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- PDB-3u9t: Crystal structure of P. aeruginosa 3-methylcrotonyl-CoA carboxyla... -

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Basic information

Entry
Database: PDB / ID: 3u9t
TitleCrystal structure of P. aeruginosa 3-methylcrotonyl-CoA carboxylase (MCC) 750 kD holoenzyme, free enzyme
Components
  • Methylcrotonyl-CoA carboxylase, alpha-subunit
  • Methylcrotonyl-CoA carboxylase, beta-subunit
KeywordsLIGASE / biotin carboxylase / carboxyltransferase / bt domain / bccp domain
Function / homology
Function and homology information


terpene catabolic process / isoprenoid catabolic process / methylcrotonoyl-CoA carboxylase complex / methylcrotonoyl-CoA carboxylase activity / L-leucine catabolic process / ATP binding / metal ion binding
Similarity search - Function
Glycoprotein, Type 4 Pilin - #40 / : / Methylcrotonyl-CoA carboxylase, alpha-subunit, BT domain / Methylcrotonoyl-CoA carboxylase beta chain MCCB/AccD1-like / Glycoprotein, Type 4 Pilin / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase ...Glycoprotein, Type 4 Pilin - #40 / : / Methylcrotonyl-CoA carboxylase, alpha-subunit, BT domain / Methylcrotonoyl-CoA carboxylase beta chain MCCB/AccD1-like / Glycoprotein, Type 4 Pilin / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / 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 / Rossmann fold - #20 / 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 / ATP-grasp fold, A domain / Single hybrid motif / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 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 / ClpP/crotonase-like domain superfamily / Dna Ligase; domain 1 / Carbamoyl-phosphate synthase subdomain signature 2. / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Methylcrotonyl-CoA carboxylase, beta-subunit / Methylcrotonyl-CoA carboxylase, alpha-subunit (Biotin-containing)
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHuang, C.S. / Tong, L.
CitationJournal: Nature / Year: 2012
Title: An unanticipated architecture of the 750-kDa {alpha}6{beta}6 holoenzyme of 3-methylcrotonyl-CoA carboxylase
Authors: Huang, C.S. / Ge, P. / Zhou, Z.H. / Tong, L.
History
DepositionOct 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references / Structure summary
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methylcrotonyl-CoA carboxylase, alpha-subunit
B: Methylcrotonyl-CoA carboxylase, beta-subunit


Theoretical massNumber of molelcules
Total (without water)131,0492
Polymers131,0492
Non-polymers00
Water0
1
A: Methylcrotonyl-CoA carboxylase, alpha-subunit
B: Methylcrotonyl-CoA carboxylase, beta-subunit
x 6


Theoretical massNumber of molelcules
Total (without water)786,29312
Polymers786,29312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area53260 Å2
ΔGint-102 kcal/mol
Surface area213890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.930, 158.930, 311.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Methylcrotonyl-CoA carboxylase, alpha-subunit / / MCC alpha


Mass: 71378.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: liuD, PA2012 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9I299, methylcrotonoyl-CoA carboxylase
#2: Protein Methylcrotonyl-CoA carboxylase, beta-subunit / / MCC beta


Mass: 59670.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: liuB, PA2014 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9I297, methylcrotonoyl-CoA carboxylase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.8556.78
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931under oil720% PEG3350, 0.2 M sodium malonate, pH 7.0, UNDER OIL, temperature 293K
2932under oil720% PEG3350, 0.2 M sodium sulfate, pH 7.0, UNDER OIL, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2011 / 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: 2.9→50 Å / Num. all: 33584 / Num. obs: 31522 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 95.9 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.0215
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2.369 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→46.23 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 582849.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1583 5 %RANDOM
Rwork0.209 ---
obs0.209 31522 92.9 %-
all-31522 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.6364 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 82.9 Å2
Baniso -1Baniso -2Baniso -3
1-6.2 Å20 Å20 Å2
2--6.2 Å20 Å2
3----12.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.9→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7635 0 0 0 7635
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.354 160 5.8 %
Rwork0.324 2599 -
obs--82.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2bti.par

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