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- PDB-7bbx: Neisseria gonorrhoeae transaldolase, variant K8A -

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Basic information

Entry
Database: PDB / ID: 7bbx
TitleNeisseria gonorrhoeae transaldolase, variant K8A
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: 0.85 Å
AuthorsRabe von Pappenheim, F. / Wensien, M. / Funk, L.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
DepositionDec 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1May 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 1.2May 19, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 2, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 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

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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)37,7953
Polymers37,5411
Non-polymers2542
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint7 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.420, 82.890, 90.250
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: 37540.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria)
Gene: tal, E8M68_10680, F9Z35_1423, TUM15744_11190, TUM15745_13730, TUM15746_13410, TUM15747_14120, TUM15749_15370, TUM15750_11410, TUM15751_15520, TUM15759_11670, TUM15760_12360, TUM15761_09930, ...Gene: tal, E8M68_10680, F9Z35_1423, TUM15744_11190, TUM15745_13730, TUM15746_13410, TUM15747_14120, TUM15749_15370, TUM15750_11410, TUM15751_15520, TUM15759_11670, TUM15760_12360, TUM15761_09930, TUM15764_14310, TUM15765_13050, TUM15766_06460, TUM15768_14740, TUM15770_09320, TUM15771_08190, TUM15772_10900, TUM15774_13280, TUM15776_12130, TUM15780_14920, TUM15781_07470, TUM15782_07520, TUM15784_12210, TUM15785_13660, TUM15786_07850, TUM15787_13260, TUM15789_13310, TUM15790_01750, TUM15791_13450, TUM15792_03840, TUM15793_14160, TUM15796_12040, TUM15797_11040, TUM15798_01870, WHOO_01512, WHOO_01712
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D3FXY0, transaldolase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 41.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: PEG8000, Sodium citrate, Sodium phosphate, Sodium chloride

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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: 0.6888 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 0.85→38.391 Å / Num. obs: 276361 / % possible obs: 99.2 % / Redundancy: 12.796 % / Biso Wilson estimate: 11.227 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.05 / Χ2: 0.881 / Net I/σ(I): 22.75
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
0.85-0.879.9792.2271.11177310.462.34795.2
0.87-0.910.491.6521.54240610.6211.73796.5
0.9-0.9512.4551.0112.71346280.8431.05499.3
0.95-113.4940.5695.13281900.9540.59199.9
1-1.113.5130.25510.87422550.9910.26599.9
1.1-1.213.4120.12120.94294300.9970.12699.9
1.2-1.513.5420.07233.44483680.9990.075100
1.5-213.410.03857.292959010.04100
2-313.1250.02973.141541610.03100
3-412.3250.03474.7438270.9980.03699.9
4-510.5280.0386913820.9960.04199.2
5-109.9690.03466.613060.9960.03697.8
10-504.6950.03642.91770.9950.04281.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CLM

3clm


Resolution: 0.85→38.39 Å / SU ML: 0.0695 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.2657
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1191 8288 3 %
Rwork0.1078 267995 -
obs0.1081 276283 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.02 Å2
Refinement stepCycle: LAST / Resolution: 0.85→38.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2638 0 17 524 3179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793293
X-RAY DIFFRACTIONf_angle_d1.14174546
X-RAY DIFFRACTIONf_chiral_restr0.0801513
X-RAY DIFFRACTIONf_plane_restr0.0078621
X-RAY DIFFRACTIONf_dihedral_angle_d16.69711289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.85-0.860.31152620.30518437X-RAY DIFFRACTION94.64
0.86-0.870.30112620.2868480X-RAY DIFFRACTION95.3
0.87-0.880.26862650.26288566X-RAY DIFFRACTION95.81
0.88-0.890.23672680.24788674X-RAY DIFFRACTION96.64
0.89-0.90.2412690.22578672X-RAY DIFFRACTION97.3
0.9-0.920.21462700.2078784X-RAY DIFFRACTION98.38
0.92-0.930.20762760.18848914X-RAY DIFFRACTION99.8
0.93-0.940.16642770.16938954X-RAY DIFFRACTION99.87
0.94-0.960.17182750.1578886X-RAY DIFFRACTION99.76
0.96-0.970.15672750.13698939X-RAY DIFFRACTION99.85
0.97-0.990.14492780.1268959X-RAY DIFFRACTION99.91
0.99-1.010.11762760.11438949X-RAY DIFFRACTION99.81
1.01-1.030.1372760.10958923X-RAY DIFFRACTION99.98
1.03-1.050.10722770.09728933X-RAY DIFFRACTION99.76
1.05-1.070.09682770.08688957X-RAY DIFFRACTION99.87
1.07-1.10.09012770.07798955X-RAY DIFFRACTION99.83
1.1-1.120.09062770.07468980X-RAY DIFFRACTION99.97
1.12-1.150.0852770.07058955X-RAY DIFFRACTION99.83
1.15-1.190.08512790.07099015X-RAY DIFFRACTION99.97
1.19-1.230.08172780.07318973X-RAY DIFFRACTION99.95
1.23-1.270.09162780.0768977X-RAY DIFFRACTION99.92
1.27-1.320.09162790.07719024X-RAY DIFFRACTION100
1.32-1.380.08322790.07819041X-RAY DIFFRACTION99.99
1.38-1.450.08352790.07759020X-RAY DIFFRACTION100
1.45-1.540.09772800.07879029X-RAY DIFFRACTION99.92
1.54-1.660.09952800.0859076X-RAY DIFFRACTION99.99
1.66-1.830.10472820.09519116X-RAY DIFFRACTION100
1.83-2.10.10172830.09979139X-RAY DIFFRACTION99.98
2.1-2.640.11342850.1059230X-RAY DIFFRACTION99.97
2.64-38.390.15292920.13699438X-RAY DIFFRACTION99.04

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