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- PDB-3u9s: Crystal structure of P. aeruginosa 3-methylcrotonyl-CoA carboxyla... -

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Basic information

Entry
Database: PDB / ID: 3u9s
TitleCrystal structure of P. aeruginosa 3-methylcrotonyl-CoA carboxylase (MCC) 750 kD holoenzyme, CoA complex
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 activity / methylcrotonoyl-CoA carboxylase complex / 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 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Carbamoyl-phosphate synthase subdomain signature 2. / Alpha-Beta Complex / Beta Barrel / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-BTI / COENZYME A / 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: 3.5 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylcrotonyl-CoA carboxylase, alpha-subunit
B: Methylcrotonyl-CoA carboxylase, beta-subunit
C: Methylcrotonyl-CoA carboxylase, alpha-subunit
D: Methylcrotonyl-CoA carboxylase, beta-subunit
E: Methylcrotonyl-CoA carboxylase, alpha-subunit
F: Methylcrotonyl-CoA carboxylase, beta-subunit
G: Methylcrotonyl-CoA carboxylase, alpha-subunit
H: Methylcrotonyl-CoA carboxylase, beta-subunit
I: Methylcrotonyl-CoA carboxylase, alpha-subunit
J: Methylcrotonyl-CoA carboxylase, beta-subunit
K: Methylcrotonyl-CoA carboxylase, alpha-subunit
L: Methylcrotonyl-CoA carboxylase, beta-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)791,35520
Polymers786,29312
Non-polymers5,0628
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area75240 Å2
ΔGint-245 kcal/mol
Surface area221850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.510, 255.340, 152.670
Angle α, β, γ (deg.)90.00, 95.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 71378.875 Da / Num. of mol.: 6
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.: 6
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
#3: 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
#4: Chemical
ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.1961.45
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: Apr 19, 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: 3.5→50 Å / Num. all: 118359 / Num. obs: 104480 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 105.4 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.2537
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 1.736 / % possible all: 75.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→48.9 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 340196.4 / 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
Rfree0.292 5256 5 %RANDOM
Rwork0.234 ---
obs0.234 104480 83 %-
all-104480 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.9385 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 105.4 Å2
Baniso -1Baniso -2Baniso -3
1-66.37 Å20 Å2-7.3 Å2
2---41.5 Å20 Å2
3----24.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.51 Å
Luzzati d res low-5 Å
Luzzati sigma a1.1 Å1.05 Å
Refinement stepCycle: LAST / Resolution: 3.5→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49621 0 318 0 49939
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.19
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.252.5
X-RAY DIFFRACTIONc_mcangle_it3.833
X-RAY DIFFRACTIONc_scbond_it3.654
X-RAY DIFFRACTIONc_scangle_it5.995
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3.5→3.63 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.425 389 5.1 %
Rwork0.396 7311 -
obs--61.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2bti.parbti.top

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