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- PDB-7ra4: Crystal structure of Neisseria gonorrhoeae serine acetyltransfera... -

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Basic information

Entry
Database: PDB / ID: 7ra4
TitleCrystal structure of Neisseria gonorrhoeae serine acetyltransferase (CysE) in complex with serine
ComponentsSerine acetyltransferase
KeywordsTRANSFERASE / CysE
Function / homology
Function and homology information


serine O-acetyltransferase / serine O-acetyltransferase activity / cysteine biosynthetic process from serine / cytoplasm
Similarity search - Function
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 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
SERINE / Serine acetyltransferase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHicks, J.L. / Oldham, K.E. / Prentice, E.J. / Summers, E.L.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Health Research Council (HRC)19/602 New Zealand
CitationJournal: Biochem.J. / Year: 2022
Title: Serine acetyltransferase from Neisseria gonorrhoeae; structural and biochemical basis of inhibition.
Authors: Oldham, K.E.A. / Prentice, E.J. / Summers, E.L. / Hicks, J.L.
History
DepositionJun 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 19, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1885
Polymers94,9773
Non-polymers2102
Water70339
1
A: Serine acetyltransferase
B: Serine acetyltransferase
C: Serine acetyltransferase
hetero molecules

A: Serine acetyltransferase
B: Serine acetyltransferase
C: Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,37510
Polymers189,9556
Non-polymers4204
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area17840 Å2
ΔGint-107 kcal/mol
Surface area46230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.857, 94.587, 79.254
Angle α, β, γ (deg.)90.000, 92.178, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 6 or (resid 7...
d_2ens_1(chain "B" and (resid 3 through 6 or (resid 7...
d_3ens_1(chain "C" and ((resid 3 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSLEUA1 - 70
d_12ens_1SERSERA72 - 184
d_13ens_1GLUILEA187 - 219
d_14ens_1ALAPROA221 - 242
d_21ens_1LYSASNB1 - 5
d_22ens_1PHELEUB7 - 71
d_23ens_1SERILEB73 - 218
d_24ens_1ALAPROB220 - 241
d_31ens_1LYSSERC2 - 184
d_32ens_1GLUPROC186 - 240

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Components

#1: Protein Serine acetyltransferase


Mass: 31659.129 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) (bacteria)
Strain: ATCC 700825 / FA 1090 / Gene: NGO_1423 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5F6X0, serine O-acetyltransferase
#2: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.03 Å3/Da / Density % sol: 39.35 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.4 / Details: 0.1M TRIS pH 8.4, 26% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→43.88 Å / Num. obs: 18772 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 58.13 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.061 / Net I/σ(I): 9.1
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.915 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2723 / CC1/2: 0.829 / Rpim(I) all: 0.367 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874model building
PHASER1.18.2_3874phasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WYE

6wye


Resolution: 2.8→43.88 Å / SU ML: 0.3655 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.4247
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2672 1873 9.99 %
Rwork0.2345 16874 -
obs0.2378 18747 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.19 Å2
Refinement stepCycle: LAST / Resolution: 2.8→43.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5001 0 14 39 5054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00225118
X-RAY DIFFRACTIONf_angle_d0.58326956
X-RAY DIFFRACTIONf_chiral_restr0.0506766
X-RAY DIFFRACTIONf_plane_restr0.0046940
X-RAY DIFFRACTIONf_dihedral_angle_d14.55691616
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.313028864659
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.321861100235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.880.30061490.28811273X-RAY DIFFRACTION100
2.88-2.960.34431340.27161303X-RAY DIFFRACTION99.93
2.96-3.060.30671510.27481304X-RAY DIFFRACTION99.79
3.06-3.160.26741440.24691297X-RAY DIFFRACTION99.93
3.17-3.290.28491360.23321268X-RAY DIFFRACTION99.86
3.29-3.440.27481470.24231302X-RAY DIFFRACTION100
3.44-3.620.29511390.22821290X-RAY DIFFRACTION99.86
3.62-3.850.22041460.1991307X-RAY DIFFRACTION99.93
3.85-4.150.21911430.2161296X-RAY DIFFRACTION100
4.15-4.560.24281420.21431299X-RAY DIFFRACTION99.86
4.56-5.220.29121490.23621298X-RAY DIFFRACTION99.38
5.22-6.580.3011450.27321309X-RAY DIFFRACTION99.86
6.58-43.880.25581480.22961328X-RAY DIFFRACTION99.26
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)
11.259230890020.2892321718580.462238425882.070121511960.5001342833651.438251036110.0379385779262-0.04136481142930.1211571532140.1600107617990.0622426505371-0.6619858960680.002249135786170.2644470813830.0001309547592560.348855824294-0.03902516952070.02793432452160.4500976494950.00391886848830.59298218340826.14362681271.509243696554.23986794225
22.343017962170.208753237460.2956099665491.79894576247-0.317249201011.586530612120.0411155039533-0.191953826856-0.2478009410620.318219832444-0.0458482402779-0.5077119866830.1052289440930.0978818243734-0.0002431047153120.4673989125880.0157345872221-0.06571338173120.3758180727010.002304692171920.43230521583715.0940758261-20.754500442316.337566769
31.4130153445-0.1490387271420.5275797321232.50122602281-0.3643606994660.701049545932-0.0436684273497-0.321912087520.1941054359340.704735437217-0.0335110458082-0.312404859847-0.05035595056580.01644566408920.0001989377669160.6280646524090.003732150578450.003487288195370.528034340652-0.08436109597420.3802072541338.049366846694.6887247555224.2661662302
40.473474082559-0.486212665508-0.3963190550281.46552243130.446480741680.8188443501820.241308444748-0.302324104291-0.07907189137440.1622545771550.0453303716774-0.0635768190822-0.242673829091-0.218842829260.2927638865130.880609262033-0.303965403617-0.0746287598130.5969834263190.08672542539970.50705578852127.668286323-0.54791979569215.295925533
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resseq 3:248)AA3 - 2481 - 243
22(chain B and resseq 3:251)BB3 - 2471 - 241
33(chain C and resseq 2:251)CC2 - 2491 - 242
44(chain A and resseq 301:302)AD301 - 3021 - 2

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