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- PDB-5lhe: Phosphoribosyl anthranilate isomerase from Thermococcus kodakaraensis -

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Basic information

Entry
Database: PDB / ID: 5lhe
TitlePhosphoribosyl anthranilate isomerase from Thermococcus kodakaraensis
ComponentsN-(5'-phosphoribosyl)anthranilate isomerase
KeywordsISOMERASE / tryptophan biosynthesis / TIM barrel / protein stability
Function / homology
Function and homology information


phosphoribosylanthranilate isomerase / phosphoribosylanthranilate isomerase activity / tryptophan biosynthetic process
Similarity search - Function
N-(5'-phosphoribosyl)anthranilate isomerase family / N-(5'phosphoribosyl) anthranilate isomerase (PRAI) domain / N-(5'phosphoribosyl)anthranilate (PRA) isomerase / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
N-(5'-phosphoribosyl)anthranilate isomerase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPerveen, S. / Rashid, N. / Papageorgiou, A.C.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Crystal structure of a phosphoribosyl anthranilate isomerase from the hyperthermophilic archaeon Thermococcus kodakaraensis.
Authors: Perveen, S. / Rashid, N. / Papageorgiou, A.C.
History
DepositionJul 11, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...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_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-(5'-phosphoribosyl)anthranilate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9943
Polymers22,9481
Non-polymers462
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-15 kcal/mol
Surface area9990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.696, 29.096, 83.946
Angle α, β, γ (deg.)90.00, 114.16, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-302-

NA

21A-424-

HOH

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Components

#1: Protein N-(5'-phosphoribosyl)anthranilate isomerase / PRAI


Mass: 22948.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HYPERTHERMOPHILE
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Gene: trpF, TK0256 / Plasmid: TKtRPf-pET-28 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9YGB1, phosphoribosylanthranilate isomerase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.15 Å3/Da / Density % sol: 42.95 % / Description: Rods
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl pH 8, 0.2 M Sodium Formate, 12% PEG 4000

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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: 1.85→38.31 Å / Num. obs: 15362 / % possible obs: 89.8 % / Redundancy: 2.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.085 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.85-1.892.50.4140.74187.8
8.92-38.312.80.0430.996191.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.5.1data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4aaj

4aaj


Resolution: 1.85→24.72 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2622 754 4.92 %
Rwork0.2192 --
obs0.2215 15340 89.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→24.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1608 0 2 182 1792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071640
X-RAY DIFFRACTIONf_angle_d1.1282219
X-RAY DIFFRACTIONf_dihedral_angle_d13.719625
X-RAY DIFFRACTIONf_chiral_restr0.042255
X-RAY DIFFRACTIONf_plane_restr0.005286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.99280.30291270.25192822X-RAY DIFFRACTION88
1.9928-2.19320.33681420.24462846X-RAY DIFFRACTION88
2.1932-2.51030.34171490.24522899X-RAY DIFFRACTION90
2.5103-3.16170.29991580.23622969X-RAY DIFFRACTION91
3.1617-24.72250.20161780.18963050X-RAY DIFFRACTION91
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)
11.5547-0.13110.03871.4026-0.34890.88720.0325-0.1814-0.0575-0.27170.27020.24760.1104-0.339-0.07360.1495-0.0632-0.05540.20920.06840.197797.805121.54678.801
23.83382.2722-2.30966.5576-3.52645.2103-0.12020.00120.0509-0.5338-0.1376-0.38140.32560.1755-0.07140.1721-0.03170.02840.1647-0.03830.1687107.258116.98673.6473
31.27650.3408-0.42691.54020.48071.52970.26010.07360.1244-0.3574-0.147-0.4906-0.16790.036-0.03510.1199-0.01060.02010.12480.03710.2059109.820726.02267.5998
41.2430.2402-0.69630.3123-0.25531.46550.186-0.1190.19150.2674-0.1534-0.2562-0.36570.03390.01050.1773-0.0332-0.03470.1370.00950.239112.894928.921218.5957
50.88390.3410.26530.3980.59290.99150.2518-0.5302-0.55320.1038-0.0442-0.38960.64130.6112-0.06520.56980.0139-0.09610.33950.05770.3507104.828918.557439.6037
61.26110.6316-0.07410.98650.32021.51980.2103-0.4724-0.12910.3247-0.0019-0.09210.0180.28640.01220.3413-0.1451-0.09130.3158-0.0330.0753107.672828.681128.4491
70.4659-0.01930.1851.4971-0.14581.35470.0183-0.01380.02210.39040.08980.40650.0198-0.3741-0.03930.2435-0.0750.05520.2248-0.01670.14993.6319.521123.4727
81.99970.68670.1160.2740.2511.1960.082-0.08370.5975-0.0423-0.07770.2787-0.2369-0.2517-0.25570.0377-0.0590.14840.28770.16560.845883.985624.988118.1924
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:34)
2X-RAY DIFFRACTION2(chain A and resid 35:45)
3X-RAY DIFFRACTION3(chain A and resid 46:78)
4X-RAY DIFFRACTION4(chain A and resid 79:107)
5X-RAY DIFFRACTION5(chain A and resid 108:115)
6X-RAY DIFFRACTION6(chain A and resid 116:135)
7X-RAY DIFFRACTION7(chain A and resid 136:201)
8X-RAY DIFFRACTION8(chain A and resid 202:208)

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