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- PDB-7oey: Neisseria gonnorhoeae variant E93Q at 1.35 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 7oey
TitleNeisseria gonnorhoeae variant E93Q at 1.35 angstrom resolution
ComponentsTransaldolase
KeywordsTRANSFERASE / SUGAR METABOLISM / POST-TRANSLATIONAL MODIFICATION
Function / homology
Function and homology information


transaldolase / transaldolase activity / pentose-phosphate shunt / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Transaldolase type 2 / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase-type TIM barrel
Similarity search - Domain/homology
SUCCINIC ACID / Transaldolase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsRabe von Pappenheim, F. / Wensien, M. / Tittmann, K.
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Widespread occurrence of covalent lysine-cysteine redox switches in proteins.
Authors: Rabe von Pappenheim, F. / Wensien, M. / Ye, J. / Uranga, J. / Irisarri, I. / de Vries, J. / Funk, L.M. / Mata, R.A. / Tittmann, K.
History
DepositionMay 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 13, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transaldolase
B: Transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7638
Polymers75,2272
Non-polymers5356
Water17,330962
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-8 kcal/mol
Surface area27480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.400, 55.040, 84.370
Angle α, β, γ (deg.)90.000, 108.690, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-757-

HOH

21B-943-

HOH

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Components

#1: Protein Transaldolase


Mass: 37613.703 Da / Num. of mol.: 2 / Mutation: E93Q
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: tal, NGO1610 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5F6E9, transaldolase
#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 962 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG8000, Sodium citrate, sodium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.6888 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 1.35→45.88 Å / Num. obs: 160849 / % possible obs: 97.8 % / Redundancy: 4.552 % / Biso Wilson estimate: 24.417 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.064 / Χ2: 0.904 / Net I/σ(I): 11.85 / Num. measured all: 732213 / Scaling rejects: 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.35-1.394.6830.79525577312144119090.8510.89698.1
1.39-1.424.6940.6422.425387711732114780.8960.72497.8
1.42-1.464.6850.5033.035284311514112780.9280.56898
1.46-1.514.6530.3723.945101011163109620.9650.4298.2
1.51-1.564.6920.3024.844941610821105330.970.34197.3
1.56-1.614.6490.2276.094702310482101140.9830.25796.5
1.61-1.674.6010.1897.25453101007398470.9860.21597.8
1.67-1.744.4480.1488.8442563969795690.9890.16998.7
1.74-1.824.7010.11711.1743182933191860.9930.13298.4
1.82-1.914.6650.09413.6140957893787790.9940.10698.2
1.91-2.014.5630.07816.1238213851183750.9950.08998.4
2.01-2.134.4220.06618.7334829802478770.9950.07598.2
2.13-2.284.2510.06120.2731561756674250.9950.0798.1
2.28-2.464.1980.05321.8328987705169050.9960.0697.9
2.46-2.74.2190.04823.6926886648063730.9970.05598.3
2.7-3.024.2370.04625.2324484593257780.9970.05297.4
3.02-3.494.450.04627.1422680520150970.9970.05298
3.49-4.274.530.04528.4219642441943360.9950.05198.1
4.27-6.044.6640.0429.0415680347433620.9970.04596.8
6.04-45.884.380.03428.067297194416660.9960.03985.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZX4

6zx4


Resolution: 1.35→45.88 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.162 4823 3 %
Rwork0.1363 155941 -
obs0.1371 160764 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.54 Å2 / Biso mean: 25.5297 Å2 / Biso min: 13.85 Å2
Refinement stepCycle: final / Resolution: 1.35→45.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5266 0 67 982 6315
Biso mean--45.18 35.2 -
Num. residues----700
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.370.30631600.2485166532698
1.37-1.380.291600.24315171533198
1.38-1.40.27721610.22265191535298
1.4-1.420.24121600.20225174533497
1.42-1.430.24111600.19155181534198
1.43-1.450.21291610.18735183534497
1.45-1.480.23691600.17525186534699
1.48-1.50.19511590.15885134529398
1.5-1.520.18171610.14615231539298
1.52-1.550.17551590.13765140529998
1.55-1.570.18231590.13535110526996
1.57-1.60.18791570.12795115527297
1.6-1.630.17071590.1285150530997
1.63-1.660.16641610.12625177533898
1.66-1.70.16561610.1255233539499
1.7-1.740.15031610.12495185534698
1.74-1.780.15341600.12395219537998
1.78-1.830.1611630.1345246540999
1.83-1.890.17421620.13025241540399
1.89-1.950.151610.12925211537298
1.95-2.020.15821620.12825250541298
2.02-2.10.16491610.12245214537598
2.1-2.190.16261620.12535228539098
2.19-2.310.14121600.12645180534098
2.31-2.450.16411630.12485241540498
2.45-2.640.14441630.12785275543898
2.64-2.910.14931620.13295247540998
2.91-3.330.17441610.13645214537597
3.33-4.190.14381640.12445311547598
4.19-45.880.14911600.1525137529793
Refinement TLS params.Method: refined / Origin x: 19.2 Å / Origin y: 6.62 Å / Origin z: 11.237 Å
111213212223313233
T0.2264 Å20.0062 Å2-0.0061 Å2-0.1762 Å2-0.0121 Å2--0.2483 Å2
L0.3065 °20.0718 °2-0.0488 °2-0.2472 °2-0.0698 °2--0.7059 °2
S-0.0117 Å °-0.0249 Å °0.0428 Å °0.0053 Å °0.0146 Å °-0.0028 Å °0.0011 Å °0.0031 Å °-0.0052 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 501:939 OR RESID 402:402 ) ) OR ( CHAIN B AND ( RESID 501:1023 OR RESID 402:403 OR RESID 404:404 ) )A501 - 939
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 501:939 OR RESID 402:402 ) ) OR ( CHAIN B AND ( RESID 501:1023 OR RESID 402:403 OR RESID 404:404 ) )A402
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 501:939 OR RESID 402:402 ) ) OR ( CHAIN B AND ( RESID 501:1023 OR RESID 402:403 OR RESID 404:404 ) )B501 - 1023
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 501:939 OR RESID 402:402 ) ) OR ( CHAIN B AND ( RESID 501:1023 OR RESID 402:403 OR RESID 404:404 ) )B402 - 403
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 501:939 OR RESID 402:402 ) ) OR ( CHAIN B AND ( RESID 501:1023 OR RESID 402:403 OR RESID 404:404 ) )B404

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