, M.-C. / Spraggon, G. / Mills, S.E.
History
DepositionNov 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anthranilate phosphoribosyltransferase
B: Anthranilate phosphoribosyltransferase
C: Anthranilate phosphoribosyltransferase
D: Anthranilate phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)148,2284
Polymers148,2284
Non-polymers00
Water16,159897
1
A: Anthranilate phosphoribosyltransferase
D: Anthranilate phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)74,1142
Polymers74,1142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-13 kcal/mol
Surface area24960 Å2
MethodPISA
2
B: Anthranilate phosphoribosyltransferase
C: Anthranilate phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)74,1142
Polymers74,1142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-13 kcal/mol
Surface area25340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.870, 82.342, 200.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Anthranilate phosphoribosyltransferase


Mass: 37057.117 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium carotovorum (bacteria) / Gene: trpD / Plasmid: pUC13 / Production host: Escherichia coli (E. coli) / Strain (production host): JMB9 r-m+.trpLDl02 leu-Thi-
References: UniProt: Q8VP84, anthranilate phosphoribosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 897 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3000, MnCl2, glutamine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH6.5
210 %glycerol1drop
31 mMdithiothreitol1drop
41 mMEDTA1drop
520 mg/mlprotein1drop
625 %PEG30001reservoir
70.2 MHEPES1reservoirpH6.5
84.5 mMglutamine1reservoir
910.0 mM1reservoirMnCl2
101.25 mMPRPP1reservoir
110.0012 mManthranilate1reservoir
121 mMdithiothreitol1reservoir
131 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jun 27, 2001
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→25 Å / Num. all: 107405 / Num. obs: 99609 / % possible obs: 92.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 25 % / Rmerge(I) obs: 0.063 / Rsym value: 0.06 / Net I/σ(I): 38.6
Reflection
*PLUS
Highest resolution: 1.86 Å / Lowest resolution: 50 Å / % possible obs: 92 % / Redundancy: 25 % / Num. measured all: 107405 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
Rmerge(I) obs: 0.372

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KGZ

1kgz


Resolution: 1.86→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2614 4800 RANDOM
Rwork0.223 --
all-94966 -
obs-94966 -
Refinement stepCycle: LAST / Resolution: 1.86→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9732 0 0 897 10629
Refinement
*PLUS
Highest resolution: 1.86 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.2633 / Rfactor Rwork: 0.2211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.0057
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.2
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg21.3
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg0.79

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