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- PDB-6k31: Crystal structure of pyrophosphate-dependent phosphoenolpyruvate ... -

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Basic information

Entry
Database: PDB / ID: 6k31
TitleCrystal structure of pyrophosphate-dependent phosphoenolpyruvate carboxykinase (PPi-PEPCK)
ComponentsAiPEPCK
KeywordsLYASE / phosphoenolpyruvate carboxykinase
Function / homology:
Function and homology information
Biological speciesActinomyces israelii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsChiba, Y. / Miyakawa, T. / Tanokura, M.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural comparisons of phosphoenolpyruvate carboxykinases reveal the evolutionary trajectories of these phosphodiester energy conversion enzymes.
Authors: Chiba, Y. / Miyakawa, T. / Shimane, Y. / Takai, K. / Tanokura, M. / Nozaki, T.
History
DepositionMay 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Jan 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AiPEPCK
B: AiPEPCK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,1124
Polymers253,9942
Non-polymers1182
Water6,395355
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.439, 160.439, 200.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 11 - 1149 / Label seq-ID: 15 - 1153

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein AiPEPCK


Mass: 126997.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomyces israelii (bacteria) / Production host: Escherichia coli (E. coli) / References: EC: 4.1.1.38
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: HEPES, PEG 400, magnesium chloride

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97887 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97887 Å / Relative weight: 1
ReflectionResolution: 2.6→48.12 Å / Num. obs: 91847 / % possible obs: 100 % / Redundancy: 20.1 % / CC1/2: 0.999 / Rpim(I) all: 0.049 / Net I/σ(I): 19.2
Reflection shellResolution: 2.6→2.64 Å / Num. unique obs: 4505 / CC1/2: 0.837 / Rpim(I) all: 0.389

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→48.12 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.261 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.061 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2414 4595 5 %RANDOM
Rwork0.19576 ---
obs0.19803 87201 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.565 Å2
Baniso -1Baniso -2Baniso -3
1--24.11 Å2-0 Å2-0 Å2
2---24.11 Å2-0 Å2
3---48.21 Å2
Refinement stepCycle: 1 / Resolution: 2.6→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17120 0 2 355 17477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01917517
X-RAY DIFFRACTIONr_bond_other_d0.0060.0216558
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.97423843
X-RAY DIFFRACTIONr_angle_other_deg1.323338035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0145.0092211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50122.834801
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17152650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.77315176
X-RAY DIFFRACTIONr_chiral_restr0.0930.22632
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02120016
X-RAY DIFFRACTIONr_gen_planes_other0.0050.024008
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6155.2388860
X-RAY DIFFRACTIONr_mcbond_other4.6125.2378859
X-RAY DIFFRACTIONr_mcangle_it6.8127.85111061
X-RAY DIFFRACTIONr_mcangle_other6.8137.85211062
X-RAY DIFFRACTIONr_scbond_it4.8635.7018657
X-RAY DIFFRACTIONr_scbond_other4.8635.7018657
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3848.37212784
X-RAY DIFFRACTIONr_long_range_B_refined9.97441.97219138
X-RAY DIFFRACTIONr_long_range_B_other9.97141.9819073
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 129138 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 328 -
Rwork0.27 6360 -
obs--99.75 %

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