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- PDB-4qsh: Crystal Structure of L. monocytogenes Pyruvate Carboxylase in com... -

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Basic information

Entry
Database: PDB / ID: 4qsh
TitleCrystal Structure of L. monocytogenes Pyruvate Carboxylase in complex with Cyclic-di-AMP
ComponentsPyruvate carboxylase
KeywordsLIGASE / TIM BARREL / Pyruvate Carboxylase / Acetyl-CoA / Biotin
Function / homology
Function and homology information


pyruvate carboxylase / pyruvate carboxylase activity / pyruvate metabolic process / gluconeogenesis / ATP binding / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #2790 / Conserved carboxylase domain / Pyruvate carboxylase / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Rossmann fold - #20 / Biotin carboxylase-like, N-terminal domain ...Arc Repressor Mutant, subunit A - #2790 / Conserved carboxylase domain / Pyruvate carboxylase / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Rossmann fold - #20 / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Cyclin A; domain 1 / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Aldolase class I / Carbamoyl-phosphate synthase subdomain signature 2. / Arc Repressor Mutant, subunit A / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-2BA / CITRATE ANION / : / Pyruvate carboxylase / :
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsChoi, P.H. / Tong, L.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: The Cyclic Dinucleotide c-di-AMP Is an Allosteric Regulator of Metabolic Enzyme Function.
Authors: Sureka, K. / Choi, P.H. / Precit, M. / Delince, M. / Pensinger, D.A. / Huynh, T.N. / Jurado, A.R. / Goo, Y.A. / Sadilek, M. / Iavarone, A.T. / Sauer, J.D. / Tong, L. / Woodward, J.J.
History
DepositionJul 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_seq_id / _struct_conn.ptnr2_label_asym_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)517,06015
Polymers514,1084
Non-polymers2,95111
Water9,116506
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25900 Å2
ΔGint-71 kcal/mol
Surface area155820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.778, 153.296, 221.240
Angle α, β, γ (deg.)90.00, 101.58, 90.00
Int Tables number4
Space group name H-MP1211
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: ARG / End label comp-ID: ARG / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETAA0 - 11452 - 1147
21METMETBB0 - 11452 - 1147
12HISHISAA-1 - 11451 - 1147
22HISHISCC-1 - 11451 - 1147
13METMETAA0 - 11452 - 1147
23METMETDD0 - 11452 - 1147
14METMETBB0 - 11452 - 1147
24METMETCC0 - 11452 - 1147
15METMETBB0 - 11452 - 1147
25METMETDD0 - 11452 - 1147
16METMETCC0 - 11452 - 1147
26METMETDD0 - 11452 - 1147

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Pyruvate carboxylase


Mass: 128527.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: AX24_02755 / Production host: Escherichia coli (E. coli)
References: UniProt: W6G6F5, UniProt: A0A1C7Q2R5*PLUS, pyruvate carboxylase
#2: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: 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.: 3 / Source method: obtained synthetically / Formula: C20H24N10O12P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 3.13 Å3/Da / Density % sol: 60.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 19% PEG 3350, 0.2M Ammonium Citrate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 24, 2013 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 209169 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.3 / % possible all: 87.3

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BG5

3bg5


Resolution: 2.51→49.8 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.679 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23336 10520 5 %RANDOM
Rwork0.19454 ---
obs0.1965 198499 96.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.768 Å2
Baniso -1Baniso -2Baniso -3
1-2.93 Å2-0 Å2-3.51 Å2
2---4.1 Å2-0 Å2
3---1.75 Å2
Refinement stepCycle: LAST / Resolution: 2.51→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33830 0 188 506 34524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01934698
X-RAY DIFFRACTIONr_bond_other_d0.0060.0233108
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.96647042
X-RAY DIFFRACTIONr_angle_other_deg1.083376191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.19454287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89524.6361620
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.523156012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.90315201
X-RAY DIFFRACTIONr_chiral_restr0.0930.25279
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02139285
X-RAY DIFFRACTIONr_gen_planes_other0.0060.027762
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)
11A687270.05
12B687270.05
21A690950.05
22C690950.05
31A691930.05
32D691930.05
41B689980.06
42C689980.06
51B690220.05
52D690220.05
61C688660.06
62D688660.06
LS refinement shellResolution: 2.507→2.643 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.345 1468 -
Rwork0.295 26177 -
obs--87.83 %

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