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- PDB-4j9j: Structure of designed HisF -

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Basic information

Entry
Database: PDB / ID: 4j9j
TitleStructure of designed HisF
ComponentsImidazole glycerol phosphate synthase subunit HisF
KeywordsLYASE / beta barrel / protein engineering
Function / homology
Function and homology information


imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / L-histidine biosynthetic process / lyase activity / cytoplasm
Similarity search - Function
Histidine biosynthesis, HisF / : / Histidine biosynthesis protein / Histidine biosynthesis protein / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Imidazole glycerol phosphate synthase subunit HisF
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSterner, R. / Rajendran, C. / Sperl, J.
CitationJournal: Febs Lett. / Year: 2013
Title: Establishing catalytic activity on an artificial ( beta alpha )8-barrel protein designed from identical half-barrels.
Authors: Sperl, J.M. / Rohweder, B. / Rajendran, C. / Sterner, R.
History
DepositionFeb 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Imidazole glycerol phosphate synthase subunit HisF


Theoretical massNumber of molelcules
Total (without water)26,3261
Polymers26,3261
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.212, 63.142, 56.260
Angle α, β, γ (deg.)90.00, 99.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Imidazole glycerol phosphate synthase subunit HisF / IGP synthase cyclase subunit / IGP synthase subunit HisF / ImGP synthase subunit HisF / IGPS subunit HisF


Mass: 26326.293 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: S6I,V45A,T76A,D81G,D156G,D202V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: hisF, TM_1036 / Plasmid: pET24 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X0C6, Lyases; Carbon-carbon lyases; Oxo-acid-lyases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN IS AN ENGINEERED CONSTRUCT COMPRISING UNP RESIDUES 97-216 COUPLED TO UNP RESIDUES 96-220 (Q9X0C6).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.58 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.7 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 1.805→41.712 Å / Num. obs: 10548 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OG3

3og3


Resolution: 2.3→41.712 Å / SU ML: 0.32 / σ(F): 1.01 / Phase error: 32.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.297 528 5.01 %
Rwork0.2415 --
obs0.2443 10542 96.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→41.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 0 0 147 1862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021731
X-RAY DIFFRACTIONf_angle_d0.6552343
X-RAY DIFFRACTIONf_dihedral_angle_d11.207615
X-RAY DIFFRACTIONf_chiral_restr0.043282
X-RAY DIFFRACTIONf_plane_restr0.002297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.53160.36341350.25442564X-RAY DIFFRACTION99
2.5316-2.89780.33941310.29012491X-RAY DIFFRACTION97
2.8978-3.65060.29981310.24782486X-RAY DIFFRACTION96
3.6506-41.71910.25321310.21052473X-RAY DIFFRACTION94

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