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- PDB-7odp: Neisseria gonorrhoeae transaldolase at 2.7 MGy dose -

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Basic information

Entry
Database: PDB / ID: 7odp
TitleNeisseria gonorrhoeae transaldolase at 2.7 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 1.4Oct 23, 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 area14420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.170, 82.820, 89.400
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, sitting 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→38.14 Å / Num. obs: 61991 / % possible obs: 99.1 % / Redundancy: 13.429 % / Biso Wilson estimate: 23.061 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.096 / Χ2: 0.828 / Net I/σ(I): 15.69 / Num. measured all: 832453 / Scaling rejects: 72
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
1.4-1.4413.3331.5531.7159773454144830.7391.61398.7
1.44-1.4813.4751.2812.0858468443843390.811.33197.8
1.48-1.5213.5210.9752.7857855436042790.8691.01398.1
1.52-1.5713.6590.8083.4256495419741360.9040.83998.5
1.57-1.6213.6280.6494.2555194407540500.9450.67499.4
1.62-1.6713.6030.5375.1153514395839340.9570.55799.4
1.67-1.7413.5510.4216.4751141380737740.9740.43799.1
1.74-1.8113.4890.337.9549114366836410.9850.34299.3
1.81-1.8913.4760.25810.0847329355335120.990.26898.8
1.89-1.9813.3420.19213.1644681338933490.9940.298.8
1.98-2.0913.1760.14117.242439323132210.9960.14799.7
2.09-2.2113.0750.10522.4940126307530690.9970.1199.8
2.21-2.3713.830.09126.4339720287928720.9980.09599.8
2.37-2.5613.7270.07830.4736775268026790.9990.081100
2.56-2.813.4940.06834.8233910251325130.9990.071100
2.8-3.1313.1510.05739.3429484224222420.9990.06100
3.13-3.6112.9890.04546.7126342202820280.9990.047100
3.61-4.4313.2840.0453.7922583172117000.9990.04198.8
4.43-6.2613.2130.0453.7318128137213720.9990.042100
6.26-38.1411.7570.03552.6793828237980.9990.03797

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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: 6ZX4

6zx4


Resolution: 1.4→38.14 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1664 3094 5 %
Rwork0.1418 58821 -
obs0.143 61915 99.11 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.54 Å2 / Biso mean: 21.6421 Å2 / Biso min: 12.22 Å2
Refinement stepCycle: final / Resolution: 1.4→38.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2645 0 18 434 3097
Biso mean--26.12 31.73 -
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 (%)
1.4-1.420.31531330.28162584271798
1.42-1.450.32781370.26292609274698
1.45-1.470.24111380.242613275198
1.47-1.50.24831390.21672624276398
1.5-1.530.21811370.20362624276199
1.53-1.560.22651400.18832641278199
1.56-1.590.18971380.1782623276199
1.59-1.630.17911410.16832661280298
1.63-1.670.19151380.15926372775100
1.67-1.710.19391390.14912643278299
1.71-1.760.17961420.14422692283499
1.76-1.820.17011400.137126662806100
1.82-1.890.161380.13462628276699
1.89-1.960.15671380.12972645278399
1.96-2.050.15751420.123126712813100
2.05-2.160.14181420.11627082850100
2.16-2.290.14371410.115227032844100
2.29-2.470.14911440.12127342878100
2.47-2.720.14241430.123927032846100
2.72-3.110.16021450.135427482893100
3.11-3.920.15671460.12862766291299
3.92-38.140.15881530.14812898305199
Refinement TLS params.Method: refined / Origin x: -13.3532 Å / Origin y: 17.1135 Å / Origin z: -17.597 Å
111213212223313233
T0.1283 Å20.0021 Å2-0.0026 Å2-0.1457 Å2-0.0015 Å2--0.1726 Å2
L0.3338 °20.0618 °2-0.0049 °2-0.7808 °20.0818 °2--0.3775 °2
S-0.0031 Å °0.0138 Å °-0.0059 Å °-0.0093 Å °-0.0045 Å °-0.016 Å °-0.0105 Å °-0.0013 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 351
2X-RAY DIFFRACTION1allA401
3X-RAY DIFFRACTION1allS1 - 500

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