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- PDB-2v59: CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E.COLI IN COMPLEX WI... -

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Basic information

Entry
Database: PDB / ID: 2v59
TitleCRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E.COLI IN COMPLEX WITH POTENT INHIBITOR 2
ComponentsBIOTIN CARBOXYLASE
KeywordsLIGASE / FATTY ACID BIOSYNTHESIS / BIOTIN CARBOXYLASE / NUCLEOTIDE-BINDING / ATP-BINDING / ANTIBACTERIAL / LIPID SYNTHESIS / FAS / BIOTIN / BACTERIAL / INHIBITOR
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 / : / 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, 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
Chem-LZK / Biotin carboxylase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMochalkin, I. / Miller, J.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: A Class of Selective Antibacterials Derived from a Protein Kinase Inhibitor Pharmacophore.
Authors: Miller, J.R. / Dunham, S. / Mochalkin, I. / Banotai, C. / Bowman, M. / Buist, S. / Dunkle, B. / Hanna, D. / Harwood, H.J. / Huband, M.D. / Karnovsky, A. / Kuhn, M. / Limberakis, C. / Liu, J. ...Authors: Miller, J.R. / Dunham, S. / Mochalkin, I. / Banotai, C. / Bowman, M. / Buist, S. / Dunkle, B. / Hanna, D. / Harwood, H.J. / Huband, M.D. / Karnovsky, A. / Kuhn, M. / Limberakis, C. / Liu, J.Y. / Mehrens, S. / Mueller, W.T. / Narasimhan, L. / Ogden, A. / Ohren, J. / Prasad, J.V. / Shelly, J.A. / Skerlos, L. / Sulavik, M. / Thomas, V.H. / Vanderroest, S. / Wang, L. / Wang, Z. / Whitton, A. / Zhu, T. / Stover, C.K.
History
DepositionOct 2, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)99,3684
Polymers98,7732
Non-polymers5952
Water4,252236
1
A: BIOTIN CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6842
Polymers49,3871
Non-polymers2971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BIOTIN CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6842
Polymers49,3871
Non-polymers2971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)84.190, 106.203, 123.055
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 / 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
#2: Chemical ChemComp-LZK / 6-(2,6-DIMETHOXYPHENYL)PYRIDO[2,3-D]PYRIMIDINE-2,7-DIAMINE


Mass: 297.312 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.75 Å3/Da / Density % sol: 54.99 % / Description: NONE
Crystal growDetails: WELL: 0.1 M POTASSIUM CHLORIDE, 4% (W/V) PEG 8000 PROTEIN: 12 MG/ML, 250 MM POTASSIUM CHLORIDE, 10 MM HEPES, PH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 31, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 40822 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 4.06 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.28
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.38 / % possible all: 71.3

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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 1DV2

1dv2


Resolution: 2.4→80.32 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.903 / SU B: 14.092 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.437 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2055 5 %RANDOM
Rwork0.208 ---
obs0.21 38720 93.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.4→80.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6850 0 44 236 7130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227034
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0231.9729496
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0895889
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45223.631314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.229151225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3291558
X-RAY DIFFRACTIONr_chiral_restr0.070.21037
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025346
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1730.23146
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.24826
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2357
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3581.54567
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.60627079
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.89532829
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5224.52417
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: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.26 115
Rwork0.218 2110
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.58210.13590.10450.47680.14640.4409-0.0097-0.03910.0133-0.01460.00940.0189-0.02050.00730.0002-0.07440.0094-0.0058-0.0811-0.0052-0.023618.7789-19.542424.6026
20.6846-0.32780.29641.04980.02511.1413-0.0333-0.1401-0.0190.110.04790.1378-0.0233-0.2527-0.0146-0.0858-0.01030.0147-0.03720.0143-0.0024-0.0396-0.6987-6.985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 445
2X-RAY DIFFRACTION2B1 - 445

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