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- PDB-7b0l: Neisseria gonorrhoeae transaldolase, low-dose inhouse -

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Basic information

Entry
Database: PDB / ID: 7b0l
TitleNeisseria gonorrhoeae transaldolase, low-dose inhouse
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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsRabe 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
DepositionNov 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_validate_close_contact ...entity_src_gen / pdbx_validate_close_contact / 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)37,8072
Polymers37,6151
Non-polymers1921
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint2 kcal/mol
Surface area14400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.150, 82.910, 89.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, Sodium citrate, Sodium Phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.65→44.77 Å / Num. obs: 37104 / % possible obs: 96.2 % / Redundancy: 7.266 % / Biso Wilson estimate: 21.546 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.092 / Χ2: 0.915 / Net I/σ(I): 15.33
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.72.0480.6471.3725340.6220.81578.2
1.7-1.753.1490.5862.1327290.7080.69694.2
1.75-1.84.6740.5422.9524720.8720.60896
1.8-1.96.3750.4314.3742210.9430.46896.1
1.9-26.7390.36.4434410.9690.32496.8
2-37.8290.12215.24150360.9950.1398.8
3-510.7690.0540.2351400.9990.053100
5-2013.880.04349.67150510.045100
20-44.777.4620.03829.472610.0483.9

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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: 3CLM

3clm


Resolution: 1.65→38.14 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1909 1855 5 %
Rwork0.1508 35244 -
obs0.1528 37099 96.21 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.86 Å2 / Biso mean: 15.4932 Å2 / Biso min: 6.26 Å2
Refinement stepCycle: final / Resolution: 1.65→38.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2645 0 13 461 3119
Biso mean--16.11 27.76 -
Num. residues----352
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.690.35691130.29612132224577
1.69-1.740.27921360.21932597273394
1.74-1.80.23141400.19032650279096
1.8-1.870.2171410.17072676281796
1.87-1.940.19981420.15332698284096
1.94-2.030.18221410.14772682282397
2.03-2.130.18091430.13552720286398
2.13-2.270.16131460.13642773291999
2.27-2.440.19541470.14262786293399
2.44-2.690.19941470.15052802294999
2.69-3.080.22441500.150328392989100
3.08-3.880.15411510.132628843035100
3.88-38.140.16681580.14230053163100
Refinement TLS params.Method: refined / Origin x: -13.3152 Å / Origin y: 17.0347 Å / Origin z: -17.6497 Å
111213212223313233
T0.0612 Å20.0024 Å2-0.0052 Å2-0.0851 Å20.0001 Å2--0.0663 Å2
L0.3505 °20.0602 °2-0.0094 °2-0.8597 °20.0834 °2--0.4193 °2
S0.0032 Å °0.0164 Å °-0.0069 Å °-0.004 Å °-0.008 Å °-0.0167 Å °-0.0071 Å °0.0016 Å °0.0034 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 351
2X-RAY DIFFRACTION1allA401
3X-RAY DIFFRACTION1allS1 - 474

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