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- PDB-3gvd: Crystal Structure of Serine Acetyltransferase CysE from Yersinia ... -

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Basic information

Entry
Database: PDB / ID: 3gvd
TitleCrystal Structure of Serine Acetyltransferase CysE from Yersinia pestis
ComponentsSerine acetyltransferase
KeywordsTRANSFERASE / left-handed beta-helix / Structural Genomics of National Institute of Allergy and Infectious Diseases / Acyltransferase / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


serine O-acetyltransferase / serine O-acetyltransferase activity / L-cysteine biosynthetic process from L-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 transferase, conserved site ...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 transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Hexapeptide repeat proteins / 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
ACETIC ACID / CYSTEINE / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Serine acetyltransferase / Serine acetyltransferase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKim, Y. / Zhou, M. / Peterson, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Serine Acetyltransferase CysE from Yersinia pestis
Authors: Kim, Y. / Zhou, M. / Peterson, S. / Anderson, W.F. / Joachimiak, A.
History
DepositionMar 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Sep 6, 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

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Assembly

Deposited unit
A: Serine acetyltransferase
B: Serine acetyltransferase
C: Serine acetyltransferase
D: Serine acetyltransferase
E: Serine acetyltransferase
F: Serine acetyltransferase
G: Serine acetyltransferase
H: Serine acetyltransferase
I: Serine acetyltransferase
J: Serine acetyltransferase
K: Serine acetyltransferase
L: Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)356,66340
Polymers353,74412
Non-polymers2,91928
Water18,2851015
1
A: Serine acetyltransferase
B: Serine acetyltransferase
C: Serine acetyltransferase
D: Serine acetyltransferase
E: Serine acetyltransferase
F: Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,36620
Polymers176,8726
Non-polymers1,49414
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24210 Å2
ΔGint-181 kcal/mol
Surface area48090 Å2
MethodPISA
2
G: Serine acetyltransferase
H: Serine acetyltransferase
I: Serine acetyltransferase
J: Serine acetyltransferase
K: Serine acetyltransferase
L: Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,29820
Polymers176,8726
Non-polymers1,42614
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23740 Å2
ΔGint-208 kcal/mol
Surface area47980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.472, 81.228, 139.406
Angle α, β, γ (deg.)97.07, 95.32, 94.72
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Serine acetyltransferase


Mass: 29478.680 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tag with TEV cleavage site / Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: cysE, YPO0070 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 magic
References: UniProt: Q0WKM4, UniProt: A0A2U2H3H7*PLUS, serine O-acetyltransferase

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Non-polymers , 7 types, 1043 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical
ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H7NO2S
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1015 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium acetate, 20% w/v Polyethylene glycol 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.4→49.17 Å / Num. all: 112894 / Num. obs: 112894 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 32.44 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 6.1
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2.2 / % possible all: 96.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
MOLREPphasing
HKL-3000phasing
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1T3D

1t3d


Resolution: 2.4→45.986 Å / SU ML: 0.39 / Isotropic thermal model: isotropic / σ(F): 1.96 / Phase error: 32.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2649 5660 5.05 %
Rwork0.1989 --
obs0.2022 112074 96.99 %
all-112074 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.29 Å2 / ksol: 0.309 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--16.2999 Å23.9853 Å2-2.4749 Å2
2--11.0081 Å2-14.1522 Å2
3---4.4653 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23766 0 174 1015 24955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824414
X-RAY DIFFRACTIONf_angle_d1.1633094
X-RAY DIFFRACTIONf_dihedral_angle_d17.5398777
X-RAY DIFFRACTIONf_chiral_restr0.0743820
X-RAY DIFFRACTIONf_plane_restr0.0054268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42730.28991820.25683348X-RAY DIFFRACTION92
2.4273-2.45580.35682290.26213535X-RAY DIFFRACTION97
2.4558-2.48580.36591750.26613515X-RAY DIFFRACTION96
2.4858-2.51720.34891900.26013548X-RAY DIFFRACTION97
2.5172-2.55040.38392100.25613583X-RAY DIFFRACTION97
2.5504-2.58530.32891680.25343503X-RAY DIFFRACTION97
2.5853-2.62220.34191790.25713629X-RAY DIFFRACTION97
2.6222-2.66140.3921700.28523441X-RAY DIFFRACTION96
2.6614-2.70290.40341960.29953426X-RAY DIFFRACTION93
2.7029-2.74730.3492010.22713577X-RAY DIFFRACTION98
2.7473-2.79460.31351930.22493524X-RAY DIFFRACTION97
2.7946-2.84540.32351830.22713623X-RAY DIFFRACTION98
2.8454-2.90010.31671880.23153561X-RAY DIFFRACTION98
2.9001-2.95930.28611970.21833565X-RAY DIFFRACTION98
2.9593-3.02370.32731770.23283566X-RAY DIFFRACTION98
3.0237-3.0940.2661970.22643611X-RAY DIFFRACTION98
3.094-3.17130.29342090.20073567X-RAY DIFFRACTION98
3.1713-3.25710.25042060.21023605X-RAY DIFFRACTION98
3.2571-3.35290.31011800.20663572X-RAY DIFFRACTION98
3.3529-3.46110.30691700.21343472X-RAY DIFFRACTION95
3.4611-3.58470.26311940.20183599X-RAY DIFFRACTION98
3.5847-3.72820.26192160.19133393X-RAY DIFFRACTION94
3.7282-3.89780.23391840.17653469X-RAY DIFFRACTION95
3.8978-4.10320.21361670.16223566X-RAY DIFFRACTION97
4.1032-4.36010.20031900.14253578X-RAY DIFFRACTION98
4.3601-4.69640.16681860.13353539X-RAY DIFFRACTION98
4.6964-5.16840.19611720.13583659X-RAY DIFFRACTION98
5.1684-5.9150.20711970.16143599X-RAY DIFFRACTION99
5.915-7.44710.22851810.16973660X-RAY DIFFRACTION99
7.4471-45.99420.20491730.16983581X-RAY DIFFRACTION97

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