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- PDB-8g1y: Crystal Structure of the Threonine Synthase from Streptococcus pn... -

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Basic information

Entry
Database: PDB / ID: 8g1y
TitleCrystal Structure of the Threonine Synthase from Streptococcus pneumoniae in complex with Pyridoxal 5-phosphate.
ComponentsThreonine synthase
KeywordsLYASE / Center for Structural Biology of Infectious Diseases (CSBID) / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / threonine synthase / PLP
Function / homology
Function and homology information


threonine synthase / threonine synthase activity
Similarity search - Function
Threonine synthase, N-terminal / Threonine synthase, N-terminal domain superfamily / Threonine synthase N terminus / Threonine synthase-like / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme
Similarity search - Domain/homology
D-MALATE / PYRIDOXAL-5'-PHOSPHATE / Threonine synthase
Similarity search - Component
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.43 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID) / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00035 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal Structure of the Threonine Synthase from Streptococcus pneumoniae in complex with Pyridoxal 5-phosphate.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID) / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Threonine synthase
B: Threonine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,72320
Polymers109,1162
Non-polymers1,60818
Water19,0241056
1
A: Threonine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,50412
Polymers54,5581
Non-polymers94611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Threonine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2198
Polymers54,5581
Non-polymers6617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.464, 81.413, 139.465
Angle α, β, γ (deg.)90.000, 94.600, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Threonine synthase /


Mass: 54557.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria)
Gene: thrC, SP_2066 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl-21 Magic / References: UniProt: A0A0H2US33, threonine synthase

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Non-polymers , 6 types, 1074 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1056 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 8.5 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3, 2mM PLP; Screen: Classics II (B11), 2.1M DL-Malic acid pH 7.0; Cryo: 25% glycerol in screen solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 29, 2021 / Details: Be
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.43→30 Å / Num. obs: 167626 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 13.9 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.039 / Rrim(I) all: 0.087 / Rsym value: 0.078 / Χ2: 1.336 / Net I/σ(I): 19.5
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 8061 / CC1/2: 0.792 / CC star: 0.94 / Rpim(I) all: 0.434 / Rrim(I) all: 0.96 / Rsym value: 0.853 / Χ2: 1.003 / % possible all: 90.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.43→29.29 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.33 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1769 8365 5 %RANDOM
Rwork0.1568 ---
obs0.1578 159092 94.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.94 Å2 / Biso mean: 16.724 Å2 / Biso min: 8.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20.02 Å2
2---0.47 Å20 Å2
3---0.78 Å2
Refinement stepCycle: final / Resolution: 1.43→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7592 0 99 1113 8804
Biso mean--27.97 30.59 -
Num. residues----991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0138296
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177856
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.64711327
X-RAY DIFFRACTIONr_angle_other_deg0.3731.57818173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.09551090
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.34325.135370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.198151330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4131518
X-RAY DIFFRACTIONr_chiral_restr0.0690.21133
X-RAY DIFFRACTIONr_gen_planes_refined0.0560.029672
X-RAY DIFFRACTIONr_gen_planes_other0.0510.021782
LS refinement shellResolution: 1.43→1.467 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 520 -
Rwork0.297 11317 -
all-11837 -
obs--90.6 %
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)
10.42820.095-0.01190.7784-0.0610.6991-0.0069-0.0155-0.05510.0250.01650.04190.0899-0.0743-0.00960.0319-0.00940.00530.01090.00380.011710.533374.540619.1304
20.6691-0.4470.09730.7827-0.12610.39880.0365-0.0015-0.0328-0.0176-0.04970.00220.00330.05030.01310.0502-0.00980.00060.02770.00810.004627.520975.940120.8943
30.4310.17060.04630.87540.18550.6515-0.02450.0836-0.0127-0.11490.00950.01030.00960.01610.0150.062-0.0008-0.00090.0178-0.00230.001221.006384.25751.9618
41.12320.080.26340.5388-0.0620.55990.00710.0210.12570.0312-0.0331-0.0989-0.09920.05960.02590.0725-0.0241-0.00210.01070.00770.037733.144498.696315.0287
50.8674-0.9382-0.34553.55480.42230.85990.0471-0.00090.07940.159-0.0159-0.3430.00620.1409-0.03120.02060.0005-0.01760.08540.02570.042542.358875.249623.857
60.35410.18780.06351.452-0.26990.4788-0.0225-0.0042-0.0908-0.04550.0192-0.08030.10910.05930.00340.04280.01510.01630.02220.0040.028227.269849.96654.5029
70.81360.42390.10840.61860.0770.32930.01230.0363-0.0726-0.0486-0.0347-0.01810.0127-0.01250.02230.0525-0.00050.00290.0172-0.00890.011212.158252.580647.8331
80.4863-0.1540.11580.8787-0.20660.5856-0.0268-0.0843-0.00280.09470.0112-0.0052-0.0074-0.01750.01560.0481-0.00110.00290.01540.00020.001115.496862.741166.2599
90.7126-0.1147-0.00230.44080.02540.36130.01670.03120.0978-0.01-0.02980.1136-0.0469-0.05350.0130.05580.0115-0.00350.020100.05532.366971.882951.1099
102.9077-0.003-0.52143.21330.77941.17020.0701-0.0199-0.0863-0.0505-0.07840.02070.08460.11450.00830.0643-0.0369-0.00740.0808-0.00160.0617-4.782138.574150.5571
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 74
2X-RAY DIFFRACTION2A75 - 259
3X-RAY DIFFRACTION3A260 - 380
4X-RAY DIFFRACTION4A381 - 453
5X-RAY DIFFRACTION5A454 - 494
6X-RAY DIFFRACTION6B0 - 50
7X-RAY DIFFRACTION7B51 - 259
8X-RAY DIFFRACTION8B260 - 393
9X-RAY DIFFRACTION9B394 - 473
10X-RAY DIFFRACTION10B474 - 494

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