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- PDB-6zwh: Neisseria gonorrhoeae transaldolase at 1.5 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 6zwh
TitleNeisseria gonorrhoeae transaldolase at 1.5 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
ACETATE ION / Transaldolase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.1Apr 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 1.6Oct 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

Downloads & links

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Assembly

Deposited unit
A: Transaldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8284
Polymers37,6151
Non-polymers2133
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint4 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.255, 82.980, 90.337
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 41.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: PEG8000, Ammonium acetate, Sodium chloride, Glycylglycine, DTT

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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: 1.001 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: 1.001 Å / Relative weight: 1
ReflectionResolution: 1.5→41.49 Å / Num. obs: 51609 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 16.18 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.141 / Net I/σ(I): 11.33
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 1.3 % / Num. unique obs: 8931 / CC1/2: 0.785 / Rrim(I) all: 1.609 / % possible all: 99.8

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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: 1.5→41.49 Å / SU ML: 0.1602 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.2537 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1805 2581 5 %
Rwork0.1501 49026 -
obs0.1517 51607 99.88 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.55 Å2
Refinement stepCycle: LAST / Resolution: 1.5→41.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2645 0 14 389 3048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00723182
X-RAY DIFFRACTIONf_angle_d0.99744366
X-RAY DIFFRACTIONf_chiral_restr0.0696492
X-RAY DIFFRACTIONf_plane_restr0.0059593
X-RAY DIFFRACTIONf_dihedral_angle_d15.23611218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.33671400.27132655X-RAY DIFFRACTION99.86
1.53-1.560.25561420.24782693X-RAY DIFFRACTION99.75
1.56-1.590.27171400.22972672X-RAY DIFFRACTION99.89
1.59-1.630.27071420.20672700X-RAY DIFFRACTION99.89
1.63-1.670.23181420.19532690X-RAY DIFFRACTION99.96
1.67-1.720.21831410.18542677X-RAY DIFFRACTION99.82
1.72-1.770.21691430.17242713X-RAY DIFFRACTION99.72
1.77-1.820.22871420.16862699X-RAY DIFFRACTION99.79
1.82-1.890.21461410.16222679X-RAY DIFFRACTION99.82
1.89-1.970.20791420.14612707X-RAY DIFFRACTION99.86
1.97-2.060.17441430.1372718X-RAY DIFFRACTION99.93
2.06-2.160.1651440.12922730X-RAY DIFFRACTION99.97
2.16-2.30.15111420.12442703X-RAY DIFFRACTION99.93
2.3-2.480.15551450.12352751X-RAY DIFFRACTION99.93
2.48-2.730.15181440.13252733X-RAY DIFFRACTION99.9
2.73-3.120.14881450.13522767X-RAY DIFFRACTION99.79
3.12-3.930.15171480.13252804X-RAY DIFFRACTION100
3.93-41.490.18471550.15672935X-RAY DIFFRACTION99.97

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