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- PDB-5vyw: Crystal structure of Lactococcus lactis pyruvate carboxylase -

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Basic information

Entry
Database: PDB / ID: 5vyw
TitleCrystal structure of Lactococcus lactis pyruvate carboxylase
ComponentsPyruvate carboxylase
KeywordsLIGASE / biotin-dependent carboxylase TIM-barrel cyclic-di-AMP
Function / homology
Function and homology information


Rossmann fold - #20 / ATP-grasp fold, A domain / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsChoi, P.H. / Tong, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI116669 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural and functional studies of pyruvate carboxylase regulation by cyclic di-AMP in lactic acid bacteria.
Authors: Choi, P.H. / Vu, T.M.N. / Pham, H.T. / Woodward, J.J. / Turner, M.S. / Tong, L.
History
DepositionMay 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Pyruvate carboxylase
B: Pyruvate carboxylase
C: Pyruvate carboxylase
D: Pyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)509,6909
Polymers509,2264
Non-polymers4645
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18430 Å2
ΔGint-35 kcal/mol
Surface area145550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.664, 139.664, 610.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 1052
2010B1 - 1052
1020A1 - 1052
2020C1 - 1052
1030A1 - 1053
2030D1 - 1053
1040B1 - 1052
2040C1 - 1052
1050B1 - 1052
2050D1 - 1052
1060C1 - 1052
2060D1 - 1052

NCS ensembles :
ID
6
1
2
3
4
5

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Components

#1: Protein
Pyruvate carboxylase


Mass: 127306.578 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Gene: pycA, LG36_0614 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A089XIW4, pyruvate carboxylase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S

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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: 3.39 Å3/Da / Density % sol: 63.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 15% (w/v) PEG 3350 and 0.2 M ammonium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.1→49.75 Å / Num. obs: 123876 / % possible obs: 99.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 12
Reflection shellResolution: 3.1→3.15 Å / Rmerge(I) obs: 0.76

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→49.75 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.901 / SU B: 18.702 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24824 6206 5 %RANDOM
Rwork0.1995 ---
obs0.20195 117581 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.466 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.52 Å2-0 Å2
2--0.52 Å2-0 Å2
3----1.69 Å2
Refinement stepCycle: 1 / Resolution: 3.1→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31405 0 20 0 31425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01932060
X-RAY DIFFRACTIONr_bond_other_d0.0070.0230805
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.96143400
X-RAY DIFFRACTIONr_angle_other_deg1.103370823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43253977
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.74524.4341547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.718155561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.66815205
X-RAY DIFFRACTIONr_chiral_restr0.0820.24826
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02136559
X-RAY DIFFRACTIONr_gen_planes_other0.0060.027340
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A647050.04
12B647050.04
21A645580.05
22C645580.05
31A645100.05
32D645100.05
41B646220.05
42C646220.05
51B643380.05
52D643380.05
61C643650.05
62D643650.05
LS refinement shellResolution: 3.1→3.268 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.349 898 -
Rwork0.296 17029 -
obs--99.82 %

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