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- PDB-4n6b: Soybean Serine Acetyltransferase Complexed with CoA -

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Basic information

Entry
Database: PDB / ID: 4n6b
TitleSoybean Serine Acetyltransferase Complexed with CoA
ComponentsSerine Acetyltransferase Apoenzyme
KeywordsTRANSFERASE / acetyltransferase
Function / homology
Function and homology information


serine O-acetyltransferase / serine O-acetyltransferase activity / cysteine biosynthetic process from serine / cytosol
Similarity search - Function
serine acetyltransferase, domain 1 / serine acetyltransferase, domain 1 / Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / : / Serine acetyltransferase, N-terminal domain superfamily / Serine acetyltransferase, LbH domain / Hexapeptide repeat of succinyl-transferase ...serine acetyltransferase, domain 1 / serine acetyltransferase, domain 1 / Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / : / Serine acetyltransferase, N-terminal domain superfamily / Serine acetyltransferase, LbH domain / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COENZYME A / serine O-acetyltransferase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.005 Å
AuthorsYi, H. / Dey, S. / Kumaran, S. / Krishnan, H.B. / Jez, J.M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structure of soybean serine acetyltransferase and formation of the cysteine regulatory complex as a molecular chaperone.
Authors: Yi, H. / Dey, S. / Kumaran, S. / Lee, S.G. / Krishnan, H.B. / Jez, J.M.
History
DepositionOct 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Jan 8, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Serine Acetyltransferase Apoenzyme
B: Serine Acetyltransferase Apoenzyme
C: Serine Acetyltransferase Apoenzyme
D: Serine Acetyltransferase Apoenzyme
E: Serine Acetyltransferase Apoenzyme
F: Serine Acetyltransferase Apoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,24711
Polymers182,4106
Non-polymers3,8385
Water00
1
A: Serine Acetyltransferase Apoenzyme
D: Serine Acetyltransferase Apoenzyme
E: Serine Acetyltransferase Apoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5076
Polymers91,2053
Non-polymers2,3033
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint-22 kcal/mol
Surface area25610 Å2
MethodPISA
2
B: Serine Acetyltransferase Apoenzyme
C: Serine Acetyltransferase Apoenzyme
F: Serine Acetyltransferase Apoenzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7405
Polymers91,2053
Non-polymers1,5352
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-18 kcal/mol
Surface area25760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.077, 99.181, 120.256
Angle α, β, γ (deg.)90.00, 117.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Serine Acetyltransferase Apoenzyme


Mass: 30401.605 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Production host: Escherichia coli (E. coli) / References: UniProt: I1KHY6, serine O-acetyltransferase
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
Sequence detailsTHE DISCREPANCIES ARE ARISING FROM THE DIFFERENT UNPROT SEQUENCE AND THE SPECIFIC CLONE USED FOR ...THE DISCREPANCIES ARE ARISING FROM THE DIFFERENT UNPROT SEQUENCE AND THE SPECIFIC CLONE USED FOR STRUCTURAL STUDIES

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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: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 12% ethanol, 100 mM Tris (pH 7.8), 200 mM MgCl2, 1 mM Tris(2-carboxyethyl)phosphine hydrochloride, and 10 mM CoA, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2012
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→37.96 Å / Num. all: 42487 / Num. obs: 33560 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.005→37.956 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 33.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 1630 4.67 %random
Rwork0.2144 ---
obs0.2169 33560 98.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.005→37.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10525 0 240 0 10765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910978
X-RAY DIFFRACTIONf_angle_d0.95214938
X-RAY DIFFRACTIONf_dihedral_angle_d13.2923915
X-RAY DIFFRACTIONf_chiral_restr0.061731
X-RAY DIFFRACTIONf_plane_restr0.0041875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0052-3.08030.40691260.34572614X-RAY DIFFRACTION90
3.0803-3.16360.43651420.32642915X-RAY DIFFRACTION100
3.1636-3.25660.36711430.30332932X-RAY DIFFRACTION100
3.2566-3.36170.33631420.26982922X-RAY DIFFRACTION100
3.3617-3.48170.34781440.25772937X-RAY DIFFRACTION100
3.4817-3.6210.43681410.33922868X-RAY DIFFRACTION98
3.621-3.78570.52671390.37622803X-RAY DIFFRACTION95
3.7857-3.98510.27591450.22942926X-RAY DIFFRACTION99
3.9851-4.23440.21361430.18422928X-RAY DIFFRACTION100
4.2344-4.56090.22241450.15772948X-RAY DIFFRACTION100
4.5609-5.01890.21451420.15632902X-RAY DIFFRACTION99
5.0189-5.7430.26351450.18592956X-RAY DIFFRACTION100
5.743-7.22740.28691450.22432956X-RAY DIFFRACTION100
7.2274-37.95940.19211430.17762895X-RAY DIFFRACTION95
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)
12.02451.27020.24440.9692-0.26431.46830.07910.27260.3639-0.1387-0.09010.4737-0.1266-0.20070.0460.44940.11820.04480.0756-0.0120.3196-25.8346-47.962-55.9257
23.4574-1.26890.10560.9389-0.31460.96390.1081-0.6194-0.07160.1255-0.0275-0.04620.12750.4747-0.14540.3964-0.06230.03370.55280.02040.2586.0159-62.5789-18.4277
31.9960.90330.46221.05680.09881.28290.0438-0.1221-0.143-0.13730.0372-0.18180.27530.467-0.03050.3172-0.00560.14820.5022-0.01750.248513.8621-51.1686-42.6288
42.775-0.3094-0.23660.7097-0.26020.7330.3323-0.5788-0.428-0.1465-0.12380.41270.1272-0.2213-0.18640.4424-0.0733-0.02450.3740.0350.3975-30.4512-63.4708-33.4314
53.0481-0.91211.10720.9801-0.19911.18630.1691-0.73790.25570.2129-0.0310.4309-0.1523-0.18120.10320.38970.05480.10930.247-0.05030.4843-31.2939-36.843-31.5107
62.00150.11911.27240.8070.04881.98140.1716-0.420.32240.0719-0.193-0.1103-0.20390.524-0.00010.453-0.09750.11640.6004-0.08250.28968.442-34.9192-19.7324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 17:255 OR RESID 300:300 ) )A17 - 255
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 17:255 OR RESID 300:300 ) )A300
3X-RAY DIFFRACTION2( CHAIN B AND RESID 16:255 ) OR ( CHAIN E AND RESID 400:400 )B16 - 255
4X-RAY DIFFRACTION2( CHAIN B AND RESID 16:255 ) OR ( CHAIN E AND RESID 400:400 )E400
5X-RAY DIFFRACTION3( CHAIN C AND RESID 15:255 ) OR ( CHAIN D AND RESID 500:500 )C15 - 255
6X-RAY DIFFRACTION3( CHAIN C AND RESID 15:255 ) OR ( CHAIN D AND RESID 500:500 )D500
7X-RAY DIFFRACTION4( CHAIN D AND RESID 17:255 ) OR ( CHAIN F AND RESID 600:600 )D17 - 255
8X-RAY DIFFRACTION4( CHAIN D AND RESID 17:255 ) OR ( CHAIN F AND RESID 600:600 )F600
9X-RAY DIFFRACTION5( CHAIN C AND RESID 700:700 ) OR ( CHAIN E AND RESID 17:255 )C700
10X-RAY DIFFRACTION5( CHAIN C AND RESID 700:700 ) OR ( CHAIN E AND RESID 17:255 )E17 - 255
11X-RAY DIFFRACTION6( CHAIN F AND RESID 17:255 )F17 - 255

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