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- PDB-6cyz: Mycobacterial homoserine kinase ThrB in complex with AMPPNP -

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Basic information

Entry
Database: PDB / ID: 6cyz
TitleMycobacterial homoserine kinase ThrB in complex with AMPPNP
ComponentsHomoserine kinase
KeywordsTRANSFERASE / Threonine biosynthesis / ATP-binding / Mycobacterium abscessus / Rv1296
Function / homology
Function and homology information


homoserine kinase / homoserine kinase activity / threonine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Homoserine kinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Homoserine kinase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.04 Å
AuthorsLi, J. / Korotkov, K.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110787 United States
CitationJournal: To Be Published
Title: Mycobacterial homoserine kinase ThrB
Authors: Li, J. / Korotkov, K.V.
History
DepositionApr 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homoserine kinase
B: Homoserine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1845
Polymers62,1362
Non-polymers1,0483
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-32 kcal/mol
Surface area22610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.350, 62.700, 84.630
Angle α, β, γ (deg.)90.000, 104.400, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 306 or resid 401))
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 306 or resid 401))A0
211chain BB2 - 306

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Components

#1: Protein Homoserine kinase / HSK / ThrB


Mass: 31068.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543) (bacteria)
Strain: ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543
Gene: thrB, MAB_1437 / Plasmid: pRSF-28T / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2(DE3) / References: UniProt: B1MLU6, homoserine kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 48.14 % / Description: rectangular prism
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 0.6 M sodium chloride, 0.1 M MES, pH 6.5, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 5, 2018
Details: Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→81.971 Å / Num. obs: 36994 / % possible obs: 99.2 % / Redundancy: 3.707 % / Biso Wilson estimate: 29.13 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.14 / Rrim(I) all: 0.164 / Χ2: 0.96 / Net I/σ(I): 9.5 / Num. measured all: 137127 / Scaling rejects: 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.04-2.093.2061.131.0826170.4091.35595.8
2.09-2.153.7120.9781.4726700.4631.14799.6
2.15-2.213.7120.811.8525700.5970.9599.5
2.21-2.283.690.7242.2325180.7010.85199.3
2.28-2.363.6990.5822.8324160.750.68399.1
2.36-2.443.7650.4973.3923700.8380.58199.8
2.44-2.533.7490.4233.9322650.8930.49499.5
2.53-2.633.7770.3674.4922020.9160.42899.9
2.63-2.753.7850.2856.0321240.9430.33399.7
2.75-2.893.7830.2187.7119910.9710.25499.8
2.89-3.043.8020.1719.4219430.9760.299.7
3.04-3.233.8080.11912.4918120.9880.13899.7
3.23-3.453.7650.08916.2516950.9930.10498.9
3.45-3.723.7590.07119.5115910.9940.08399.8
3.72-4.083.7610.05623.214710.9960.06598.9
4.08-4.563.7820.04128.6813210.9980.04899.8
4.56-5.273.7480.04428.7811870.9970.05199.6
5.27-6.453.7240.04725.2210100.9970.05699.6
6.45-9.123.6460.03131.597770.9990.03799.6
9.12-81.9713.450.02537.74440.9990.02998.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.95 Å41.58 Å
Translation3.95 Å41.58 Å

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Processing

Software
NameVersionClassification
XDSVERSION Jan 26, 2018 BUILT=20180319data reduction
XSCALEVERSION Jan 26, 2018 BUILT=20180319data scaling
PHASER2.8.2phasing
PHENIX1.13rc2_2975refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5WAT

