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- PDB-6at2: E. coli phosphoenolpyruvate carboxykinase G209N mutant bound to t... -

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Basic information

Entry
Database: PDB / ID: 6at2
TitleE. coli phosphoenolpyruvate carboxykinase G209N mutant 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
ADENOSINE-5'-TRIPHOSPHATE / : / THIOSULFATE / Phosphoenolpyruvate carboxykinase (ATP)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.444 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)61,4166
Polymers60,5951
Non-polymers8215
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.171, 94.360, 46.559
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-985-

HOH

21A-1007-

HOH

31A-1106-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoenolpyruvate carboxykinase (ATP) / PEPCK


Mass: 60595.121 Da / Num. of mol.: 1 / Mutation: G209N
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 , 6 types, 347 molecules

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


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


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-THJ / THIOSULFATE


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


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 24% 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: 12.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.444→47.18 Å / Num. obs: 182988 / % possible obs: 96.3 % / Redundancy: 3.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.48
Reflection shellResolution: 1.444→1.52 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.371 / Mean I/σ(I) obs: 1.04 / Num. unique obs: 28555 / CC1/2: 0.53 / % possible all: 92.8

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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: 1.444→47.18 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.89
RfactorNum. reflection% reflection
Rfree0.1911 3952 2.16 %
Rwork0.1712 --
obs0.1716 182893 96.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.444→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4065 0 46 342 4453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084229
X-RAY DIFFRACTIONf_angle_d1.0355776
X-RAY DIFFRACTIONf_dihedral_angle_d16.9441486
X-RAY DIFFRACTIONf_chiral_restr0.077646
X-RAY DIFFRACTIONf_plane_restr0.007745
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4442-1.46180.3491250.3825728X-RAY DIFFRACTION85
1.4618-1.48030.33571410.33866286X-RAY DIFFRACTION95
1.4803-1.49980.29831360.32246260X-RAY DIFFRACTION94
1.4998-1.52040.33651380.31416226X-RAY DIFFRACTION95
1.5204-1.54210.28541400.30096299X-RAY DIFFRACTION95
1.5421-1.56510.30591370.29156332X-RAY DIFFRACTION95
1.5651-1.58960.30041420.27486281X-RAY DIFFRACTION95
1.5896-1.61560.28541380.25826378X-RAY DIFFRACTION96
1.6156-1.64350.271380.24866288X-RAY DIFFRACTION95
1.6435-1.67340.2571410.22516372X-RAY DIFFRACTION96
1.6734-1.70560.23461400.21656346X-RAY DIFFRACTION96
1.7056-1.74040.28461440.21296417X-RAY DIFFRACTION96
1.7404-1.77820.25031410.19966416X-RAY DIFFRACTION96
1.7782-1.81960.21971410.19436463X-RAY DIFFRACTION97
1.8196-1.86510.22441400.17866354X-RAY DIFFRACTION96
1.8651-1.91550.20021440.16776430X-RAY DIFFRACTION98
1.9155-1.97190.18311400.1666430X-RAY DIFFRACTION97
1.9719-2.03550.16411440.16166446X-RAY DIFFRACTION97
2.0355-2.10830.19671450.15336497X-RAY DIFFRACTION97
2.1083-2.19270.14821450.14486499X-RAY DIFFRACTION98
2.1927-2.29250.19651400.14636438X-RAY DIFFRACTION98
2.2925-2.41340.15911420.14496496X-RAY DIFFRACTION98
2.4134-2.56460.16731450.14856532X-RAY DIFFRACTION98
2.5646-2.76260.16281420.15186508X-RAY DIFFRACTION98
2.7626-3.04050.16141440.15556511X-RAY DIFFRACTION98
3.0405-3.48040.18221470.14936529X-RAY DIFFRACTION98
3.4804-4.38440.12251460.13266577X-RAY DIFFRACTION99
4.3844-47.20520.19211460.15046602X-RAY DIFFRACTION99

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