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- PDB-6zwj: Neisseria gonorrhoeae transaldolase at 1.35 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 6zwj
TitleNeisseria gonorrhoeae transaldolase 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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CITRIC 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. / 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
Revision 1.5Oct 16, 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

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Assembly

Deposited unit
A: Transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8993
Polymers37,6151
Non-polymers2842
Water8,161453
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint2 kcal/mol
Surface area14420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.205, 82.955, 90.502
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Transaldolase


Mass: 37614.688 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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: PEG8000, Citrate, Sodium Phosphate, Sodium Chloride, Glycylglycine

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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: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 1.35→39.73 Å / Num. obs: 67040 / % possible obs: 95 % / Redundancy: 3.5 % / Biso Wilson estimate: 14.3 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.08 / Net I/σ(I): 10.3
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6987 / CC1/2: 0.5 / Rrim(I) all: 1.21 / % possible all: 97.2

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Processing

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

3clm


Resolution: 1.35→39.73 Å / SU ML: 0.1607 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.6332 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1825 3351 5 %
Rwork0.1463 63680 -
obs0.148 67031 94.98 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.34 Å2
Refinement stepCycle: LAST / Resolution: 1.35→39.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2645 0 16 453 3114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513212
X-RAY DIFFRACTIONf_angle_d0.86374413
X-RAY DIFFRACTIONf_chiral_restr0.0624496
X-RAY DIFFRACTIONf_plane_restr0.0048601
X-RAY DIFFRACTIONf_dihedral_angle_d16.54651241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.35671410.32752689X-RAY DIFFRACTION97.28
1.37-1.390.33971400.30522649X-RAY DIFFRACTION97.01
1.39-1.410.33381420.27782700X-RAY DIFFRACTION96.93
1.41-1.430.3291380.27252623X-RAY DIFFRACTION96.5
1.43-1.460.24671390.24432639X-RAY DIFFRACTION94.55
1.46-1.490.23621380.21762627X-RAY DIFFRACTION96.27
1.49-1.510.2261410.21132682X-RAY DIFFRACTION96.51
1.51-1.550.26361420.19732689X-RAY DIFFRACTION96.99
1.55-1.580.21881400.18232667X-RAY DIFFRACTION96.89
1.58-1.620.19671420.16452695X-RAY DIFFRACTION96.73
1.62-1.660.20351400.15812661X-RAY DIFFRACTION96.65
1.66-1.70.22271400.14992666X-RAY DIFFRACTION96.56
1.7-1.750.18521420.13712689X-RAY DIFFRACTION96.23
1.75-1.810.21121390.13982655X-RAY DIFFRACTION95.91
1.81-1.870.17591390.13872649X-RAY DIFFRACTION95.45
1.87-1.950.19441400.13722667X-RAY DIFFRACTION95.44
1.95-2.040.1941400.13422656X-RAY DIFFRACTION94.94
2.04-2.140.17551390.11992626X-RAY DIFFRACTION94.11
2.14-2.280.13421380.11462638X-RAY DIFFRACTION93.5
2.28-2.450.16191380.11382616X-RAY DIFFRACTION92.82
2.45-2.70.13661380.11652631X-RAY DIFFRACTION93.23
2.7-3.090.16441390.1242630X-RAY DIFFRACTION92.27
3.09-3.890.13761380.12332615X-RAY DIFFRACTION90.95
3.89-39.730.17551380.15252621X-RAY DIFFRACTION86.87

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