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- PDB-5vip: Crystal structure of Pseudomonas malonate decarboxylase MdcD-MdcE... -

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Basic information

Entry
Database: PDB / ID: 5vip
TitleCrystal structure of Pseudomonas malonate decarboxylase MdcD-MdcE hetero-dimer
Components
  • MdcD
  • MdcE
KeywordsTRANSFERASE / acyl carrier protein / acetyl-CoA carboxylase
Function / homology
Function and homology information


malonyl-S-ACP:biotin-protein carboxyltransferase / carboxy-lyase activity / transferase activity / carbohydrate metabolic process
Similarity search - Function
Biotin-dependent malonate decarboxylase, gamma subunit / Biotin-independent malonate decarboxylase, beta subunit / Malonate decarboxylase gamma subunit (MdcE) / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
Malonate decarboxylase subunit beta / Malonate decarboxylase subunit gamma / Malonate decarboxylase gamma subunit / Malonate decarboxylase beta subunit
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.857 Å
AuthorsMaderbocus, R. / Tong, L.
CitationJournal: Nat Commun / Year: 2017
Title: Crystal structure of a Pseudomonas malonate decarboxylase holoenzyme hetero-tetramer.
Authors: Maderbocus, R. / Fields, B.L. / Hamilton, K. / Luo, S. / Tran, T.H. / Dietrich, L.E.P. / Tong, L.
History
DepositionApr 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MdcE
B: MdcD
C: MdcE
D: MdcD


Theoretical massNumber of molelcules
Total (without water)122,1964
Polymers122,1964
Non-polymers00
Water3,891216
1
A: MdcE
B: MdcD


Theoretical massNumber of molelcules
Total (without water)61,0982
Polymers61,0982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-39 kcal/mol
Surface area18270 Å2
MethodPISA
2
C: MdcE
D: MdcD


Theoretical massNumber of molelcules
Total (without water)61,0982
Polymers61,0982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-40 kcal/mol
Surface area18230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.310, 60.076, 91.277
Angle α, β, γ (deg.)89.87, 88.77, 68.80
Int Tables number1
Space group name H-MP1

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Components

#1: Protein MdcE / Biotin-independent malonate decarboxylase subunit gamma / Malonate decarboxylase / gamma subunit / ...Biotin-independent malonate decarboxylase subunit gamma / Malonate decarboxylase / gamma subunit / Malonyl-S-ACP:biotin-protein carboxyltransferase MADD


Mass: 30632.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: madD, AO964_31595, AOY09_06293, PAERUG_E15_London_28_01_14_07062, PAERUG_P32_London_17_VIM_2_10_11_04128
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0C6EV56, UniProt: Q9I6S6*PLUS, malonyl-S-ACP:biotin-protein carboxyltransferase
#2: Protein MdcD / Biotin-independent malonate decarboxylase subunit beta / Malonate decarboxylase subunit beta / ...Biotin-independent malonate decarboxylase subunit beta / Malonate decarboxylase subunit beta / Malonyl-S-ACP:biotin-protein carboxyltransferase MADC / Methylmalonyl-CoA carboxyltransferase 12S subunit


Mass: 30465.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: madC, mdcD, AO964_31600, AOY09_06294, BH593_13640, PAERUG_E15_London_28_01_14_07061, PAERUG_P32_London_17_VIM_2_10_11_04127, PAMH19_0209
Production host: Escherichia coli (E. coli)
References: UniProt: A0A071KS24, UniProt: Q9I6S7*PLUS, malonyl-S-ACP:biotin-protein carboxyltransferase, methylmalonyl-CoA carboxytransferase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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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: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.1 M Bis-Tris (pH 5.8), 18% (w/v) PEG 3350, and 0.2 M ammonium acetate
PH range: 5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2014 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 90024 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 12.7
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.5 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.857→45.937 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.17 / Phase error: 20.42 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2075 2012 2.28 %
Rwork0.1806 --
obs0.1813 88297 93.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.857→45.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7477 0 0 216 7693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087596
X-RAY DIFFRACTIONf_angle_d1.0510313
X-RAY DIFFRACTIONf_dihedral_angle_d12.7142772
X-RAY DIFFRACTIONf_chiral_restr0.0451166
X-RAY DIFFRACTIONf_plane_restr0.0051384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8567-1.90310.24991260.22515371X-RAY DIFFRACTION82
1.9031-1.95460.27731330.21825765X-RAY DIFFRACTION88
1.9546-2.01210.24291450.20635856X-RAY DIFFRACTION89
2.0121-2.0770.22821320.19495944X-RAY DIFFRACTION90
2.077-2.15130.19211370.18376006X-RAY DIFFRACTION92
2.1513-2.23740.22591340.1776116X-RAY DIFFRACTION93
2.2374-2.33920.19861440.1736227X-RAY DIFFRACTION94
2.3392-2.46260.19721620.17446280X-RAY DIFFRACTION96
2.4626-2.61680.21531450.18336371X-RAY DIFFRACTION97
2.6168-2.81880.21011520.18296421X-RAY DIFFRACTION98
2.8188-3.10250.20281540.19186436X-RAY DIFFRACTION98
3.1025-3.55130.21291470.18596501X-RAY DIFFRACTION99
3.5513-4.47360.20131560.16356474X-RAY DIFFRACTION99
4.4736-45.9510.18311450.16996517X-RAY DIFFRACTION99

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