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- PDB-2w71: Crystal structure of Biotin carboxylase from E. coli in complex w... -

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Basic information

Entry
Database: PDB / ID: 2w71
TitleCrystal structure of Biotin carboxylase from E. coli in complex with the imidazole-pyrimidine inhibitor
ComponentsBIOTIN CARBOXYLASE
KeywordsLIGASE / ATP-BINDING / FATTY ACID BIOSYNTHESIS / NUCLEOTIDE-BINDING / LIPID SYNTHESIS / ATP-GRASP DOMAIN / FRAGMENT SCREENING
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 / : / Rossmann fold - #20 / 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 ...Acetyl-CoA carboxylase, biotin carboxylase / : / Rossmann fold - #20 / 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 / 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, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold, B domain / 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
Chem-L23 / Biotin carboxylase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsMochalkin, I. / Miller, J.R.
CitationJournal: Acs Chem.Biol. / Year: 2009
Title: Discovery of Antibacterial Biotin Carboxylase Inhibitors by Virtual Screening and Fragment-Based Approaches.
Authors: Mochalkin, I. / Miller, J.R. / Narasimhan, L.S. / Thanabal, V. / Erdman, P. / Cox, P. / Prasad, J.V. / Lightle, S. / Huband, M. / Stover, K.
History
DepositionDec 19, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Data collection / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BIOTIN CARBOXYLASE
C: BIOTIN CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5136
Polymers98,7732
Non-polymers7394
Water12,088671
1
A: BIOTIN CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7563
Polymers49,3871
Non-polymers3702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: BIOTIN CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7563
Polymers49,3871
Non-polymers3702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.664, 113.740, 121.786
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BIOTIN CARBOXYLASE / ACC / ACETYL-COA CARBOXYLASE SUBUNIT A


Mass: 49386.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P24182, biotin carboxylase, acetyl-CoA carboxylase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-L23 / 4-[1-(2,6-dichlorobenzyl)-2-methyl-1H-imidazol-4-yl]pyrimidin-2-amine


Mass: 334.203 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H13Cl2N5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 52.84 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→80 Å / Num. obs: 75853 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 4.47 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.34
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.63 / % possible all: 92.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J9G

2j9g


Resolution: 1.99→83.05 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.373 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3807 5 %RANDOM
Rwork0.194 ---
obs0.195 72012 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.99→83.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6868 0 46 671 7585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227048
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0421.9739515
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9855890
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40623.587315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.701151229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2431559
X-RAY DIFFRACTIONr_chiral_restr0.0720.21038
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025369
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1780.23336
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.24854
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2623
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4861.54584
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82727089
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.35332795
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2544.52426
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.99→2.04 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.308 261
Rwork0.263 5083

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