5wat


Resolution: 2.04→81.971 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0.91 / Phase error: 26.88
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 3428 4.98 %RANDOM SELECTION
Rwork0.197 ---
obs0.1989 36986 94.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.4 Å2 / Biso mean: 38.8277 Å2 / Biso min: 15.51 Å2
Refinement stepCycle: final / Resolution: 2.04→81.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4188 0 96 236 4520
Biso mean--97.97 34.65 -
Num. residues----590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_d0.0040.0344314
X-RAY DIFFRACTIONf_angle_d0.786.4985912
X-RAY DIFFRACTIONf_dihedral_angle_d0.0490.149740
X-RAY DIFFRACTIONf_chiral_restr0.0040.037790
X-RAY DIFFRACTIONf_plane_restr13.485179.9182604
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2646X-RAY DIFFRACTION7.854TORSIONAL
12B2646X-RAY DIFFRACTION7.854TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0399-2.06910.44241190.38292202232176
2.0691-2.10.36811470.33592640278793
2.1-2.13280.30761460.32992712285894
2.1328-2.16780.33221410.31362681282294
2.1678-2.20510.33611460.29782723286994
2.2051-2.24520.32731430.28512698284194
2.2452-2.28840.35421430.29312693283692
2.2884-2.33510.27631450.26732625277093
2.3351-2.38590.32841380.24892736287496
2.3859-2.44140.29981320.23842800293296
2.4414-2.50250.30371400.23992766290695
2.5025-2.57010.31511400.22592737287795
2.5701-2.64580.22271400.22232790293096
2.6458-2.73120.22341410.21112796293796
2.7312-2.82880.26551460.20282728287496
2.8288-2.94210.26761390.2072801294097
2.9421-3.0760.21181500.20162766291697
3.076-3.23810.2581580.17742782294097
3.2381-3.4410.19761220.17412815293796
3.441-3.70670.25211390.1632753289296
3.7067-4.07970.18571260.14712821294796
4.0797-4.670.15481630.11922766292998
4.67-5.88350.15521580.14382799295797
5.8835-82.03740.18381660.17262766293297
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)
10.907-0.2491-0.17971.0956-0.5762.26130.01610.1417-0.0206-0.2234-0.025-0.0188-0.1956-0.0267-0.02980.3353-0.023-0.00540.2277-0.0190.240916.500712.43139.7729
21.2932-0.23450.05580.88760.13251.66490.03740.14270.0598-0.2579-0.02210.0469-0.1383-0.1785-0.0090.353-0.0138-0.00160.2947-0.01450.238216.7878.7169-0.3492
31.06140.2971-0.15570.9967-0.47722.3489-0.01060.003-0.08870.02960.04780.0204-0.1473-0.2147-0.04960.26590.0395-0.01320.2565-0.01790.25628.87610.202313.9379
41.41240.6763-0.41491.89740.10721.4847-0.0974-0.06690.0582-0.30850.03060.011-0.07540.17870.07220.22510.0583-0.01180.19910.01880.231323.63520.559923.5488
50.7658-0.2279-0.09510.69220.01181.5029-0.0458-0.1205-0.01720.01190.0547-0.11360.0240.2386-0.00890.19270.0180.00680.2374-0.01750.238327.76811.592327.4688
60.8430.58470.2530.73790.30842.99720.07980.02350.04640.0991-0.08970.02-0.2144-0.06090.00270.2540.03720.00830.17750.01480.245610.74015.438859.9312
73.1194-1.19980.57541.7924-1.00981.82660.1983-0.3021-0.24830.2279-0.11370.11880.2308-0.194-0.09260.3219-0.03940.00360.24060.07120.31746.6134-3.110772.4965
81.0328-0.1283-0.03210.42220.07981.62420.0830.0261-0.04650.0558-0.0028-0.02880.03830.0797-0.09240.25080.02540.00290.18250.00190.244115.54281.983658.8163
91.35560.2199-0.72331.28610.05751.74740.03890.05850.01860.06530.03710.0655-0.0763-0.4225-0.06520.22460.0445-0.03230.33230.02170.24791.06650.198937.6475
101.07051.08410.06511.29580.15880.47670.1801-0.1030.234-0.022-0.12040.2889-0.2244-0.90340.00660.2620.16690.05390.58540.02480.3614-5.83787.002147.0289
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 43 )A2 - 43
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 101 )A44 - 101
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 172 )A102 - 172
4X-RAY DIFFRACTION4chain 'A' and (resid 173 through 203 )A173 - 203
5X-RAY DIFFRACTION5chain 'A' and (resid 204 through 306 )A204 - 306
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 43 )B2 - 43
7X-RAY DIFFRACTION7chain 'B' and (resid 44 through 66 )B44 - 66
8X-RAY DIFFRACTION8chain 'B' and (resid 67 through 172 )B67 - 172
9X-RAY DIFFRACTION9chain 'B' and (resid 173 through 257 )B173 - 257
10X-RAY DIFFRACTION10chain 'B' and (resid 258 through 306 )B258 - 306

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