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- PDB-5noe: Anthranilate phosphoribosyltransferase from Thermococcus kodakaraensis -

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Basic information

Entry
Database: PDB / ID: 5noe
TitleAnthranilate phosphoribosyltransferase from Thermococcus kodakaraensis
ComponentsAnthranilate phosphoribosyltransferase
KeywordsTRANSFERASE / tryptophan biosynthesis / phosphoribosyltransferase / archaea / zinc binding
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 speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsPerveen, S. / Rashid, N. / Papageorgiou, A.C.
CitationJournal: FEBS Open Bio / Year: 2017
Title: Anthranilate phosphoribosyltransferase from the hyperthermophilic archaeon Thermococcus kodakarensis shows maximum activity with zinc and forms a unique dimeric structure.
Authors: Perveen, S. / Rashid, N. / Tang, X.F. / Imanaka, T. / Papageorgiou, A.C.
History
DepositionApr 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_assembly / pdbx_struct_assembly_auth_evidence / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.details / _pdbx_struct_assembly_auth_evidence.details / _pdbx_struct_assembly_auth_evidence.experimental_support / _refine_hist.d_res_low
Revision 1.2Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)137,5244
Polymers137,5244
Non-polymers00
Water17,493971
1
A: Anthranilate phosphoribosyltransferase
C: Anthranilate phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)68,7622
Polymers68,7622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-17 kcal/mol
Surface area23600 Å2
MethodPISA
2
B: Anthranilate phosphoribosyltransferase
D: Anthranilate phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)68,7622
Polymers68,7622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-18 kcal/mol
Surface area24140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.870, 85.613, 180.758
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: 34381.070 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: HYPERTHERMOPHILE
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Gene: trpD, TK0253 / Plasmid: TkTpD-pET21a / Details (production host): E.coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon plus RIL
References: UniProt: Q9YGB4, anthranilate phosphoribosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 971 / 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: 2.36 Å3/Da / Density % sol: 47.87 % / Description: Rods
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% w/v PEG 3350, 0.2M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96598 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96598 Å / Relative weight: 1
ReflectionResolution: 1.91→49.27 Å / Num. obs: 100253 / % possible obs: 98.8 % / Redundancy: 4.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.91-1.984.61.0031.50.536195.9
7.4-49.274.40.0640.996198.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
Aimless0.5.15data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2gvq

2gvq


Resolution: 1.91→49.27 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2364 4930 4.92 %
Rwork0.1872 --
obs0.1896 100170 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.91→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9613 0 0 971 10584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139797
X-RAY DIFFRACTIONf_angle_d1.313280
X-RAY DIFFRACTIONf_dihedral_angle_d16.1515990
X-RAY DIFFRACTIONf_chiral_restr0.0691551
X-RAY DIFFRACTIONf_plane_restr0.0071750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.93170.31091600.2863023X-RAY DIFFRACTION95
1.9317-1.95440.3331540.28543061X-RAY DIFFRACTION96
1.9544-1.97830.34891530.27033051X-RAY DIFFRACTION96
1.9783-2.00330.3011740.26613110X-RAY DIFFRACTION98
2.0033-2.02970.3021740.24433120X-RAY DIFFRACTION98
2.0297-2.05750.26841370.2233173X-RAY DIFFRACTION99
2.0575-2.08690.24791670.21943128X-RAY DIFFRACTION98
2.0869-2.1180.27941690.21783150X-RAY DIFFRACTION100
2.118-2.15110.28371640.21753135X-RAY DIFFRACTION98
2.1511-2.18640.25211490.21523185X-RAY DIFFRACTION99
2.1864-2.22410.281690.20763142X-RAY DIFFRACTION99
2.2241-2.26450.26591880.19913152X-RAY DIFFRACTION98
2.2645-2.30810.23661490.20153171X-RAY DIFFRACTION99
2.3081-2.35520.23761600.19323112X-RAY DIFFRACTION98
2.3552-2.40640.26181560.2053133X-RAY DIFFRACTION98
2.4064-2.46240.24851470.20533193X-RAY DIFFRACTION99
2.4624-2.5240.27451580.19653185X-RAY DIFFRACTION99
2.524-2.59220.2621460.1943214X-RAY DIFFRACTION100
2.5922-2.66850.25151700.1923179X-RAY DIFFRACTION100
2.6685-2.75460.22641750.19183182X-RAY DIFFRACTION99
2.7546-2.8530.26861890.19283195X-RAY DIFFRACTION99
2.853-2.96730.23691720.19633174X-RAY DIFFRACTION99
2.9673-3.10230.21991670.18713202X-RAY DIFFRACTION100
3.1023-3.26580.24711660.1883218X-RAY DIFFRACTION100
3.2658-3.47040.22791580.17223196X-RAY DIFFRACTION98
3.4704-3.73820.19431560.16193259X-RAY DIFFRACTION99
3.7382-4.11430.20261750.15623233X-RAY DIFFRACTION100
4.1143-4.70920.18661840.1463259X-RAY DIFFRACTION100
4.7092-5.93150.21641910.17423268X-RAY DIFFRACTION99
5.9315-49.28960.24271530.18233437X-RAY DIFFRACTION98

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