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- PDB-5kia: Crystal structure of L-threonine 3-dehydrogenase from Burkholderi... -

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Basic information

Entry
Database: PDB / ID: 5kia
TitleCrystal structure of L-threonine 3-dehydrogenase from Burkholderia thailandensis
ComponentsL-threonine 3-dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


L-threonine 3-dehydrogenase / L-threonine catabolic process to glycine / L-threonine 3-dehydrogenase activity / zinc ion binding / cytoplasm
Similarity search - Function
L-threonine 3-dehydrogenase / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain ...L-threonine 3-dehydrogenase / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-threonine 3-dehydrogenase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of L-threonine 3-dehydrogenase from Burkholderia thailandensis
Authors: Abendroth, J. / Lukacs, C.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJun 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6554
Polymers38,5091
Non-polymers1463
Water2,846158
1
A: L-threonine 3-dehydrogenase
hetero molecules

A: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3108
Polymers77,0192
Non-polymers2916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,x,-z1
Buried area2450 Å2
ΔGint-56 kcal/mol
Surface area26330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.770, 91.770, 173.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-642-

HOH

21A-654-

HOH

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Components

#1: Protein L-threonine 3-dehydrogenase / TDH


Mass: 38509.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264) (bacteria)
Strain: ATCC 700388 / DSM 13276 / CIP 106301 / E264 / Gene: tdh, BTH_II0006 / Plasmid: ButhA.10611.b.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2T9E1, L-threonine 3-dehydrogenase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytic MCSG 1 screen A10, 28% PEG 400, 200mM CaCl2, 100mM HEPES/NaOH, ButhA.10611.b.B1.PS01804 at 20mg/ml + 2.5mM NAD; cryo: direct; tray 257666a10, puck xbm5-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 12, 2014
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→48.958 Å / Num. obs: 22085 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.208 % / Biso Wilson estimate: 33.18 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.058 / Χ2: 0.971 / Net I/σ(I): 25.79 / Num. measured all: 181263 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique allNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.158.3340.4624.68133421601160116010.9210.493100
2.15-2.218.3670.3595.9613120156815680.9480.382100
2.21-2.288.320.2927.2612638151915190.9660.312100
2.28-2.358.3060.2588.1512443149814980.9810.275100
2.35-2.428.3570.2119.8911909142714250.9820.22599.9
2.42-2.518.3490.17212.0711589138913880.9880.18499.9
2.51-2.68.3070.13314.8811198134813480.9920.142100
2.6-2.718.3180.1216.7110788129712970.9930.128100
2.71-2.838.3240.08522.3810263123312330.9970.091100
2.83-2.978.2780.07225.699975120612050.9980.07799.9
2.97-3.138.30.05631.959404113511330.9980.0699.8
3.13-3.328.240.04538.048916108210820.9990.048100
3.32-3.558.1880.03944.038278101110110.9990.041100
3.55-3.838.1170.03451.0378259649640.9990.037100
3.83-4.28.0810.03155.9771688878870.9990.033100
4.2-4.78.020.02860.6164168018000.9990.0399.9
4.7-5.427.8460.02759.4157127287280.9990.029100
5.42-6.647.7770.02959.347366096090.9990.031100
6.64-9.397.4780.02564.0237094974960.9990.02699.8
9.39-48.9586.2590.02361.9118343062930.9990.02595.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(dev_2650)refinement
XDSdata reduction
XSCALEdata scaling
BALBESphasing
PHASERphasing
PHENIXmodel building
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2dq4

2dq4


Resolution: 2.1→48.958 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 2027 9.19 %Random selection
Rwork0.1748 20032 --
obs0.1795 22059 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.48 Å2 / Biso mean: 46.729 Å2 / Biso min: 16.29 Å2
Refinement stepCycle: final / Resolution: 2.1→48.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 3 161 2646
Biso mean--52.95 44.49 -
Num. residues----339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072558
X-RAY DIFFRACTIONf_angle_d0.7713476
X-RAY DIFFRACTIONf_chiral_restr0.055400
X-RAY DIFFRACTIONf_plane_restr0.006448
X-RAY DIFFRACTIONf_dihedral_angle_d17.4611500
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1001-2.15260.27921490.216713951544100
2.1526-2.21080.26921390.200214221561100
2.2108-2.27590.2711510.196613901541100
2.2759-2.34930.28171300.190114321562100
2.3493-2.43330.27191190.193714081527100
2.4333-2.53070.24791500.190214091559100
2.5307-2.64590.24141400.187114311571100
2.6459-2.78540.21041670.186813951562100
2.7854-2.95990.24651620.191114041566100
2.9599-3.18830.24641270.188614471574100
3.1883-3.50910.23461410.162414411582100
3.5091-4.01670.19561450.154414531598100
4.0167-5.05980.18571540.140414521606100
5.0598-48.97150.22371530.18661553170699
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)
12.0363-0.46350.67992.3227-2.01733.0095-0.0590.0758-0.4139-0.45140.58070.8580.6579-0.8595-0.27310.4551-0.2024-0.02330.55160.06530.53090.949-21.4189-29.1557
21.9342-0.0974-0.93711.52280.19692.4885-0.10350.0292-0.2676-0.1343-0.00360.02980.3088-0.03110.08710.2502-0.0120.02530.16140.04410.22741.3295-23.8193-3.875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 140 )A0 - 140
2X-RAY DIFFRACTION2chain 'A' and (resid 141 through 341 )A141 - 341

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