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- PDB-6jvu: Crystal structure of Klebsiella pneumoniae CysE in complex with L... -

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Basic information

Entry
Database: PDB / ID: 6jvu
TitleCrystal structure of Klebsiella pneumoniae CysE in complex with L-cysteine
ComponentsSerine acetyltransferase
KeywordsTRANSFERASE / Serine 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 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 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
CYSTEINE / PHOSPHATE ION / Serine acetyltransferase / Serine acetyltransferase
Similarity search - Component
Biological speciesKlebsiella pneumoniae MGH 78578 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsVerma, D. / Gupta, V.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (India)BT/Bio-CARe/01/79/2011-12 India
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Allosteric inhibition and kinetic characterization of Klebsiella pneumoniae CysE: An emerging drug target.
Authors: Verma, D. / Gupta, S. / Saxena, R. / Kaur, P. / R, R. / Srivastava, S. / Gupta, V.
History
DepositionApr 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,94515
Polymers181,9666
Non-polymers9799
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20620 Å2
ΔGint-138 kcal/mol
Surface area46040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.770, 110.750, 101.790
Angle α, β, γ (deg.)90.000, 96.620, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A6 - 258
2010B6 - 258
1020A7 - 256
2020C7 - 256
1030A6 - 258
2030D6 - 258
1040A6 - 257
2040E6 - 257
1050A6 - 258
2050F6 - 258
1060B7 - 256
2060C7 - 256
1070B5 - 259
2070D5 - 259
1080B6 - 257
2080E6 - 257
1090B5 - 259
2090F5 - 259
10100C7 - 256
20100D7 - 256
10110C7 - 256
20110E7 - 256
10120C7 - 256
20120F7 - 256
10130D6 - 257
20130E6 - 257
10140D5 - 259
20140F5 - 259
10150E6 - 257
20150F6 - 257

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Serine acetyltransferase


Mass: 30327.709 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae MGH 78578 (bacteria)
Strain: MGH 78578 / Gene: cysE / Variant: serotype K52 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q0ZB96, UniProt: A6TFK2*PLUS, serine O-acetyltransferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H7NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.35 Å3/Da / Density % sol: 47.7 % / Description: Cuboidal crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% v/v ethylene glycol+ 3% w/v trimethylamine N-oxide dihydrate
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9785 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Apr 15, 2015
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.8→110.75 Å / Num. obs: 37156 / % possible obs: 99.3 % / Redundancy: 7.8 % / Biso Wilson estimate: 90.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.026 / Rrim(I) all: 0.072 / Rsym value: 0.067 / Net I/av σ(I): 5.2 / Net I/σ(I): 16.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
2.8-2.957.80.9640.853760.7710.3681.0320.96499
2.95-3.137.80.5821.351190.2220.6230.58299.1
3.13-3.357.80.3032.547980.1160.3240.30399.2
3.35-3.617.80.1415.244910.0540.1510.14199.3
3.61-3.967.80.0818.440960.0310.0870.08199.4
3.96-4.437.80.05910.137480.0230.0630.05999.6
4.43-5.117.80.0519.632970.020.0550.05199.6
5.11-6.267.70.0579.728360.0220.0610.05799.7
6.26-8.857.70.04810.421770.0180.0510.04899.8
8.8-74.6727.30.04211.912180.0180.0460.04298.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 2

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Processing

Software
NameVersionClassification
MOSFLM7.2.1data reduction
SCALA3.3.22data scaling
PHASERphasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T3D

1t3d


Resolution: 2.8→101.11 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.934 / SU B: 51.054 / SU ML: 0.438 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.412
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1766 4.8 %RANDOM
Rwork0.2227 ---
obs0.2244 35368 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 244.32 Å2 / Biso mean: 119 Å2 / Biso min: 54.78 Å2
Baniso -1Baniso -2Baniso -3
1--3.59 Å20 Å26.45 Å2
2---3.93 Å20 Å2
3---5.86 Å2
Refinement stepCycle: final / Resolution: 2.8→101.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10874 0 56 50 10980
Biso mean--115.27 86.8 -
Num. residues----1517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01911298
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210807
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.95915394
X-RAY DIFFRACTIONr_angle_other_deg1.157324782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9151518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76324.264401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.404151712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0691553
X-RAY DIFFRACTIONr_chiral_restr0.1050.21806
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112948
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022371
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A146560.05
12B146560.05
21A145400.05
22C145400.05
31A147020.04
32D147020.04
41A145920.06
42E145920.06
51A145360.05
52F145360.05
61B156200.05
62C156200.05
71B159940.04
72D159940.04
81B158840.01
82E158840.01
91B158420.04
92F158420.04
101C157480.04
102D157480.04
111C155860.05
112E155860.05
121C156880.04
122F156880.04
131D158280.04
132E158280.04
141D159640.04
142F159640.04
151E157160.04
152F157160.04
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 130 -
Rwork0.35 2596 -
all-2726 -
obs--98.66 %
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)
12.61320.82490.78092.49890.69634.8287-0.64671.16830.8818-1.22880.31740.2482-1.917-0.17510.32931.7808-0.0373-0.25780.94850.41440.3029-35.513-14.7359.557
24.79861.20681.87533.02271.31634.8027-0.24440.43360.0988-0.7655-0.07360.478-0.2481-1.63740.3180.54290.009-0.18881.1224-0.05280.1008-14.9851.538-0.012
33.18820.64120.80651.58211.4245.3027-0.0131.1167-0.5659-0.76570.4534-0.35140.15840.3631-0.44030.8601-0.16990.0890.8227-0.31460.1602-12.487-26.271-1.481
43.20890.94330.87763.29141.3734.2227-0.0719-0.60370.27650.21380.3739-0.5566-1.05160.8455-0.30190.6753-0.2198-0.08380.6808-0.2780.2058-54.088-18.13-32.715
53.5131.72160.60544.45630.76024.33110.4701-0.5425-1.28940.9190.4788-1.39961.22961.2308-0.94890.59430.3364-0.51020.7556-0.09090.7513-29.406-24.15-43.971
62.13480.15470.66463.36751.68215.3880.2232-1.2148-0.17131.1254-0.32660.14780.8934-1.04780.10330.754-0.21230.01810.96050.09740.0272-36.6632.481-40.041
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 259
2X-RAY DIFFRACTION2B5 - 257
3X-RAY DIFFRACTION3C7 - 257
4X-RAY DIFFRACTION4D5 - 259
5X-RAY DIFFRACTION5E7 - 257
6X-RAY DIFFRACTION6F6 - 256

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