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- PDB-6oi8: Crystal Structure of Haemophilus Influenzae Biotin Carboxylase Co... -

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Basic information

Entry
Database: PDB / ID: 6oi8
TitleCrystal Structure of Haemophilus Influenzae Biotin Carboxylase Complexed with 7-((1R,5S,6s)-6-amino-3-azabicyclo[3.1.0]hexan-3-yl)-6-(2-chloro-6-(pyridin-3-yl)phenyl)pyrido[2,3-d]pyrimidin-2-amine
ComponentsBiotin carboxylase
KeywordsLIGASE / ATP GRASP / CARBOXYLASE / INHIBITOR
Function / homology
Function and homology information


biotin carboxylase / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / fatty acid biosynthetic process / ATP binding / metal ion binding
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 / 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 / Carbamoyl-phosphate synthase subdomain signature 2. / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MQV / Biotin carboxylase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAndrews, L.D. / Kane, T.R. / Dozzo, P. / Haglund, C.M. / Hilderbrandt, D.J. / Linsell, M.S. / Machajewski, T. / McEnroe, G. / Serio, A.W. / Wlasichuk, K.B. ...Andrews, L.D. / Kane, T.R. / Dozzo, P. / Haglund, C.M. / Hilderbrandt, D.J. / Linsell, M.S. / Machajewski, T. / McEnroe, G. / Serio, A.W. / Wlasichuk, K.B. / Neau, D.B. / Pakhomova, S. / Waldrop, G.L. / Sharp, M. / Pogliano, J. / Cirz, R. / Cohen, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI113572 United States
CitationJournal: J.Med.Chem. / Year: 2019
Title: Optimization and Mechanistic Characterization of Pyridopyrimidine Inhibitors of Bacterial Biotin Carboxylase.
Authors: Andrews, L.D. / Kane, T.R. / Dozzo, P. / Haglund, C.M. / Hilderbrandt, D.J. / Linsell, M.S. / Machajewski, T. / McEnroe, G. / Serio, A.W. / Wlasichuk, K.B. / Neau, D.B. / Pakhomova, S. / ...Authors: Andrews, L.D. / Kane, T.R. / Dozzo, P. / Haglund, C.M. / Hilderbrandt, D.J. / Linsell, M.S. / Machajewski, T. / McEnroe, G. / Serio, A.W. / Wlasichuk, K.B. / Neau, D.B. / Pakhomova, S. / Waldrop, G.L. / Sharp, M. / Pogliano, J. / Cirz, R.T. / Cohen, F.
History
DepositionApr 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Biotin carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8393
Polymers51,3471
Non-polymers4922
Water54030
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.321, 86.321, 102.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-630-

HOH

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Components

#1: Protein Biotin carboxylase / / Acetyl-CoA carboxylase subunit A / ACC


Mass: 51346.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: accC, HI_0972 / Production host: Escherichia coli (E. coli)
References: UniProt: P43873, biotin carboxylase, acetyl-CoA carboxylase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MQV / 7-[(1R,5S,6s)-6-amino-3-azabicyclo[3.1.0]hexan-3-yl]-6-[2-chloro-6-(pyridin-3-yl)phenyl]pyrido[2,3-d]pyrimidin-2-amine


Mass: 429.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H20ClN7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2M Na acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2015 / Details: KB mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.5→35.15 Å / Num. obs: 14331 / % possible obs: 96.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 38 Å2 / Rpim(I) all: 0.039 / Net I/σ(I): 20.4
Reflection shellResolution: 2.5→2.62 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1641 / Rpim(I) all: 0.488 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RZQ

4rzq


Resolution: 2.5→35.15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.915 / SU B: 26.121 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R Free: 0.329 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25301 701 4.9 %RANDOM
Rwork0.18571 ---
obs0.18889 13626 94.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å2-0 Å2
2--0.74 Å2-0 Å2
3----2.41 Å2
Refinement stepCycle: 1 / Resolution: 2.5→35.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3380 0 35 30 3445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133479
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173305
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.664705
X-RAY DIFFRACTIONr_angle_other_deg1.161.5867666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8665438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77822.184174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79515607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2521524
X-RAY DIFFRACTIONr_chiral_restr0.0520.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023891
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02691
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1053.6821758
X-RAY DIFFRACTIONr_mcbond_other1.1053.6811756
X-RAY DIFFRACTIONr_mcangle_it1.8655.522194
X-RAY DIFFRACTIONr_mcangle_other1.8655.522194
X-RAY DIFFRACTIONr_scbond_it1.0813.8261721
X-RAY DIFFRACTIONr_scbond_other1.0813.8271722
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8095.6792509
X-RAY DIFFRACTIONr_long_range_B_refined3.23543.1873725
X-RAY DIFFRACTIONr_long_range_B_other3.23543.1873726
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.497→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 46 -
Rwork0.35 773 -
obs--73.32 %
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)
14.1085-1.09890.05032.05680.19521.9158-0.0089-0.1995-0.81160.06280.1250.31590.2582-0.1596-0.11610.1024-0.0249-0.0620.02920.05950.213947.528890.074-3.5732
22.6938-0.24720.3661.8493-0.7152.3141-0.0754-0.26910.05290.13370.21280.3436-0.0738-0.4094-0.13730.02740.03470.01090.11240.0390.093946.1107106.1705-0.8003
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 158
2X-RAY DIFFRACTION2A159 - 445

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