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- PDB-3ho8: Crystal Structure of S. aureus Pyruvate Carboxylase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3ho8
TitleCrystal Structure of S. aureus Pyruvate Carboxylase in complex with Coenzyme A
ComponentsPyruvate carboxylase
KeywordsLIGASE / TIM barrel / Pyruvate
Function / homology
Function and homology information


pyruvate carboxylase / pyruvate carboxylase activity / pyruvate metabolic process / gluconeogenesis / ATP binding / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
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. ...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. / 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 / Cyclin A; domain 1 / 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 / Aldolase class I / Carbamoyl-phosphate synthase subdomain signature 2. / Aldolase-type TIM barrel / 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
Chem-BTI / COENZYME A / : / Pyruvate carboxylase / Pyruvate carboxylase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsTong, L. / Yu, L.P.C.
CitationJournal: Structure / Year: 2009
Title: A Symmetrical Tetramer for S. aureus Pyruvate Carboxylase in Complex with Coenzyme A.
Authors: Yu, L.P. / Xiang, S. / Lasso, G. / Gil, D. / Valle, M. / Tong, L.
History
DepositionJun 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
D: Pyruvate carboxylase
C: Pyruvate carboxylase
B: Pyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)518,57614
Polymers514,8304
Non-polymers3,74710
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23070 Å2
ΔGint-43 kcal/mol
Surface area143840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.586, 164.466, 373.346
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Pyruvate carboxylase


Mass: 128707.414 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Gene: pycA, Pyruvate Carboxylase, SAV1114 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star(DE3) / References: UniProt: Q99UY8, UniProt: A0A0H3JRU9*PLUS
#2: Chemical
ChemComp-COA / COENZYME A


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


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-BTI / 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL


Mass: 228.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O2S

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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: 2.88 Å3/Da / Density % sol: 57.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.2M ammonium tartrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 124420 / % possible obs: 95.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.139 / Χ2: 0.925 / Net I/σ(I): 8.65
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-34.70.478128490.97699.9
3-3.124.70.371128730.99199.9
3.12-3.274.60.297128790.99699.9
3.27-3.444.10.287116921.14190.7
3.44-3.6540.244114251.11188
3.65-3.933.70.204100001.07677.2
3.93-4.339.20.157129670.85299.7
4.33-4.95100.134130100.8999.8
4.95-6.2310.80.124131680.88399.9
6.23-3011.50.108135570.85699.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→29.97 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.817 / Occupancy max: 1 / Occupancy min: 1 / SU B: 48.823 / SU ML: 0.445 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.53 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.328 5969 5 %RANDOM
Rwork0.264 ---
obs0.268 118417 89.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 177.34 Å2 / Biso mean: 67.901 Å2 / Biso min: 23.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31007 0 226 0 31233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02231838
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.97243100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0553901
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.7124.6981522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.601155601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.70115188
X-RAY DIFFRACTIONr_chiral_restr0.0860.24807
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02124063
X-RAY DIFFRACTIONr_mcbond_it0.311.519441
X-RAY DIFFRACTIONr_mcangle_it0.578231482
X-RAY DIFFRACTIONr_scbond_it0.806312397
X-RAY DIFFRACTIONr_scangle_it1.3614.511618
LS refinement shellResolution: 2.9→2.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 375 -
Rwork0.286 7607 -
all-7982 -
obs--83.21 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8420.01760.45811.6420.18012.64310.14780.1374-0.1651-0.33520.0216-0.76720.06590.5652-0.16940.12420.06280.12380.3088-0.00030.492423.245-62.154955.3614
20.64720.6619-0.09493.3025-0.54812.66460.08240.0413-0.0554-0.7182-0.0348-0.24540.19450.4069-0.04750.40530.09360.03350.2077-0.00970.22063.244248.891438.0023
30.84430.65780.30953.24221.11751.55930.1059-0.02320.0104-0.5095-0.12950.3395-0.0995-0.24420.02360.35340.0789-0.08150.22620.01060.1752-6.3175-67.97838.4846
41.1178-0.26550.43362.7749-0.91923.07290.1487-0.16580.0095-0.360.16081.0782-0.0469-0.7525-0.30950.08870.0592-0.16810.40630.03480.7096-24.939743.563757.0993
51.1507-0.169-0.70471.8091-0.93123.3082-0.0440.14460.0912-0.49050.028-0.141-0.24440.22150.0160.8596-0.10270.10120.3608-0.04450.227613.5544-20.90495.4885
60.9612-0.07130.40112.3406-0.720.73170.01420.0217-0.0066-0.2694-0.0735-0.3062-0.02410.18440.05920.0657-0.02220.03620.1828-0.05670.091612.89436.5286.8131
70.86950.0368-0.67032.64420.94621.270.0011-0.05360.0622-0.3106-0.07310.5574-0.0503-0.08330.07190.0467-0.0081-0.07940.19770.02330.1429-13.4486-25.609887.2107
81.4418-0.32460.56111.70451.31143.5966-0.07710.1202-0.0919-0.399-0.09020.53380.0256-0.19670.16730.9662-0.0546-0.3520.30340.02080.4387-20.46134.22627.6091
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 167
2X-RAY DIFFRACTION1A239 - 494
3X-RAY DIFFRACTION2B36 - 167
4X-RAY DIFFRACTION2B239 - 494
5X-RAY DIFFRACTION3C36 - 167
6X-RAY DIFFRACTION3C239 - 494
7X-RAY DIFFRACTION4D36 - 167
8X-RAY DIFFRACTION4D239 - 494
9X-RAY DIFFRACTION5A495 - 1093
10X-RAY DIFFRACTION6B495 - 1093
11X-RAY DIFFRACTION7C495 - 1093
12X-RAY DIFFRACTION8D495 - 1093

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