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- PDB-1s80: Structure of Serine Acetyltransferase from Haemophilis influenzae Rd -

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Basic information

Entry
Database: PDB / ID: 1s80
TitleStructure of Serine Acetyltransferase from Haemophilis influenzae Rd
ComponentsSerine acetyltransferase
KeywordsTRANSFERASE / Structural Genomics / Protein Structure Initiative / Serine Acetyltransferase / Left-Handed Parallel beta-Helix / NYSGXRC / PSI / New York SGX Research Center for Structural Genomics
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 acetyltransferase, LbH domain / Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal domain superfamily / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. ...serine acetyltransferase, domain 1 / serine acetyltransferase, domain 1 / Serine acetyltransferase, LbH domain / Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal domain superfamily / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Serine acetyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsGorman, J. / Gogos, A. / Shapiro, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of serine acetyltransferase from Haemophilus influenzae Rd.
Authors: Gorman, J. / Shapiro, L.
History
DepositionJan 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)183,7936
Polymers183,7936
Non-polymers00
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18700 Å2
ΔGint-101 kcal/mol
Surface area47940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.963, 209.670, 136.569
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a hexamer shown in the asymmetric unit

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Components

#1: Protein
Serine acetyltransferase / SAT


Mass: 30632.211 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: CYSE, HI0606 / Plasmid: pET26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P43886, serine O-acetyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 3 Å3/Da / Density % sol: 58.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2M NaCl, 0.16M MgCl2, 3% PEG 400, and 0.1 M NaCitrate pH 5.6 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 2, 2003
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 51228 / Num. obs: 51228 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.102 / Net I/σ(I): 18.6
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 6.98 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.702 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 1.003 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21913 2601 5.1 %RANDOM
Rwork0.17155 ---
obs0.17401 48592 99.75 %-
all-46107 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.021 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2--2.27 Å20 Å2
3----2.87 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11094 0 0 418 11512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02211328
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210476
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.93715396
X-RAY DIFFRACTIONr_angle_other_deg0.821324348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98951434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88524.5480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.948151884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6011554
X-RAY DIFFRACTIONr_chiral_restr0.0770.21770
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212606
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022142
X-RAY DIFFRACTIONr_nbd_refined0.2080.22798
X-RAY DIFFRACTIONr_nbd_other0.1880.210852
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.090.26480
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2463
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1420.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8061.58550
X-RAY DIFFRACTIONr_mcbond_other0.1061.52952
X-RAY DIFFRACTIONr_mcangle_it1.017211544
X-RAY DIFFRACTIONr_scbond_it1.60334620
X-RAY DIFFRACTIONr_scangle_it2.4664.53852
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 194
Rwork0.234 3372

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