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- PDB-6zx4: Neisseria gonorrhoeae transaldolase -

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Basic information

Entry
Database: PDB / ID: 6zx4
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-type TIM barrel
Similarity search - Domain/homology
CITRIC ACID / Transaldolase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.96 Å
AuthorsSautner, V. / Rabe von Pappenheim, F. / Wensien, M. / 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 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: entity_src_gen / struct_conn ...entity_src_gen / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2May 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 1.3May 19, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Jun 2, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Jan 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 1.6Nov 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9914
Polymers37,6151
Non-polymers3763
Water8,989499
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint2 kcal/mol
Surface area14370 Å2
Unit cell
Length a, b, c (Å)42.260, 82.790, 90.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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 (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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.1 Å3/Da / Density % sol: 41.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: PEG 8000, sodium chloride, citric acid, sodium phosphate, 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 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 0.96→30.87 Å / Num. obs: 190503 / % possible obs: 98.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 10.47 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.04 / Net I/σ(I): 16.4
Reflection shellResolution: 0.96→0.99 Å / Redundancy: 3.27 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 54087 / CC1/2: 0.53 / Rrim(I) all: 1.27 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CLM

3clm


Resolution: 0.96→30.87 Å / SU ML: 0.0986 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.8055 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1362 9517 5 %
Rwork0.1171 180860 -
obs0.1181 190377 98.43 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.07 Å2
Refinement stepCycle: LAST / Resolution: 0.96→30.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2645 0 22 499 3166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00883361
X-RAY DIFFRACTIONf_angle_d1.18774625
X-RAY DIFFRACTIONf_chiral_restr0.0756513
X-RAY DIFFRACTIONf_plane_restr0.0072635
X-RAY DIFFRACTIONf_dihedral_angle_d17.49931307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.96-0.970.35343110.33445887X-RAY DIFFRACTION97.59
0.97-0.980.31573140.32375978X-RAY DIFFRACTION97.64
0.98-0.990.30453090.30095862X-RAY DIFFRACTION97.83
0.99-1.010.29283120.28225943X-RAY DIFFRACTION97.23
1.01-1.020.26613130.25965939X-RAY DIFFRACTION97.98
1.02-1.030.26163120.23875937X-RAY DIFFRACTION97.98
1.03-1.050.23343160.22026025X-RAY DIFFRACTION98.94
1.05-1.060.21393130.2045972X-RAY DIFFRACTION98.65
1.06-1.080.22793180.18756032X-RAY DIFFRACTION98.85
1.08-1.10.1873150.17045976X-RAY DIFFRACTION99.13
1.1-1.120.20613170.15576026X-RAY DIFFRACTION98.77
1.12-1.140.16013160.14386005X-RAY DIFFRACTION98.72
1.14-1.160.15583170.13436026X-RAY DIFFRACTION98.88
1.16-1.180.1483160.12255995X-RAY DIFFRACTION98.72
1.18-1.210.13123190.12016045X-RAY DIFFRACTION98.77
1.21-1.240.14893160.12166010X-RAY DIFFRACTION98.87
1.24-1.270.14793160.11496002X-RAY DIFFRACTION98.67
1.27-1.30.13973140.10855980X-RAY DIFFRACTION98.07
1.3-1.340.12373170.10416021X-RAY DIFFRACTION98.55
1.34-1.380.12483170.10366031X-RAY DIFFRACTION98.68
1.38-1.430.123190.09746074X-RAY DIFFRACTION99.24
1.43-1.490.11433210.09196090X-RAY DIFFRACTION98.94
1.49-1.560.11793210.08456098X-RAY DIFFRACTION99.15
1.56-1.640.10583190.08576060X-RAY DIFFRACTION98.79
1.64-1.740.10533210.08656105X-RAY DIFFRACTION99.18
1.74-1.880.10993220.08936125X-RAY DIFFRACTION98.85
1.88-2.070.10033200.08616079X-RAY DIFFRACTION98.22
2.07-2.370.10053200.0876090X-RAY DIFFRACTION97.59
2.37-2.980.11333270.09876206X-RAY DIFFRACTION98.98
2.98-30.870.14993290.1316241X-RAY DIFFRACTION95.59

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