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- PDB-3s1t: Structure of the regulatory domain of aspartokinase (Rv3709c; AK-... -

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Basic information

Entry
Database: PDB / ID: 3s1t
TitleStructure of the regulatory domain of aspartokinase (Rv3709c; AK-beta) in complex with threonine from Mycobacterium tuberculosis
Components(Aspartokinase) x 2
KeywordsTRANSFERASE / ACT domain / Threonine binding / regulatory domain of aspartokinase
Function / homology
Function and homology information


aspartate kinase / aspartate kinase activity / homoserine biosynthetic process / threonine biosynthetic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / peptidoglycan-based cell wall / ATP binding / plasma membrane / cytosol
Similarity search - Function
CASTOR, ACT domain / Aspartokinase catalytic domain / ACT domain / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / : / ACT domain / Aspartokinase signature. / ACT domain ...CASTOR, ACT domain / Aspartokinase catalytic domain / ACT domain / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / : / ACT domain / Aspartokinase signature. / ACT domain / ACT domain / ACT domain profile. / ACT domain / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / ACT-like domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
THREONINE / Aspartokinase / Aspartokinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsSchuldt, L. / Mueller-Dieckmann, J. / Weiss, M.S.
Citation
Journal: To be Published
Title: High-resolution X-ray structure of the regulatory domain of the mycobacterial aspartokinase in complex with threonine
Authors: Schuldt, L. / Mueller-Dieckmann, J. / Weiss, M.S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the regulatory domain of aspartokinase (Rv3709c) from Mycobacterium tuberculosis
Authors: Schuldt, L. / Suchowersky, R. / Veith, K. / Mueller-Dieckmann, J. / Weiss, M.S.
History
DepositionMay 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Data collection / Database references / Derived calculations
Category: diffrn_source / pdbx_struct_assembly ...diffrn_source / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly.details ..._diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.value / _struct_ref_seq_dif.details
Revision 1.2Sep 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Aspartokinase
B: Aspartokinase
C: Aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,77912
Polymers39,8683
Non-polymers9119
Water3,945219
1
A: Aspartokinase
B: Aspartokinase
hetero molecules

C: Aspartokinase


Theoretical massNumber of molelcules
Total (without water)40,77912
Polymers39,8683
Non-polymers9119
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area6310 Å2
ΔGint-99 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.700, 63.430, 108.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aspartokinase / Aspartate kinase / ASK


Mass: 19364.801 Da / Num. of mol.: 2 / Fragment: Aspartokinase beta-subunit, residues 251-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: ask, MT3812, MTV025.057c, Rv3709c / Plasmid: pETM-13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) cc2
References: UniProt: P0A4Z8, UniProt: P9WPX3*PLUS, aspartate kinase
#2: Protein/peptide Aspartokinase


Mass: 1138.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Plasmid: pETM-13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) cc2 / References: UniProt: P0A4Z8, UniProt: P9WPX3*PLUS
#3: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Compound detailsAUTHORS STATE THAT THE ASYMMETRIC UNIT OF THE CRYSTALS CONTAINS A HOMODIMER FORMED BY THE TWO ...AUTHORS STATE THAT THE ASYMMETRIC UNIT OF THE CRYSTALS CONTAINS A HOMODIMER FORMED BY THE TWO POLYPEPTIDE CHAINS A AND B (SEQUENCE RANGE 3-160). CHAIN C REPRESENTS THE C-TERMINAL TAIL OF THE POLYPEPTIDE CHAIN (SEQUENCE RANGE 163-173). DUE TO LACK OF ELECTRON DENSITY IN THE LINKER REGION, IT COULD NOT BE UNAMBIGUOUSLY ASSIGNED WHEATHER THIS FRAGMENT ORIGINATES FROM CHAIN A OR FROM CHAIN B OF A NEIGHBORING ASYMMETRIC UNIT. HENCE THE FRAGMENT WAS DECLARED AS CHAIN C. THIS IS ALSO DISCUSSED IN THE PUBLICATION.

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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: 2.32 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: ammonium sulphate, bis-tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→99 Å / Num. all: 48122 / Num. obs: 47641 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.63→1.65 Å / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.6.0091 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DTJ

2dtj


Resolution: 1.63→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.197 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21143 1450 3.1 %RANDOM
Rwork0.19258 ---
all0.19318 47148 --
obs0.19318 45214 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.877 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å2-0 Å20 Å2
2---0.2 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.63→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2409 0 51 219 2679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222522
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.9893437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9315336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.35624.64699
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68915422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0151515
X-RAY DIFFRACTIONr_chiral_restr0.1180.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211841
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 109 -
Rwork0.287 3098 -
obs--99.97 %
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)
18.56832.3167-7.47783.9301-5.268419.8820.28210.05520.25030.37040.0210.0643-0.46980.0014-0.30310.10770.0107-0.03440.0054-0.01450.063132.718541.285529.4167
24.25420.0182-0.55040.56480.37951.6372-0.01070.0940.0036-0.0233-0.0013-0.06260.09720.0380.01190.0199-0.0058-0.00390.05070.01120.039124.161344.50063.6961
31.0907-0.92760.29373.0701-0.72372.9006-0.1222-0.0303-0.14810.22960.11150.13870.048-0.16260.01060.0866-0.0109-0.01840.0443-0.0060.053126.62347.809726.9824
45.77661.05220.34841.8154-0.01858.0388-0.01640.0215-0.05120.29920.1493-0.2984-0.09690.4569-0.13290.07450.0233-0.04280.04-0.03180.080535.568148.763426.45
513.0439-13.406514.560615.312-14.343516.5579-0.56350.2630.5290.2249-0.0828-0.0664-0.74520.50050.64630.1507-0.0728-0.02080.4062-0.05960.409953.190524.788838.5691
618.7666-15.7919-5.471322.01996.96494.25920.43710.5918-0.402-0.0924-0.46780.16420.3715-0.36370.03070.2748-0.0465-0.02780.08530.03810.062214.038628.612718.018
73.02150.76850.20232.7850.74311.2393-0.03070.0330.14150.16030.0210.1975-0.0688-0.20070.00970.10290.01810.00670.06180.00760.058714.793755.295423.1079
80.2213-0.19-0.79434.74190.06512.9417-0.1127-0.0553-0.01030.22170.028-0.38280.41850.17730.08470.1255-0.0311-0.03510.0920.02360.097316.681834.744611.7683
94.3532-2.28320.02368.00662.64182.86670.0544-0.0246-0.33080.4186-0.25240.5480.6767-0.55130.1980.1941-0.1190.03930.17190.0170.09198.302732.89413.1272
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 13
2X-RAY DIFFRACTION2A14 - 94
3X-RAY DIFFRACTION3A95 - 134
4X-RAY DIFFRACTION4A135 - 160
5X-RAY DIFFRACTION5C163 - 173
6X-RAY DIFFRACTION6B3 - 13
7X-RAY DIFFRACTION7B14 - 94
8X-RAY DIFFRACTION8B95 - 134
9X-RAY DIFFRACTION9B135 - 158

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