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- PDB-3v7n: Crystal structure of Threonine synthase (thrC) from from Burkhold... -

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Basic information

Entry
Database: PDB / ID: 3v7n
TitleCrystal structure of Threonine synthase (thrC) from from Burkholderia thailandensis
ComponentsThreonine synthase
KeywordsLYASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


threonine synthase / threonine synthase activity / threonine biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Threonine synthase, C-terminal / threonine synthase, domain 1, chain A / Threonine synthase, N-terminal domain / : / Threonine synthase, N-terminal / Threonine synthase, N-terminal domain superfamily / Threonine synthase N terminus / Threonine synthase-like / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. ...Threonine synthase, C-terminal / threonine synthase, domain 1, chain A / Threonine synthase, N-terminal domain / : / Threonine synthase, N-terminal / Threonine synthase, N-terminal domain superfamily / Threonine synthase N terminus / Threonine synthase-like / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BORIC ACID / MALONIC ACID / Threonine synthase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionDec 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Apr 29, 2015Group: Non-polymer description
Revision 1.3Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Threonine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9009
Polymers53,3621
Non-polymers5388
Water8,629479
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.560, 90.240, 98.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Threonine synthase


Mass: 53361.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: thrC, BTH_I2199 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2SWH9, threonine synthase
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BH3O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5
Details: EBS internal tracking number 225991F9: Wizard3/4 F9. 25% PEG 1500, 0.1 M MIB buffer/HCl pH 5.0. ButhA.00545.a.A1 PW33400 at 44.8 mg/mL, vapor diffusion, sitting drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03318 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 7, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 97539 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.84 % / Biso Wilson estimate: 18.564 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 14.74
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.4-1.444.780.5672.834222716599.7
1.44-1.480.4463.633402698499.7
1.48-1.520.3544.532513678399.8
1.52-1.570.2795.631761661199.9
1.57-1.620.2376.530889641099.9
1.62-1.670.2017.630051621299.8
1.67-1.740.1678.929205603399.8
1.74-1.810.1311128004575099.8
1.81-1.890.10513.426897552799.7
1.89-1.980.08416.125862531199.4
1.98-2.090.06919.424490500199.2
2.09-2.210.0622.323222476399.2
2.21-2.370.05324.521986448298.9
2.37-2.560.04726.820429415798.6
2.56-2.80.04328.718929385898.7
2.8-3.130.04131.317074348198.3
3.13-3.610.03733.715214311998.7
3.61-4.430.03536.312737263098.4
4.43-6.260.03535.79968208597.8
6.26-500.03434.95248117795.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.4 Å
Translation1.4 Å48.4 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KL7

1kl7


Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.587 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.181 4871 5 %RANDOM
Rwork0.16 ---
obs0.161 97538 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.198 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2--0.14 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3546 0 35 479 4060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193673
X-RAY DIFFRACTIONr_bond_other_d0.0010.022467
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.9524973
X-RAY DIFFRACTIONr_angle_other_deg0.99635951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6715469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78623.277177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57715565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2691532
X-RAY DIFFRACTIONr_chiral_restr0.1050.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02810
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 321 -
Rwork0.225 6463 -
all-6784 -
obs--99.71 %
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)
10.3257-0.01-0.12920.0289-0.04260.2941-0.0133-0.025-0.06630.0051-0.002-0.0042-0.03120.00470.01540.00660.00080.00490.01010.00760.031110.37610.9817.75
20.32930.09570.0310.6322-0.57990.6569-0.0194-0.0126-0.0692-0.1142-0.0305-0.0660.12370.02870.04990.02910.00940.01530.0220.01890.034.948-2.84819.963
30.4886-0.03960.00220.1007-0.00130.32780.02210.0114-0.1045-0.0122-0.00020.01870.0114-0.0743-0.02180.0037-0.002-0.00720.0180.0010.0276-5.94.4731.29
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 231
2X-RAY DIFFRACTION2A232 - 382
3X-RAY DIFFRACTION3A383 - 483

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