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- PDB-3og3: Crystal structure of an artificial thermostable (BA)8-barrel prot... -

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Basic information

Entry
Database: PDB / ID: 3og3
TitleCrystal structure of an artificial thermostable (BA)8-barrel protein from identical half barrels
ComponentsImidazole glycerol phosphate synthase subunit hisF
KeywordsDE NOVO PROTEIN / LYASE / FUSION PROTEIN / TIM Barrel
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 / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsSperl, J.M. / Bocola, M. / List, F. / Kellerer, B. / Sterner, R.
CitationJournal: To be Published
Title: Design of an artificial thermostable (BA)8-barrel protein from identical half barrels
Authors: Sperl, J.M. / Bocola, M. / List, F. / Kellerer, B. / Sterner, R.
History
DepositionAug 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 6, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Imidazole glycerol phosphate synthase subunit hisF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5795
Polymers27,3161
Non-polymers2634
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.374, 82.086, 74.511
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number5
Space group name H-MC121

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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: 27316.248 Da / Num. of mol.: 1 / Mutation: A3R, Y22H, Y143H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: hisF, hisF derivative (Amino acids 99-219), TM_1036 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express (NEB)
References: UniProt: Q9X0C6, Lyases; Carbon-carbon lyases; Oxo-acid-lyases
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 1.76 Å3/Da / Density % sol: 29.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M ammonium sulfate, 18% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD RUBY CCD / Detector: CCD / Date: Dec 18, 2009 / Details: mirrors
RadiationMonochromator: Oxford MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.08→14.7 Å / Num. all: 11304 / Num. obs: 11304 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 26 Å2 / Rsym value: 0.052 / Net I/σ(I): 18.58
Reflection shellResolution: 2.04→2.14 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.168 / % possible all: 96.8

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Processing

Software
NameVersionClassification
CrysalisProdata collection
OxfordDiffraction Ltd.data collection
PHASERphasing
REFMAC5.5.0088refinement
CrysalisProdata reduction
OxfordDiffraction Ltd.data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1THF (Amino acids 99-219) dimer

1thf


Resolution: 2.08→14.65 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.717 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19591 584 5.2 %RANDOM
Rwork0.14953 ---
all0.166 11260 --
obs0.15194 10719 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.478 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.08 Å2
2---0.02 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.179 Å
Refinement stepCycle: LAST / Resolution: 2.08→14.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 12 173 2021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221871
X-RAY DIFFRACTIONr_angle_refined_deg2.0061.9642528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.335241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18423.86775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.48115331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4741513
X-RAY DIFFRACTIONr_chiral_restr0.1390.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211365
X-RAY DIFFRACTIONr_mcbond_it1.3751.51191
X-RAY DIFFRACTIONr_mcangle_it2.34521918
X-RAY DIFFRACTIONr_scbond_it3.3433680
X-RAY DIFFRACTIONr_scangle_it5.2784.5610
LS refinement shellResolution: 2.08→2.133 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.19 41 -
Rwork0.139 750 -
obs--98.38 %

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