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- PDB-8gk8: R21A Staphylococcus aureus pyruvate carboxylase -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8gk8
TitleR21A Staphylococcus aureus pyruvate carboxylase
ComponentsPyruvate carboxylase
KeywordsLIGASE / Biotin dependent ligase
Function / homology
Function and homology information


pyruvate carboxylase / pyruvate carboxylase activity / pyruvate metabolic process / gluconeogenesis / ATP binding / metal ion binding
Similarity search - Function
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 ...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 / ATP-grasp fold, A domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Pre-ATP-grasp domain superfamily / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Carbamoyl-phosphate synthase subdomain signature 2. / Aldolase-type TIM barrel / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / Chem-BTI / COENZYME A / : / Pyruvate carboxylase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsLaseke, A.J. / St.Maurice, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) United States
CitationJournal: Biochemistry / Year: 2023
Title: Allosteric Site at the Biotin Carboxylase Dimer Interface Mediates Activation and Inhibition in Staphylococcus aureus Pyruvate Carboxylase.
Authors: Laseke, A.J. / Boram, T.J. / Schneider, N.O. / Lohman, J.R. / St Maurice, M.
History
DepositionMar 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Pyruvate carboxylase
B: Pyruvate carboxylase
D: Pyruvate carboxylase
A: Pyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)517,60414
Polymers514,8944
Non-polymers2,71010
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21180 Å2
ΔGint-65 kcal/mol
Surface area147880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.976, 253.668, 125.657
Angle α, β, γ (deg.)90.00, 110.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules CBDA

#1: Protein
Pyruvate carboxylase


Mass: 128723.461 Da / Num. of mol.: 4 / Mutation: R21A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: G6Y24_05790 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3A5LTU8, pyruvate carboxylase

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Non-polymers , 5 types, 288 molecules

#2: Chemical
ChemComp-BTI / 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL


Mass: 228.311 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C10H16N2O2S
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 54.76 % / Description: cube-like
Crystal growTemperature: 295 K / Method: batch mode / pH: 7
Details: 13.3% MEPEG 2K, 133 mM KNO3-, 50 mM MOPS pH 7.0, 1.5% v/v 2-propanol, 0.625 mM acetyl CoA, 1.25 mM adenosine triphosphate (ATP)
PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.676→126.83 Å / Num. obs: 108946 / % possible obs: 70.71 % / Redundancy: 3.7 % / Biso Wilson estimate: 50.4 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.1 / Rrim(I) all: 0.194 / Net I/av σ(I): 7.1 / Net I/σ(I): 7.1
Reflection shellResolution: 2.68→2.932 Å / Num. unique obs: 108939 / CC1/2: 0.561

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessv0.7.7data scaling
XDSV10.Jan2022data reduction
PHASERv.1.20.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→60.62 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3011 5560 5.1 %
Rwork0.2485 --
obs0.2512 108946 70.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.68→60.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30599 0 163 278 31040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00431366
X-RAY DIFFRACTIONf_angle_d0.71442619
X-RAY DIFFRACTIONf_dihedral_angle_d6.5414378
X-RAY DIFFRACTIONf_chiral_restr0.0454875
X-RAY DIFFRACTIONf_plane_restr0.0065556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.710.422780.3707219X-RAY DIFFRACTION4
2.71-2.740.4655130.3279329X-RAY DIFFRACTION7
2.74-2.770.3611230.3501402X-RAY DIFFRACTION8
2.77-2.810.4039280.3307603X-RAY DIFFRACTION12
2.81-2.840.48440.338808X-RAY DIFFRACTION17
2.84-2.880.4167580.34971064X-RAY DIFFRACTION22
2.88-2.920.427690.35721439X-RAY DIFFRACTION29
2.92-2.970.3792840.33641803X-RAY DIFFRACTION37
2.97-3.010.38231100.33732193X-RAY DIFFRACTION45
3.01-3.060.36521490.3222597X-RAY DIFFRACTION54
3.06-3.120.36141480.31783044X-RAY DIFFRACTION62
3.12-3.170.37381850.31363494X-RAY DIFFRACTION72
3.17-3.230.31682130.31183789X-RAY DIFFRACTION78
3.23-3.30.34632510.30544187X-RAY DIFFRACTION87
3.3-3.370.3722400.30144559X-RAY DIFFRACTION93
3.37-3.450.34512430.28464778X-RAY DIFFRACTION98
3.45-3.540.32422550.28194856X-RAY DIFFRACTION100
3.54-3.630.34182750.27754910X-RAY DIFFRACTION100
3.63-3.740.32722660.26194828X-RAY DIFFRACTION100
3.74-3.860.31822750.254835X-RAY DIFFRACTION100
3.86-40.3132820.24654848X-RAY DIFFRACTION100
4-4.160.27842530.23134874X-RAY DIFFRACTION100
4.16-4.350.27592360.2274877X-RAY DIFFRACTION99
4.35-4.570.28842900.20884814X-RAY DIFFRACTION100
4.57-4.860.26172380.19974878X-RAY DIFFRACTION100
4.86-5.240.24732750.20724879X-RAY DIFFRACTION100
5.24-5.760.2972790.23124833X-RAY DIFFRACTION100
5.76-6.60.31892630.25274886X-RAY DIFFRACTION100
6.6-8.310.27532680.22464853X-RAY DIFFRACTION99
8.31-60.620.22652390.21824907X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -14.7259 Å / Origin y: -21.909 Å / Origin z: 85.4572 Å
111213212223313233
T0.0944 Å20.009 Å2-0.0387 Å2-0.194 Å20.0043 Å2--0.1284 Å2
L0.0917 °2-0.0557 °2-0.0299 °2-0.4447 °2-0.0391 °2--0.0834 °2
S0.0084 Å °-0.0344 Å °-0.0089 Å °0.0715 Å °0.0004 Å °-0.0065 Å °-0.0045 Å °0.0264 Å °-0.0133 Å °
Refinement TLS groupSelection details: all

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