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- PDB-4qsl: Crystal Structure of Listeria Monocytogenes Pyruvate Carboxylase -

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Basic information

Entry
Database: PDB / ID: 4qsl
TitleCrystal Structure of Listeria Monocytogenes Pyruvate Carboxylase
ComponentsPyruvate carboxylase
KeywordsLIGASE / TIM Barrell / Pyruvate Carboxylase / Acetyl-CoA / Biotin
Function / homology
Function and homology information


pyruvate carboxylase / pyruvate carboxylase activity / gluconeogenesis / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Arc Repressor Mutant, subunit A - #2790 / pyruvate carboxylase f1077a mutant fold / pyruvate carboxylase f1077a mutant domain / Conserved carboxylase domain / : / Pyruvate carboxylase / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like ...Arc Repressor Mutant, subunit A - #2790 / pyruvate carboxylase f1077a mutant fold / pyruvate carboxylase f1077a mutant domain / 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. / ATP-grasp fold, A domain / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Cyclin A; domain 1 / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / ATP-grasp fold, subdomain 1 / ATP-grasp fold, B domain / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Aldolase class I / Aldolase-type TIM barrel / Arc Repressor Mutant, subunit A / Carbamoyl-phosphate synthase subdomain signature 2. / TIM Barrel / Alpha-Beta Barrel / Roll / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Pyruvate carboxylase / :
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
H: Pyruvate carboxylase
F: Pyruvate carboxylase
E: Pyruvate carboxylase
G: Pyruvate carboxylase
D: Pyruvate carboxylase
A: Pyruvate carboxylase
B: Pyruvate carboxylase
C: Pyruvate carboxylase


Theoretical massNumber of molelcules
Total (without water)1,026,0628
Polymers1,026,0628
Non-polymers00
Water00
1
H: Pyruvate carboxylase
F: Pyruvate carboxylase
E: Pyruvate carboxylase
G: Pyruvate carboxylase


Theoretical massNumber of molelcules
Total (without water)513,0314
Polymers513,0314
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14200 Å2
ΔGint-38 kcal/mol
Surface area158470 Å2
MethodPISA
2
D: Pyruvate carboxylase
A: Pyruvate carboxylase
B: Pyruvate carboxylase
C: Pyruvate carboxylase


Theoretical massNumber of molelcules
Total (without water)513,0314
Polymers513,0314
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14250 Å2
ΔGint-37 kcal/mol
Surface area158430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.360, 132.615, 257.544
Angle α, β, γ (deg.)86.65, 79.84, 70.07
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21B
12C
22E
13C
23G
14C
24D
15C
25A
16C
26F
17C
27H
18B
28E
19B
29G
110B
210D
111B
211A
112B
212F
113B
213H
114E
214G
115E
215D
116E
216A
117E
217F
118E
218H
119G
219D
120G
220A
121G
221F
122G
222H
123D
223A
124D
224F
125D
225H
126A
226F
127A
227H
128F
228H

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 1 - 1060 / Label seq-ID: 1 - 1060

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11CH
21BG
12CH
22EC
13CH
23GD
14CH
24DE
15CH
25AF
16CH
26FB
17CH
27HA
18BG
28EC
19BG
29GD
110BG
210DE
111BG
211AF
112BG
212FB
113BG
213HA
114EC
214GD
115EC
215DE
116EC
216AF
117EC
217FB
118EC
218HA
119GD
219DE
120GD
220AF
121GD
221FB
122GD
222HA
123DE
223AF
124DE
224FB
125DE
225HA
126AF
226FB
127AF
227HA
128FB
228HA

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Pyruvate carboxylase


Mass: 128257.719 Da / Num. of mol.: 8
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

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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: 2.81 Å3/Da / Density % sol: 56.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 16% PEG 3350, 0.1M BIS-TRIS pH 6.5, 1% Tacsimate 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: Nov 21, 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: 3.3→50 Å / Num. obs: 151836 / % possible obs: 89.4 % / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 11.3
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 1.6 / % possible all: 72.2

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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: 3.28→47.16 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.909 / SU B: 34.498 / SU ML: 0.558 / Cross valid method: THROUGHOUT / ESU R Free: 0.64 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28437 7628 5 %RANDOM
Rwork0.23751 ---
obs0.23989 144205 88.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 127.681 Å2
Baniso -1Baniso -2Baniso -3
1-10.72 Å22.32 Å20.73 Å2
2---5.6 Å2-0.59 Å2
3----2.48 Å2
Refinement stepCycle: LAST / Resolution: 3.28→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms60495 0 0 0 60495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01961712
X-RAY DIFFRACTIONr_bond_other_d0.0060.0256546
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9584112
X-RAY DIFFRACTIONr_angle_other_deg1.2813129202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.76158082
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91424.4392690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.742159228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.60515334
X-RAY DIFFRACTIONr_chiral_restr0.0750.29664
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02171992
X-RAY DIFFRACTIONr_gen_planes_other0.0050.0213994
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)
11C574580.09
12B574580.09
21C507600.1
22E507600.1
31C473430.09
32G473430.09
41C631370.02
42D631370.02
51C574560.09
52A574560.09
61C506810.1
62F506810.1
71C473730.09
72H473730.09
81B512940.1
82E512940.1
91B479420.1
92G479420.1
101B574580.09
102D574580.09
111B634440.02
112A634440.02
121B511640.1
122F511640.1
131B479230.1
132H479230.1
141E450190.1
142G450190.1
151E507630.1
152D507630.1
161E512860.1
162A512860.1
171E554270.04
172F554270.04
181E450300.1
182H450300.1
191G473480.09
192D473480.09
201G479300.1
202A479300.1
211G449870.1
212F449870.1
221G523640.03
222H523640.03
231D574470.09
232A574470.09
241D506880.1
242F506880.1
251D473730.09
252H473730.09
261A511480.1
262F511480.1
271A479080.1
272H479080.1
281F450020.1
282H450020.1
LS refinement shellResolution: 3.285→3.462 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.376 889 -
Rwork0.339 16919 -
obs--71.44 %

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