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- PDB-8vhh: Engineered holo tryptophan synthase (Tm9D8*) derived from T. mari... -

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Basic information

Entry
Database: PDB / ID: 8vhh
TitleEngineered holo tryptophan synthase (Tm9D8*) derived from T. maritima TrpB
ComponentsTryptophan synthase beta chain 1
KeywordsLYASE / enzyme / synthase / tryptophan synthases / engineered enzyme
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / L-tryptophan biosynthetic process / cytoplasm
Similarity search - Function
Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme
Similarity search - Domain/homology
: / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Tryptophan synthase beta chain 1
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsPorter, N.J. / Johnston, K.E. / Almhjell, P.J. / Arnold, F.H.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0022218 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: A combinatorially complete epistatic fitness landscape in an enzyme active site.
Authors: Johnston, K.E. / Almhjell, P.J. / Watkins-Dulaney, E.J. / Liu, G. / Porter, N.J. / Yang, J. / Arnold, F.H.
History
DepositionJan 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan synthase beta chain 1
B: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7689
Polymers87,9102
Non-polymers8577
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-32 kcal/mol
Surface area26310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.698, 165.698, 83.061
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Tryptophan synthase beta chain 1


Mass: 43955.160 Da / Num. of mol.: 2 / Mutation: multiple
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: trpB1, trpB, TM_0138 / Production host: Escherichia coli (E. coli) / References: UniProt: P50909, tryptophan synthase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.24 Å3/Da / Density % sol: 62.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1.2 M sodium phosphate monobasic, 0.8 M potassium phosphate dibasic, 0.1 M N-cyclohexyl-3-aminopropanesulfonic acid (CAPS), 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→45.99 Å / Num. obs: 61153 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 39.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.049 / Net I/σ(I): 13.2
Reflection shellResolution: 2.15→2.21 Å / Rmerge(I) obs: 2.19 / Num. unique obs: 4440 / CC1/2: 0.596 / Rpim(I) all: 0.642

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6AM7

6am7


Resolution: 2.15→45.99 Å / SU ML: 0.2898 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.6438
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.237 2926 4.79 %
Rwork0.2143 58185 -
obs0.2153 61111 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.95 Å2
Refinement stepCycle: LAST / Resolution: 2.15→45.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5814 0 49 94 5957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00195981
X-RAY DIFFRACTIONf_angle_d0.48088109
X-RAY DIFFRACTIONf_chiral_restr0.0425892
X-RAY DIFFRACTIONf_plane_restr0.00311039
X-RAY DIFFRACTIONf_dihedral_angle_d6.7163844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.190.36171400.3092728X-RAY DIFFRACTION98.73
2.19-2.220.30271430.29712733X-RAY DIFFRACTION99.79
2.22-2.260.38281370.30772746X-RAY DIFFRACTION99.31
2.26-2.310.3121230.28342784X-RAY DIFFRACTION100
2.31-2.350.33211210.26862751X-RAY DIFFRACTION99.93
2.35-2.410.29611490.26042764X-RAY DIFFRACTION100
2.41-2.460.25521500.26442725X-RAY DIFFRACTION100
2.46-2.520.26041560.25582766X-RAY DIFFRACTION99.97
2.52-2.590.26471440.24862805X-RAY DIFFRACTION100
2.59-2.670.31711090.26392752X-RAY DIFFRACTION99.97
2.67-2.750.29821310.26272782X-RAY DIFFRACTION99.93
2.75-2.850.33161330.24782776X-RAY DIFFRACTION99.39
2.85-2.970.29311670.24152735X-RAY DIFFRACTION99.97
2.97-3.10.29141710.24142728X-RAY DIFFRACTION99.97
3.1-3.260.26721400.23272778X-RAY DIFFRACTION100
3.26-3.470.26231090.21682793X-RAY DIFFRACTION99.97
3.47-3.740.2071350.1952798X-RAY DIFFRACTION99.97
3.74-4.110.17681280.19132795X-RAY DIFFRACTION99.73
4.11-4.710.16361380.16472786X-RAY DIFFRACTION99.93
4.71-5.930.19181600.1762806X-RAY DIFFRACTION99.97
5.93-45.990.20231420.17992854X-RAY DIFFRACTION99.63

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