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- PDB-2gpw: Crystal Structure of the Biotin Carboxylase Subunit, F363A Mutant... -

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Basic information

Entry
Database: PDB / ID: 2gpw
TitleCrystal Structure of the Biotin Carboxylase Subunit, F363A Mutant, of Acetyl-CoA Carboxylase from Escherichia coli.
ComponentsBiotin carboxylase
KeywordsLIGASE / ATP-grasp / carboxylase / biotin-dependent / fatty acid synthesis / dimer-interface mutant
Function / homology
Function and homology information


biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / negative regulation of fatty acid biosynthetic process / fatty acid biosynthetic process / protein homodimerization activity / ATP binding / metal ion binding ...biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / negative regulation of fatty acid biosynthetic process / fatty acid biosynthetic process / protein homodimerization activity / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Acetyl-CoA carboxylase, biotin carboxylase / 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. ...Acetyl-CoA carboxylase, biotin carboxylase / 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 / ATP-grasp fold, A domain / Rudiment single hybrid motif / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Carbamoyl-phosphate synthase subdomain signature 2. / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsShen, Y. / Chou, C.Y. / Chang, G.G. / Tong, L.
CitationJournal: Mol.Cell / Year: 2006
Title: Is dimerization required for the catalytic activity of bacterial biotin carboxylase?
Authors: Shen, Y. / Chou, C.Y. / Chang, G.G. / Tong, L.
History
DepositionApr 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300 BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ... BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). ACCORDING TO AUTHORS, THE F363A MUTANT DISPLAYS EQUILIBRIUM BETWEEN THE MONOMER AND THE DIMER. IT IS A MONOMER IN SOLUTION IN GEL-FILTRATION AND LIGHT SCATTERING ASSAYS. HOWEVER, AT HIGHER CONCENTRATION, THIS MUTANT FORMS A DIMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Biotin carboxylase
B: Biotin carboxylase
C: Biotin carboxylase
D: Biotin carboxylase


Theoretical massNumber of molelcules
Total (without water)205,9284
Polymers205,9284
Non-polymers00
Water19,2941071
1
A: Biotin carboxylase


Theoretical massNumber of molelcules
Total (without water)51,4821
Polymers51,4821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Biotin carboxylase


Theoretical massNumber of molelcules
Total (without water)51,4821
Polymers51,4821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Biotin carboxylase


Theoretical massNumber of molelcules
Total (without water)51,4821
Polymers51,4821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Biotin carboxylase


Theoretical massNumber of molelcules
Total (without water)51,4821
Polymers51,4821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.351, 81.499, 176.649
Angle α, β, γ (deg.)90.00, 97.69, 90.00
Int Tables number4
Space group name H-MP1211
DetailsMolecule A and B form a biological dimer. Molecule C and D form a biological dimer.

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Components

#1: Protein
Biotin carboxylase / A subunit of acetyl-CoA carboxylase


Mass: 51481.922 Da / Num. of mol.: 4 / Mutation: F363A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: accC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/DE3 Rosetta / References: UniProt: P24182, biotin carboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1071 / 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: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M Bis-Tris (pH 7.5), 100 mM NaCl, 200 mM trimethylamine N-oxide, 8% (v/v) PEG2000 MME, 4% (v/v) glycerol, 5 mM magnesium chloride, and 2.5 mM DTT, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0999 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 91116 / Num. obs: 80638 / % possible obs: 88.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.5113
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 4.454 / Num. unique all: 6858 / % possible all: 75.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DV1

1dv1


Resolution: 2.2→29.75 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 237505.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.25 5892 7.5 %RANDOM
Rwork0.192 ---
obs0.192 78337 87.8 %-
all-84229 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.0061 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso mean: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1--5.4 Å20 Å20.92 Å2
2--4.2 Å20 Å2
3---1.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13731 0 0 1071 14802
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.012.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.302 510 7.9 %
Rwork0.221 5981 -
obs-5981 73.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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