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- PDB-1xnv: Acyl-CoA Carboxylase Beta Subunit from S. coelicolor (PccB), apo ... -

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Basic information

Entry
Database: PDB / ID: 1xnv
TitleAcyl-CoA Carboxylase Beta Subunit from S. coelicolor (PccB), apo form #1
Componentspropionyl-CoA carboxylase complex B subunit
KeywordsLIGASE / polyketide / polyketide synthase / acyl-CoA carboxylase / carboxyltransferase
Function / homology
Function and homology information


acetyl-CoA carboxylase complex / acetyl-CoA carboxylase activity / fatty acid biosynthetic process
Similarity search - Function
Acetyl-CoA carboxylase carboxyl transferase, beta subunit / 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 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Acetyl-CoA carboxylase carboxyl transferase, beta subunit / 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 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Propionyl-CoA carboxylase complex B subunit
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDiacovich, L. / Mitchell, D.L. / Pham, H. / Gago, G. / Melgar, M.M. / Khosla, C. / Gramajo, H. / Tsai, S.-C.
CitationJournal: Biochemistry / Year: 2004
Title: Crystal Structure of the beta-Subunit of Acyl-CoA Carboxylase: Structure-Based Engineering of Substrate Specificity
Authors: Diacovich, L. / Mitchell, D.L. / Pham, H. / Gago, G. / Melgar, M.M. / Khosla, C. / Gramajo, H. / Tsai, S.-C.
History
DepositionOct 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: propionyl-CoA carboxylase complex B subunit
B: propionyl-CoA carboxylase complex B subunit


Theoretical massNumber of molelcules
Total (without water)114,4482
Polymers114,4482
Non-polymers00
Water12,719706
1
A: propionyl-CoA carboxylase complex B subunit
B: propionyl-CoA carboxylase complex B subunit

A: propionyl-CoA carboxylase complex B subunit
B: propionyl-CoA carboxylase complex B subunit

A: propionyl-CoA carboxylase complex B subunit
B: propionyl-CoA carboxylase complex B subunit


Theoretical massNumber of molelcules
Total (without water)343,3456
Polymers343,3456
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area44690 Å2
ΔGint-227 kcal/mol
Surface area97750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)166.942, 166.942, 80.494
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Cell settinghexagonal
Space group name H-MP63
DetailsTwo monomers asymmetric unit that are related with the other four monomers by the 3-fold axis. In vivo this enzyme is a hexamer

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Components

#1: Protein propionyl-CoA carboxylase complex B subunit / E.C.6.4.1.3 / PCCase / Propanoyl- CoA:carbon dioxide ligase / PCC


Mass: 57224.164 Da / Num. of mol.: 2 / Fragment: B subunit
Source method: isolated from a genetically manipulated source
Details: apo form / Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3 / Plasmid: pET28c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9X4K7, propionyl-CoA carboxylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 706 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.4 M sodium citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 9, 2003 / Details: mirror
RadiationMonochromator: si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40.25 Å / Num. all: 111570 / Num. obs: 111570 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 22.6 Å2 / Rsym value: 0.13 / Net I/σ(I): 19
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.89 % / Mean I/σ(I) obs: 3.43 / Num. unique all: 2635 / Rsym value: 0.491 / % possible all: 93.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model of PccB

Resolution: 2.3→40.25 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 135118.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2728 5.1 %RANDOM
Rwork0.189 ---
all0.1891 53953 --
obs0.1891 53953 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.6117 Å2 / ksol: 0.345252 e/Å3
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1--12.38 Å2-4.58 Å20 Å2
2---12.38 Å20 Å2
3---24.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.3→40.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7905 0 0 706 8611
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d1.03
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 391 4.8 %
Rwork0.255 7798 -
obs--86.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3BIOTIN.PARBIOTIN.TOP
X-RAY DIFFRACTION4PCA3.PARPCA3.TOP

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