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- PDB-6asm: E. coli phosphoenolpyruvate carboxykinase G209S K212C mutant boun... -

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Basic information

Entry
Database: PDB / ID: 6asm
TitleE. coli phosphoenolpyruvate carboxykinase G209S K212C mutant bound to thiosulfate
ComponentsPhosphoenolpyruvate carboxykinase (ATP)Phosphoenolpyruvate 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
ADENOSINE-5'-TRIPHOSPHATE / : / THIOSULFATE / XENON / Phosphoenolpyruvate carboxykinase (ATP)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 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 25, 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 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoenolpyruvate carboxykinase (ATP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5817
Polymers60,5421
Non-polymers1,0396
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.706, 94.080, 46.596
Angle α, β, γ (deg.)90.00, 96.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-990-

HOH

21A-1067-

HOH

31A-1182-

HOH

41A-1188-

HOH

51A-1243-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoenolpyruvate carboxykinase (ATP) / Phosphoenolpyruvate carboxykinase (ATP) / PEPCK


Mass: 60542.059 Da / Num. of mol.: 1 / Mutation: G209S, K212C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: pckA, pck, b3403, JW3366 / Production host: Escherichia coli (E. coli)
References: UniProt: P22259, phosphoenolpyruvate carboxykinase (ATP)

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Non-polymers , 7 types, 463 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-XE / XENON / Xenon


Mass: 131.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Xe
#6: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#7: Chemical ChemComp-THJ / THIOSULFATE / Thiosulfate


Mass: 112.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O3S2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.4 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.008 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.55→47.04 Å / Num. obs: 145769 / % possible obs: 94.7 % / Redundancy: 2.02 % / Net I/σ(I): 9.45

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.55→47.04 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7
RfactorNum. reflection% reflection
Rfree0.1881 3831 2.63 %
Rwork0.1698 --
obs0.1702 145677 94.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4025 0 53 457 4535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134221
X-RAY DIFFRACTIONf_angle_d1.0895746
X-RAY DIFFRACTIONf_dihedral_angle_d13.6622461
X-RAY DIFFRACTIONf_chiral_restr0.06639
X-RAY DIFFRACTIONf_plane_restr0.007741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5503-1.56990.3684910.37843284X-RAY DIFFRACTION60
1.5699-1.59060.36381090.35644067X-RAY DIFFRACTION74
1.5906-1.61240.35241180.34254430X-RAY DIFFRACTION79
1.6124-1.63540.37091190.32364679X-RAY DIFFRACTION85
1.6354-1.65980.2471430.30355127X-RAY DIFFRACTION92
1.6598-1.68580.28781480.29285257X-RAY DIFFRACTION95
1.6858-1.71340.26741500.27865406X-RAY DIFFRACTION97
1.7134-1.74290.33871510.27115530X-RAY DIFFRACTION99
1.7429-1.77460.28621490.25265460X-RAY DIFFRACTION99
1.7746-1.80880.26861480.24065484X-RAY DIFFRACTION99
1.8088-1.84570.20081500.21925548X-RAY DIFFRACTION99
1.8457-1.88580.2481480.20525452X-RAY DIFFRACTION99
1.8858-1.92970.19181480.19355540X-RAY DIFFRACTION99
1.9297-1.9780.16781460.17915504X-RAY DIFFRACTION99
1.978-2.03140.1831500.17225497X-RAY DIFFRACTION99
2.0314-2.09120.20361500.16115500X-RAY DIFFRACTION99
2.0912-2.15870.16991440.15325495X-RAY DIFFRACTION99
2.1587-2.23590.19091480.14515550X-RAY DIFFRACTION99
2.2359-2.32540.17461510.14285428X-RAY DIFFRACTION99
2.3254-2.43120.1841470.14225494X-RAY DIFFRACTION99
2.4312-2.55940.17621490.14175492X-RAY DIFFRACTION99
2.5594-2.71970.20431470.14035485X-RAY DIFFRACTION99
2.7197-2.92970.14351470.13855441X-RAY DIFFRACTION98
2.9297-3.22440.14051430.13615440X-RAY DIFFRACTION98
3.2244-3.69090.14981470.13375401X-RAY DIFFRACTION98
3.6909-4.64940.13381450.12885417X-RAY DIFFRACTION97
4.6494-47.06160.19091450.17675438X-RAY DIFFRACTION98

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