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- PDB-6oi9: Crystal Structure of E. coli Biotin Carboxylase Complexed with 7-... -

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Basic information

Entry
Database: PDB / ID: 6oi9
TitleCrystal Structure of E. coli Biotin Carboxylase Complexed with 7-[3-(aminomethyl)pyrrolidin-1-yl]-6-(2,6-dichlorophenyl)pyrido[2,3-d]pyrimidin-2-amine
ComponentsBiotin carboxylase
KeywordsLIGASE / ATP GRASP / CARBOXYLASE / BIOTIN CARBOXYL CARRIER PROTEIN AND CARBOXYLTRANSFERASE
Function / homology
Function and homology information


acetyl-CoA carboxylase / 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 ...acetyl-CoA carboxylase / 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 / 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-MQM / Biotin carboxylase / Biotin carboxylase
Similarity search - Component
Biological speciesEscherichia coli UMNK88 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)104,0817
Polymers103,1162
Non-polymers9655
Water7,782432
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.352, 106.782, 122.345
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 1 - 447 / Label seq-ID: 21 - 467

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Biotin carboxylase


Mass: 51558.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli UMNK88 (bacteria) / Gene: accC, UMNK88_4016 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0E0U408, UniProt: P24182*PLUS, biotin carboxylase, acetyl-CoA carboxylase
#2: Chemical ChemComp-MQM / 7-[(3S)-3-(aminomethyl)pyrrolidin-1-yl]-6-(2,6-dichlorophenyl)pyrido[2,3-d]pyrimidin-2-amine


Mass: 389.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18Cl2N6
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 30% PEG1000

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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: 2.06→61.25 Å / Num. obs: 68531 / % possible obs: 99.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.4 Å2 / Rpim(I) all: 0.056 / Net I/σ(I): 12.8
Reflection shellResolution: 2.06→2.11 Å / Redundancy: 3.7 % / Num. unique obs: 4530 / Rpim(I) all: 0.634 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DV1

1dv1


Resolution: 2.06→61.25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.335 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.158 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22292 3382 4.9 %RANDOM
Rwork0.19457 ---
obs0.19594 65059 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å2-0 Å2
2--0.29 Å2-0 Å2
3---0.16 Å2
Refinement stepCycle: 1 / Resolution: 2.06→61.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6868 0 64 432 7364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137137
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176794
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.6569642
X-RAY DIFFRACTIONr_angle_other_deg1.3521.58515732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9321.25384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.425151250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7241563
X-RAY DIFFRACTIONr_chiral_restr0.0680.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028083
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021504
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_it0.6111.4433592
X-RAY DIFFRACTIONr_mcbond_other0.6111.4443593
X-RAY DIFFRACTIONr_mcangle_it1.0322.1614495
X-RAY DIFFRACTIONr_mcangle_other1.0322.1614495
X-RAY DIFFRACTIONr_scbond_it0.8181.5763545
X-RAY DIFFRACTIONr_scbond_other0.8181.5773546
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3212.3175141
X-RAY DIFFRACTIONr_long_range_B_refined3.79917.5737924
X-RAY DIFFRACTIONr_long_range_B_other3.79917.5797925
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14023 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.06→2.114 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 236 -
Rwork0.377 4717 -
obs--98.51 %
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)
12.2370.53240.12270.43850.16810.4333-0.01360.08690.2234-0.08540.00090.0505-0.0477-0.0460.01270.11510.02380.00170.1230.02670.025215.5776130.346316.1404
25.81150.43482.5651.95920.30244.87960.03910.0499-0.4157-0.1156-0.00470.03910.2232-0.0677-0.03440.1226-0.02020.04680.11640.0170.117642.8012134.858814.5416
32.14380.09150.27331.4032-0.88221.03970.011-0.19340.13020.1096-0.0148-0.0659-0.13470.03590.00390.1010.00280.00210.1321-0.00770.020723.2436132.988432.8463
41.10560.47720.46261.60360.34841.47660.00920.1068-0.1633-0.06160.0159-0.21780.13550.2145-0.02510.09980.03160.01310.15080.03230.054124.8283110.969930.1061
51.4743-0.816-0.02472.0042-0.091.553-0.0875-0.270.08040.23920.1027-0.2285-0.08480.2065-0.01520.0923-0.0252-0.00750.1635-0.02370.032536.3735115.2839-1.4753
63.4332-1.5185-2.37415.2103-0.66444.57570.32760.29590.9403-0.3388-0.0518-0.522-0.80910.4145-0.27580.4494-0.0544-0.08660.7079-0.12550.640360.7251114.66924.9972
72.7078-1.4775-0.46091.92210.3962.8877-0.1182-0.2491-0.12680.25610.1117-0.10350.26140.29940.00660.1340.0148-0.01890.14690.00350.034440.522498.4183-2.3558
80.2342-0.1632-0.09163.191-0.75661.09490.00550.02460.0338-0.1518-0.0519-0.43160.07260.27790.04640.07790.00660.02230.1616-0.01790.063445.1899105.4423-23.0256
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 149
2X-RAY DIFFRACTION2A150 - 201
3X-RAY DIFFRACTION3A202 - 331
4X-RAY DIFFRACTION4A332 - 447
5X-RAY DIFFRACTION5B1 - 155
6X-RAY DIFFRACTION6B156 - 199
7X-RAY DIFFRACTION7B200 - 331
8X-RAY DIFFRACTION8B332 - 447

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