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- PDB-7odo: Neisseria gonorrhoeae transaldolase at 0.27 MGy dose -

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Basic information

Entry
Database: PDB / ID: 7odo
TitleNeisseria gonorrhoeae transaldolase at 0.27 MGy dose
ComponentsTransaldolase
KeywordsTRANSFERASE / TRANSALDOLASE / CROSS-LINK / REGULATION
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: 1.4 Å
AuthorsRabe von Pappenheim, F. / Wensien, M. / Tittmann, K.
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Widespread occurrence of covalent lysine-cysteine redox switches in proteins.
Authors: Rabe von Pappenheim, F. / Wensien, M. / Ye, J. / Uranga, J. / Irisarri, I. / de Vries, J. / Funk, L.M. / Mata, R.A. / Tittmann, K.
History
DepositionApr 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 13, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 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
Water7,710428
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)42.140, 82.780, 89.360
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 (bacteria) / Gene: tal, E8M68_10680, WHOO_01512, WHOO_01712 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D3FXY0, 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.: 428 / 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: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG8000, Sodium citrate, Sodium Phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.4→38.11 Å / Num. obs: 61924 / % possible obs: 99.2 % / Redundancy: 13.41 % / Biso Wilson estimate: 21.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.088 / Χ2: 0.854 / Net I/σ(I): 17.5 / Num. measured all: 830401 / Scaling rejects: 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.4413.3221.122.3959737453744840.8511.16498.8
1.44-1.4813.4380.9232.9358537444843560.8930.95997.9
1.48-1.5213.5050.7143.7857532433642600.9290.74198.2
1.52-1.5713.6620.6084.5256533419441380.9480.63198.7
1.57-1.6213.6050.4875.5654855406140320.9680.50599.3
1.62-1.6713.5770.4186.5153399395139330.9750.43499.5
1.67-1.7413.5480.3238.2351050379937680.9830.33699.2
1.74-1.8113.4630.2639.7949004366636400.9890.27399.3
1.81-1.8913.4540.20712.2147277355235140.9930.21598.9
1.89-1.9813.3580.15915.6544669338533440.9950.16698.8
1.98-2.0913.1230.1219.9842045321232040.9970.12599.8
2.09-2.2113.0630.09225.4840115307730710.9980.09599.8
2.21-2.3713.8080.0829.4139546287028640.9990.08399.8
2.37-2.5613.7240.07133.5336739267826770.9990.073100
2.56-2.813.4410.06437.6333669250525050.9990.066100
2.8-3.1313.1120.05341.8529436224522450.9990.056100
3.13-3.6112.9890.04348.8526251202120210.9990.045100
3.61-4.4313.2720.03955.3522549172016990.9990.04198.8
4.43-6.2613.2080.03855.0118121137213720.9990.04100
6.26-38.1111.7150.03453.5693378207970.9990.03597.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZX4

6zx4


Resolution: 1.4→38.11 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1633 3094 5 %
Rwork0.139 58756 -
obs0.1402 61850 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.59 Å2 / Biso mean: 19.9498 Å2 / Biso min: 10.74 Å2
Refinement stepCycle: final / Resolution: 1.4→38.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2645 0 18 434 3097
Biso mean--22.77 29.35 -
Num. residues----352
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.420.27891370.24062597273499
1.42-1.450.23761370.22142607274498
1.45-1.470.2341380.20592618275698
1.47-1.50.20571390.19032622276198
1.5-1.530.20951380.17692622276099
1.53-1.560.2081370.16442610274799
1.56-1.590.16561390.15872647278699
1.59-1.630.16621400.15272648278898
1.63-1.670.17541390.14626342773100
1.67-1.710.15791390.13752651279099
1.71-1.760.17471410.13592673281499
1.76-1.820.16671390.130426632802100
1.82-1.890.1521380.13212625276399
1.89-1.960.1621400.13222647278799
1.96-2.050.15611400.12326632803100
2.05-2.160.13271430.119927022845100
2.16-2.290.14641400.117726942834100
2.29-2.470.15051440.121927332877100
2.47-2.720.14341420.127626942836100
2.72-3.110.1531450.133427492894100
3.11-3.920.16291460.13082763290999
3.92-38.110.16621530.149328943047100

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