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- PDB-6zwf: Neisseria gonorrhoeae transaldolase -

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Basic information

Entry
Database: PDB / ID: 6zwf
TitleNeisseria gonorrhoeae transaldolase
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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / CITRIC ACID / OXYGEN MOLECULE / Transaldolase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsRabe von Pappenheim, F. / Wensien, M. / Funk, L.-M. / Sautner, V. / Tittmann, K.
CitationJournal: Nature / Year: 2021
Title: A lysine-cysteine redox switch with an NOS bridge regulates enzyme function.
Authors: Wensien, M. / von Pappenheim, F.R. / Funk, L.M. / Kloskowski, P. / Curth, U. / Diederichsen, U. / Uranga, J. / Ye, J. / Fang, P. / Pan, K.T. / Urlaub, H. / Mata, R.A. / Sautner, V. / Tittmann, K.
History
DepositionJul 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
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.title / _citation.year
Revision 1.2May 19, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 2, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 31, 2024Group: 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: Transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1978
Polymers37,5991
Non-polymers5997
Water8,557475
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint7 kcal/mol
Surface area14420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.087, 82.910, 89.465
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Transaldolase


Mass: 37598.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: tal, E8M68_10680, WHOO_01512, WHOO_01712 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D3FXY0, transaldolase

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Non-polymers , 5 types, 482 molecules

#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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: PEG8000, Citrate, Sodium phosphate, Sodium chloride, Glycylglycin

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.7293 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 1.05→41.455 Å / Num. obs: 145716 / % possible obs: 99.6 % / Redundancy: 4.5 % / Biso Wilson estimate: 11.22 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.074 / Net I/σ(I): 10.91
Reflection shellResolution: 1.05→1.1 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.04 / Num. unique obs: 18762 / CC1/2: 0.506 / Rrim(I) all: 1.98 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CLM

3clm


Resolution: 1.05→41.455 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1532 7286 5 %
Rwork0.1327 138374 -
obs0.1337 145660 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.33 Å2 / Biso mean: 16.1688 Å2 / Biso min: 7.5 Å2
Refinement stepCycle: final / Resolution: 1.05→41.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2644 0 84 496 3224
Biso mean--24.95 29.59 -
Num. residues----352
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.05-1.06190.35992390.35614526100
1.0619-1.07440.35712420.32754588100
1.0744-1.08750.3292380.30464525100
1.0875-1.10130.31072420.28924587100
1.1013-1.11580.28692410.26984577100
1.1158-1.13110.29262410.2526458099
1.1311-1.14720.2342420.24144589100
1.1472-1.16440.25722400.22634568100
1.1644-1.18260.26062400.21074551100
1.1826-1.2020.21642430.20574612100
1.202-1.22270.26312410.20044569100
1.2227-1.24490.21092410.19174589100
1.2449-1.26890.20422420.17484585100
1.2689-1.29480.17472390.16894572100
1.2948-1.32290.18892430.16114615100
1.3229-1.35370.18872420.14894588100
1.3537-1.38750.16882430.14124615100
1.3875-1.42510.16632410.13584574100
1.4251-1.4670.1522420.12444599100
1.467-1.51440.13932430.10374625100
1.5144-1.56850.12752440.09954620100
1.5685-1.63130.1282430.09344624100
1.6313-1.70550.12762420.0921460399
1.7055-1.79540.11112430.0935460699
1.7954-1.90790.11552450.09724666100
1.9079-2.05520.12312440.09584628100
2.0552-2.26210.11132470.0944688100
2.2621-2.58930.13022460.0981469199
2.5893-3.26210.12282500.10934740100
3.2621-41.4550.14242570.135487498

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