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- PDB-6at4: E. coli phosphoenolpyruvate carboxykinase bound to thiosulfate -

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Basic information

Entry
Database: PDB / ID: 6at4
TitleE. coli phosphoenolpyruvate carboxykinase bound to thiosulfate
ComponentsPhosphoenolpyruvate carboxykinase (ATP)
KeywordsLYASE / Nonnative ligand
Function / homology
Function and homology information


phosphoenolpyruvate carboxykinase (ATP) / phosphoenolpyruvate carboxykinase (ATP) activity / gluconeogenesis / calcium ion binding / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Phosphoenolpyruvate carboxykinase, ATP-utilising / Phosphoenolpyruvate carboxykinase (ATP), conserved site / Phosphoenolpyruvate carboxykinase / Phosphoenolpyruvate carboxykinase (ATP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate carboxykinase, C-terminal ...Phosphoenolpyruvate carboxykinase, ATP-utilising / Phosphoenolpyruvate carboxykinase (ATP), conserved site / Phosphoenolpyruvate carboxykinase / Phosphoenolpyruvate carboxykinase (ATP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate carboxykinase, C-terminal / Phosphoenolpyruvate carboxykinase, N-terminal / Phosphoenolpyruvate Carboxykinase; domain 3 / Beta Complex / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
THIOSULFATE / Phosphoenolpyruvate carboxykinase (ATP)
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.332 Å
AuthorsTang, H.Y.H. / Shin, D.S. / Tainer, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)ARPA-E REMOTE United States
Department of Energy (DOE, United States)Integrated Diffraction Analysis Technologies United States
CitationJournal: Biochemistry / Year: 2018
Title: Structural Control of Nonnative Ligand Binding in Engineered Mutants of Phosphoenolpyruvate Carboxykinase.
Authors: Tang, H.Y.H. / Shin, D.S. / Hura, G.L. / Yang, Y. / Hu, X. / Lightstone, F.C. / McGee, M.D. / Padgett, H.S. / Yannone, S.M. / Tainer, J.A.
History
DepositionAug 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / 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.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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

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Assembly

Deposited unit
A: Phosphoenolpyruvate carboxykinase (ATP)
B: Phosphoenolpyruvate carboxykinase (ATP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,6377
Polymers121,0762
Non-polymers5615
Water16,682926
1
A: Phosphoenolpyruvate carboxykinase (ATP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8744
Polymers60,5381
Non-polymers3363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoenolpyruvate carboxykinase (ATP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7623
Polymers60,5381
Non-polymers2242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.720, 103.614, 119.156
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphoenolpyruvate carboxykinase (ATP) / PEPCK


Mass: 60538.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: pckA, pck, b3403, JW3366 / Production host: Escherichia coli (E. coli)
References: UniProt: P22259, phosphoenolpyruvate carboxykinase (ATP)
#2: Chemical
ChemComp-THJ / THIOSULFATE


Mass: 112.128 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: O3S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 926 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.4 M sodium chloride, 0.1 M Bis-Tris pH 5.5, 0.1 M sodium thiosulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.332→119.156 Å / Num. obs: 470294 / % possible obs: 90.7 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Net I/σ(I): 13.78
Reflection shellResolution: 1.332→1.4 Å / Redundancy: 2.21 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 1 / Num. unique obs: 48895 / CC1/2: 0.436 / % possible all: 58.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OLQ

2olq


Resolution: 1.332→78.188 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.39
RfactorNum. reflection% reflection
Rfree0.1514 3850 0.82 %
Rwork0.135 --
obs0.1352 470167 90.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.332→78.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8216 0 25 926 9167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058494
X-RAY DIFFRACTIONf_angle_d0.80311568
X-RAY DIFFRACTIONf_dihedral_angle_d16.1433030
X-RAY DIFFRACTIONf_chiral_restr0.0711283
X-RAY DIFFRACTIONf_plane_restr0.0051506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3318-1.34860.3463670.35228554X-RAY DIFFRACTION45
1.3486-1.36640.3797850.327310456X-RAY DIFFRACTION55
1.3664-1.38510.3028920.308611671X-RAY DIFFRACTION61
1.3851-1.40490.32591080.28512783X-RAY DIFFRACTION67
1.4049-1.42580.27631160.251714064X-RAY DIFFRACTION74
1.4258-1.44810.28321260.230415542X-RAY DIFFRACTION82
1.4481-1.47190.25541450.202117242X-RAY DIFFRACTION91
1.4719-1.49720.21631530.175518360X-RAY DIFFRACTION96
1.4972-1.52450.21171550.154518672X-RAY DIFFRACTION98
1.5245-1.55380.16781540.14818664X-RAY DIFFRACTION98
1.5538-1.58550.18281540.139418730X-RAY DIFFRACTION98
1.5855-1.620.15471510.139618711X-RAY DIFFRACTION99
1.62-1.65770.17721530.133318846X-RAY DIFFRACTION98
1.6577-1.69910.18771550.127618787X-RAY DIFFRACTION99
1.6991-1.74510.14281590.12118745X-RAY DIFFRACTION99
1.7451-1.79640.14921590.115318877X-RAY DIFFRACTION99
1.7964-1.85440.1271580.112518837X-RAY DIFFRACTION99
1.8544-1.92070.14891550.105618835X-RAY DIFFRACTION99
1.9207-1.99760.13251550.105918829X-RAY DIFFRACTION99
1.9976-2.08850.14031540.104918856X-RAY DIFFRACTION99
2.0885-2.19870.11531540.104118908X-RAY DIFFRACTION99
2.1987-2.33640.11341590.108718857X-RAY DIFFRACTION99
2.3364-2.51680.13731550.114718887X-RAY DIFFRACTION99
2.5168-2.77010.12751580.122618959X-RAY DIFFRACTION99
2.7701-3.1710.12661580.126718896X-RAY DIFFRACTION99
3.171-3.99510.14441540.129318840X-RAY DIFFRACTION99
3.9951-78.32270.16381580.165218909X-RAY DIFFRACTION99

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