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- PDB-5vit: Crystal structure of a Pseudomonas malonate decarboxylase hetero-... -

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Basic information

Entry
Database: PDB / ID: 5vit
TitleCrystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer in complex with malonate
Components
  • MdcA
  • MdcC
  • MdcD
  • MdcE
KeywordsTRANSFERASE / acyl carrier protein / acetyl-CoA carboxylase
Function / homology
Function and homology information


malonyl-S-ACP:biotin-protein carboxyltransferase / biotin-independent malonate decarboxylase / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / carboxy-lyase activity / acyl carrier activity / fatty acid biosynthetic process / transferase activity / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Malonate decarboxylase delta subunit / Malonate decarboxylase/citrate lyase acyl carrier protein / Malonate decarboxylase delta subunit (MdcD) / Acetyl-S-ACP:malonate ACP transferase / Biotin-dependent malonate decarboxylase, gamma subunit / Biotin-independent malonate decarboxylase, beta subunit / Malonate decarboxylase gamma subunit / Malonate decarboxylase, alpha subunit, transporter / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. ...Malonate decarboxylase delta subunit / Malonate decarboxylase/citrate lyase acyl carrier protein / Malonate decarboxylase delta subunit (MdcD) / Acetyl-S-ACP:malonate ACP transferase / Biotin-dependent malonate decarboxylase, gamma subunit / Biotin-independent malonate decarboxylase, beta subunit / Malonate decarboxylase gamma subunit / Malonate decarboxylase, alpha subunit, transporter / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / NagB/RpiA transferase-like / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
MALONATE ION / Biotin-independent malonate decarboxylase subunit beta / Malonyl-S-ACP:biotin-protein carboxyltransferase MADD / Malonate decarboxylase acyl carrier protein / Malonate decarboxylase gamma subunit / Malonate decarboxylase beta subunit / Malonate decarboxylase alpha subunit
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Pseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.203 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
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MdcA
C: MdcC
D: MdcD
E: MdcE
P: MdcA
R: MdcC
S: MdcD
T: MdcE
I: MdcA
K: MdcC
L: MdcD
M: MdcE
V: MdcA
X: MdcC
Y: MdcD
Z: MdcE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)532,07720
Polymers531,66916
Non-polymers4084
Water26,2841459
1
A: MdcA
C: MdcC
D: MdcD
E: MdcE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,0195
Polymers132,9174
Non-polymers1021
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
P: MdcA
R: MdcC
S: MdcD
T: MdcE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,0195
Polymers132,9174
Non-polymers1021
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: MdcA
K: MdcC
L: MdcD
M: MdcE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,0195
Polymers132,9174
Non-polymers1021
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
V: MdcA
X: MdcC
Y: MdcD
Z: MdcE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,0195
Polymers132,9174
Non-polymers1021
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: MdcA
C: MdcC
P: MdcA
R: MdcC
Y: MdcD
Z: MdcE
hetero molecules

L: MdcD
M: MdcE


Theoretical massNumber of molelcules
Total (without water)266,03810
Polymers265,8348
Non-polymers2042
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_566x,y+1,z+11
Buried area30830 Å2
ΔGint-148 kcal/mol
Surface area77170 Å2
MethodPISA
6
I: MdcA
K: MdcC
V: MdcA
X: MdcC
hetero molecules

S: MdcD
T: MdcE

D: MdcD
E: MdcE


Theoretical massNumber of molelcules
Total (without water)266,03810
Polymers265,8348
Non-polymers2042
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation1_545x,y-1,z1
Buried area30770 Å2
ΔGint-142 kcal/mol
Surface area76690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.510, 161.450, 102.720
Angle α, β, γ (deg.)90.80, 93.76, 90.11
Int Tables number1
Space group name H-MP1

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Components

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Protein , 4 types, 16 molecules APIVCRKXDSLYETMZ

#1: Protein
MdcA / Malonate decarboxylase alpha subunit


Mass: 61501.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: mdcA, PA0208 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I6T0
#2: Protein
MdcC / Malonate decarboxylase acyl carrier protein / Malonate decarboxylase subunit delta


Mass: 10692.981 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5) (bacteria)
Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: mdcC, PFL_5818 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4K4F7
#3: 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: 30371.320 Da / Num. of mol.: 4
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
#4: 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: 30351.605 Da / Num. of mol.: 4
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

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Non-polymers , 2 types, 1463 molecules

#5: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1459 / 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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% (w/v) PEG3350 and 8% Tacsimate / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2015 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 294135 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 1.6 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.203→49.043 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2322 14608 4.97 %
Rwork0.1857 --
obs0.188 294062 97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.203→49.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35976 0 28 1459 37463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00936724
X-RAY DIFFRACTIONf_angle_d1.19249852
X-RAY DIFFRACTIONf_dihedral_angle_d15.20813680
X-RAY DIFFRACTIONf_chiral_restr0.0455516
X-RAY DIFFRACTIONf_plane_restr0.0066680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2028-2.22790.33064060.27297801X-RAY DIFFRACTION81
2.2279-2.25410.32364640.26589099X-RAY DIFFRACTION96
2.2541-2.28160.31035310.25449354X-RAY DIFFRACTION96
2.2816-2.31040.31174770.24949255X-RAY DIFFRACTION97
2.3104-2.34080.29184750.24519360X-RAY DIFFRACTION97
2.3408-2.37290.29824720.24459312X-RAY DIFFRACTION97
2.3729-2.40680.29994910.2379380X-RAY DIFFRACTION98
2.4068-2.44270.29295290.2359379X-RAY DIFFRACTION98
2.4427-2.48090.29565170.23299316X-RAY DIFFRACTION98
2.4809-2.52160.28444960.23099434X-RAY DIFFRACTION98
2.5216-2.5650.2955350.22259284X-RAY DIFFRACTION98
2.565-2.61170.27365160.22069350X-RAY DIFFRACTION98
2.6117-2.66190.28984790.21929404X-RAY DIFFRACTION98
2.6619-2.71620.28794820.21479407X-RAY DIFFRACTION98
2.7162-2.77530.26584830.20919453X-RAY DIFFRACTION98
2.7753-2.83980.29534860.21429391X-RAY DIFFRACTION98
2.8398-2.91090.25864830.21799399X-RAY DIFFRACTION98
2.9109-2.98960.2674650.21779421X-RAY DIFFRACTION98
2.9896-3.07750.27934800.21949404X-RAY DIFFRACTION98
3.0775-3.17680.27864840.22159451X-RAY DIFFRACTION98
3.1768-3.29030.25975230.21339397X-RAY DIFFRACTION98
3.2903-3.42210.25254690.20679401X-RAY DIFFRACTION98
3.4221-3.57780.23654960.19189419X-RAY DIFFRACTION98
3.5778-3.76630.22154370.17319447X-RAY DIFFRACTION98
3.7663-4.00220.2074810.15569309X-RAY DIFFRACTION97
4.0022-4.3110.17054840.13639377X-RAY DIFFRACTION97
4.311-4.74450.15344880.12479299X-RAY DIFFRACTION97
4.7445-5.43030.15864880.13129314X-RAY DIFFRACTION97
5.4303-6.83870.17764910.14469458X-RAY DIFFRACTION98
6.8387-49.05480.15885000.12819379X-RAY DIFFRACTION98

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