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- PDB-5ks8: Crystal structure of two-subunit pyruvate carboxylase from Methyl... -

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Basic information

Entry
Database: PDB / ID: 5ks8
TitleCrystal structure of two-subunit pyruvate carboxylase from Methylobacillus flagellatus
Components
  • Pyruvate carboxylase subunit alpha
  • Pyruvate carboxylase subunit beta
KeywordsLIGASE / Biotin / TIM Barrel / Pyruvate
Function / homology
Function and homology information


pyruvate carboxylase activity / biotin carboxylase / oxaloacetate decarboxylase activity / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / sodium ion transport / fatty acid biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Oxaloacetate decarboxylase, alpha subunit / : / Acetyl-CoA carboxylase, biotin carboxylase / : / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Biotin-binding site ...Oxaloacetate decarboxylase, alpha subunit / : / Acetyl-CoA carboxylase, biotin carboxylase / : / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Biotin-binding site / Biotin-requiring enzymes attachment site. / 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 / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / 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 / Carbamoyl-phosphate synthase subdomain signature 2. / Aldolase-type TIM barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BTI / : / PYRUVIC ACID / Oxaloacetate decarboxylase alpha subunit / Biotin carboxylase
Similarity search - Component
Biological speciesMethylobacillus flagellatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsChoi, P.H. / Tong, L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK067238 United States
National Institutes of Health/Office of the DirectorOD012018 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI103369 United States
CitationJournal: Nat Commun / Year: 2016
Title: A distinct holoenzyme organization for two-subunit pyruvate carboxylase.
Authors: Choi, P.H. / Jo, J. / Lin, Y.C. / Lin, M.H. / Chou, C.Y. / Dietrich, L.E. / Tong, L.
History
DepositionJul 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: database_2 / diffrn_radiation_wavelength ...database_2 / diffrn_radiation_wavelength / pdbx_audit_support / struct_conn / struct_conn_type
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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_type.id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_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
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate carboxylase subunit alpha
B: Pyruvate carboxylase subunit alpha
C: Pyruvate carboxylase subunit beta
D: Pyruvate carboxylase subunit beta
E: Pyruvate carboxylase subunit beta
F: Pyruvate carboxylase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)358,94012
Polymers358,3716
Non-polymers5696
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23880 Å2
ΔGint-122 kcal/mol
Surface area112480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)285.760, 285.760, 274.873
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13C
23E
14D
24E
15D
25F
16E
26F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLYGLYAA1 - 4711 - 404
21METMETGLYGLYBB1 - 4711 - 404
12LYSLYSPROPROCC3 - 6163 - 616
22LYSLYSPROPRODD3 - 6163 - 616
13LYSLYSVALVALCC3 - 5103 - 510
23LYSLYSVALVALEE3 - 5103 - 510
14LYSLYSVALVALDD3 - 5103 - 510
24LYSLYSVALVALEE3 - 5103 - 510
15LYSLYSPROPRODD3 - 6163 - 616
25LYSLYSPROPROFF3 - 6163 - 616
16LYSLYSVALVALEE3 - 5103 - 510
26LYSLYSVALVALFF3 - 5103 - 510

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein Pyruvate carboxylase subunit alpha


Mass: 45053.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacillus flagellatus (bacteria), (gene. exp.) Methylobacillus flagellatus (strain KT / ATCC 51484 / DSM 6875) (bacteria)
Strain: KT / ATCC 51484 / DSM 6875 / Gene: Mfla_1511 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1H158
#2: Protein
Pyruvate carboxylase subunit beta


Mass: 67066.023 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacillus flagellatus (strain KT / ATCC 51484 / DSM 6875) (bacteria)
Strain: KT / ATCC 51484 / DSM 6875 / Gene: Mfla_1512 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1H157
#3: Chemical ChemComp-BTI / 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL


Mass: 228.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O2S
#4: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn

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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: 3.01 Å3/Da / Density % sol: 63.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 19% (w/v) PEG3350, 2% tacsimate (pH 6.0) (Hampton), and 3% (v/v) ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2015 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.01→50 Å / Num. obs: 81321 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 11
Reflection shellResolution: 3.01→3.11 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 1.8 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
SnBTHEN SOLVE/RESOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: S. aureus pyruvate carboxylase

Resolution: 3.01→47.44 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.912 / SU B: 18.734 / SU ML: 0.346 / Cross valid method: THROUGHOUT / ESU R Free: 0.447 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27151 4072 5 %RANDOM
Rwork0.22527 ---
obs0.22761 77247 95.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 106.271 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.03 Å20 Å2
2---0.03 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 3.01→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21654 0 30 0 21684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01922057
X-RAY DIFFRACTIONr_bond_other_d0.0050.0220811
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.96129987
X-RAY DIFFRACTIONr_angle_other_deg1.166347702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67552882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93924.38920
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.446153498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.66115134
X-RAY DIFFRACTIONr_chiral_restr0.0780.23502
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02125371
X-RAY DIFFRACTIONr_gen_planes_other0.0040.024814
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)
11A241100.1
12B241100.1
21C320500.15
22D320500.15
31C162220.16
32E162220.16
41D160850.16
42E160850.16
51D244220.13
52F244220.13
61E135390.16
62F135390.16
LS refinement shellResolution: 3.008→3.17 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.335 603 -
Rwork0.291 11129 -
obs--95.52 %

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