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- PDB-5vyz: Crystal structure of Lactococcus lactis pyruvate carboxylase in c... -

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Basic information

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


Rossmann fold - #20 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-2BA / ADENOSINE-5'-DIPHOSPHATE / : / :
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChoi, P.H. / Tong, L.
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: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / entity / pdbx_entity_nonpoly / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _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_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

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)513,25018
Polymers509,9074
Non-polymers3,34314
Water16,556919
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26320 Å2
ΔGint-121 kcal/mol
Surface area168870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.270, 130.431, 133.367
Angle α, β, γ (deg.)66.08, 89.05, 70.60
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA-6 - 11372 - 1145
21LEULEUBB-6 - 11372 - 1145
12LEULEUAA-6 - 11372 - 1145
22LEULEUCC-6 - 11372 - 1145
13LEULEUAA-6 - 11372 - 1145
23LEULEUDD-6 - 11372 - 1145
14GLYGLYBB-7 - 11371 - 1145
24GLYGLYCC-7 - 11371 - 1145
15GLYGLYBB-7 - 11371 - 1145
25GLYGLYDD-7 - 11371 - 1145
16GLYGLYCC-7 - 11371 - 1145
26GLYGLYDD-7 - 11371 - 1145

NCS ensembles :
ID
6
1
2
3
4
5

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Pyruvate carboxylase


Mass: 127476.781 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

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Non-polymers , 5 types, 933 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O12P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 919 / 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: 2.87 Å3/Da / Density % sol: 57.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG3350, and 0.2 M ammonium formate

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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: Dec 18, 2015 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.3→48.6 Å / Num. obs: 223863 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 1.7 / % possible all: 89.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.6 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.508 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.222 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 11256 5 %RANDOM
Rwork0.1831 ---
obs0.185 212577 89.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.733 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å21.77 Å2-0.81 Å2
2--0.06 Å20.24 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35356 0 204 919 36479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01936259
X-RAY DIFFRACTIONr_bond_other_d0.0070.0234853
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.96949110
X-RAY DIFFRACTIONr_angle_other_deg1.236380177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64754506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78624.5931709
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.719156295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.30715221
X-RAY DIFFRACTIONr_chiral_restr0.090.25474
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02141222
X-RAY DIFFRACTIONr_gen_planes_other0.0060.028177
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)
11A715960.09
12B715960.09
21A684410.09
22C684410.09
31A717160.09
32D717160.09
41B683690.08
42C683690.08
51B717240.09
52D717240.09
61C680760.09
62D680760.09
LS refinement shellResolution: 2.296→2.42 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.308 1583 -
Rwork0.274 29892 -
obs--86.1 %

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