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- PDB-2w6z: Crystal structure of Biotin carboxylase from E. coli in complex w... -

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Basic information

Entry
Database: PDB / ID: 2w6z
TitleCrystal structure of Biotin carboxylase from E. coli in complex with the 3-(3-Methyl-but-2-enyl)-3H-purin-6-ylamine fragment
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 / cytosol / cytoplasm
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 ...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, 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
3-(3-methylbut-2-en-1-yl)-3H-purin-6-amine / Biotin carboxylase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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
B: BIOTIN CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0475
Polymers98,7732
Non-polymers2743
Water9,188510
1
A: BIOTIN CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6253
Polymers49,3871
Non-polymers2392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BIOTIN CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4222
Polymers49,3871
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.482, 106.895, 122.413
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-L21 / 3-(3-methylbut-2-en-1-yl)-3H-purin-6-amine


Mass: 203.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details3-(3-METHYL-BUT-2-ENYL)-3H-PURIN-6-YLAMINE (LIG): INITIAL SCREENING FRAGMENT

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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: 2.66 Å3/Da / Density % sol: 53.39 % / Description: NONE
Crystal growDetails: 0.1M KCL AND 2-8% PEG 800

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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: 1.9→80 Å / Num. obs: 67879 / % possible obs: 77.4 % / Observed criterion σ(I): 0 / Redundancy: 5.82 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.58
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.76 / % possible all: 81.2

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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: 1.9→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.171 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3407 5 %RANDOM
Rwork0.185 ---
obs0.186 64336 77.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2--0.86 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6860 0 17 510 7387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227038
X-RAY DIFFRACTIONr_bond_other_d0.0010.026557
X-RAY DIFFRACTIONr_angle_refined_deg1.1091.9689494
X-RAY DIFFRACTIONr_angle_other_deg1.215315243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9115889
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02323.668319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.363151247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0151559
X-RAY DIFFRACTIONr_chiral_restr0.0870.21038
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027890
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021408
X-RAY DIFFRACTIONr_nbd_refined0.190.21238
X-RAY DIFFRACTIONr_nbd_other0.1780.26366
X-RAY DIFFRACTIONr_nbtor_refined0.1670.23370
X-RAY DIFFRACTIONr_nbtor_other0.0810.24004
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2376
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0830.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7151.55761
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.78427093
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.33233002
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9744.52401
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.226 246
Rwork0.208 4788

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