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- PDB-6nw4: Evolution of a computationally designed Kemp eliminase -

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Basic information

Entry
Database: PDB / ID: 6nw4
TitleEvolution of a computationally designed Kemp eliminase
ComponentsIndole-3-glycerol phosphate synthase
KeywordsBIOSYNTHETIC PROTEIN / Kemp elimination / evolution
Function / homology
Function and homology information


indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / tryptophan biosynthetic process
Similarity search - Function
Indole-3-glycerol phosphate synthase / Indole-3-glycerol phosphate synthase, conserved site / Indole-3-glycerol phosphate synthase signature. / Indole-3-glycerol phosphate synthase domain / Indole-3-glycerol phosphate synthase / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
6-NITROBENZOTRIAZOLE / Indole-3-glycerol phosphate synthase
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBunzel, A. / Mittl, P. / Hilvert, D.
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Emergence of a Negative Activation Heat Capacity during Evolution of a Designed Enzyme.
Authors: Bunzel, H.A. / Kries, H. / Marchetti, L. / Zeymer, C. / Mittl, P.R.E. / Mulholland, A.J. / Hilvert, D.
History
DepositionFeb 6, 2019Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 20, 2019Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.process_site
Revision 1.3Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.4Jan 24, 2024Group: 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: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0726
Polymers28,5241
Non-polymers5485
Water37821
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-45 kcal/mol
Surface area11020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.304, 61.304, 121.278
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Indole-3-glycerol phosphate synthase / IGPS


Mass: 28523.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: trpC, SSO0895 / Production host: Escherichia coli (E. coli)
References: UniProt: Q06121, indole-3-glycerol-phosphate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-6NT / 6-NITROBENZOTRIAZOLE


Mass: 164.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4N4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate, 20 mM sodium sulfate, 43% v/v PEG 300, pH 5.6
PH range: 4.2 - 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→48.63 Å / Num. obs: 5650 / % possible obs: 99.8 % / Redundancy: 9.626 % / Biso Wilson estimate: 74.22 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.413 / Rrim(I) all: 0.437 / Χ2: 0.71 / Net I/σ(I): 5.09 / Num. measured all: 54388 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3-3.110.2652.1231.415200.7312.234100
3.1-3.210.2131.8591.644460.7451.95699.8
3.2-3.310.1551.4791.914060.7891.558100
3.3-3.510.0251.0912.446670.8791.1599.9
3.5-49.6580.6253.7511500.9620.6699.8
4-4.58.9150.3186.117140.9810.33899.4
4.5-59.9550.2617.734440.9850.275100
5-69.7070.2637.515320.9780.27899.6
6-79.2380.2028.332730.9890.214100
7-87.9680.11711.041540.9920.125100
8-108.1880.11713.321600.9940.12599.4
10-48.638.5330.10214.61840.9990.10999.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NZ1

3nz1


Resolution: 3→48.63 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.78 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.536
RfactorNum. reflection% reflectionSelection details
Rfree0.295 296 5.24 %RANDOM
Rwork0.187 ---
obs0.192 5651 99.8 %-
Displacement parametersBiso max: 153.16 Å2 / Biso mean: 64.52 Å2 / Biso min: 22.18 Å2
Baniso -1Baniso -2Baniso -3
1--15.5199 Å20 Å20 Å2
2---15.5199 Å20 Å2
3---31.0398 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 3→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 32 21 2058
Biso mean--88.51 40.62 -
Num. residues----247
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d757SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes345HARMONIC5
X-RAY DIFFRACTIONt_it2067HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion270SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2513SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2067HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2787HARMONIC21.16
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion21.86
LS refinement shellResolution: 3→3.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2595 25 6.19 %
Rwork0.2279 379 -
all0.23 404 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -22.1451 Å / Origin y: 16.6641 Å / Origin z: -9.9762 Å
111213212223313233
T0.0286 Å20.0075 Å2-0.0133 Å2--0.0804 Å2-0.0009 Å2---0.1348 Å2
L1.2494 °20.1459 °20.3671 °2-0.7454 °20.2813 °2--2.0876 °2
S0.0171 Å °-0.0673 Å °-0.0396 Å °-0.0473 Å °-0.0365 Å °-0.0111 Å °-0.12 Å °0.0075 Å °0.0194 Å °
Refinement TLS groupSelection details: { A|* }

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