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

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Basic information

Entry
Database: PDB / ID: 6ojh
TitleCrystal Structure of Haemophilus Influenzae Biotin Carboxylase Complexed with (R)-7-(3-aminopyrrolidin-1-yl)-6-(naphthalen-1-yl)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 / metal ion binding / ATP binding
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
ACETATE ION / Chem-MV4 / Biotin carboxylase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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: To Be Published
Title: Crystal Structure of Haemophilus Influenzae Biotin Carboxylase Complexed with (R)-7-(3-aminopyrrolidin-1-yl)-6-(naphthalen-1-yl)pyrido[2,3-d]pyrimidin-2-amine
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. / Cohen, F.
History
DepositionApr 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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)51,8024
Polymers51,3471
Non-polymers4563
Water3,081171
1
A: Biotin carboxylase
hetero molecules

A: Biotin carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,6048
Polymers102,6932
Non-polymers9116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)85.688, 85.688, 104.830
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-628-

HOH

21A-753-

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-MV4 / 7-[(3R)-3-aminopyrrolidin-1-yl]-6-(naphthalen-1-yl)pyrido[2,3-d]pyrimidin-2-amine


Mass: 356.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20N6
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2M Ca acetate, 14% PEG3350

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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: 2.05→39.69 Å / Num. obs: 27210 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rpim(I) all: 0.035 / Net I/σ(I): 18.7
Reflection shellResolution: 2.05→2.11 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2045 / Rpim(I) all: 0.532 / % possible all: 97.9

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Processing

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

4rzq


Resolution: 2.05→39.69 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.425 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.175 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22244 1376 5.1 %RANDOM
Rwork0.1756 ---
obs0.17795 25814 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.725 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0.16 Å2-0 Å2
2---0.33 Å20 Å2
3---1.07 Å2
Refinement stepCycle: 1 / Resolution: 2.05→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3413 0 32 171 3616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133541
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173362
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.6574792
X-RAY DIFFRACTIONr_angle_other_deg1.3351.5867802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7675454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89222180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.38415624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3981526
X-RAY DIFFRACTIONr_chiral_restr0.0750.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023997
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02716
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_it0.8281.7981793
X-RAY DIFFRACTIONr_mcbond_other0.8161.7951790
X-RAY DIFFRACTIONr_mcangle_it1.3052.6892242
X-RAY DIFFRACTIONr_mcangle_other1.3012.6892242
X-RAY DIFFRACTIONr_scbond_it1.0741.9631748
X-RAY DIFFRACTIONr_scbond_other1.0741.9651749
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6732.8892547
X-RAY DIFFRACTIONr_long_range_B_refined4.28321.9853924
X-RAY DIFFRACTIONr_long_range_B_other4.28321.9973925
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 76 -
Rwork0.344 1871 -
obs--97.69 %
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)
14.73870.3738-1.24782.3078-3.44919.51220.0231-1.3101-0.79520.61210.19550.1775-0.00990.2292-0.21860.45320.11350.02320.46190.18280.299620.2114-14.7517-1.2148
23.44880.7250.57192.9901-0.52581.8616-0.01230.1148-0.2-0.22190.13930.520.1443-0.1522-0.1270.0618-0.0367-0.05080.08080.03180.130117.6461-4.1899-8.3414
31.9209-0.3516-0.03456.2671-0.36571.3414-0.21390.07060.2182-0.04760.1360.6703-0.4111-0.44820.0780.33490.06630.08220.3589-0.02770.37219.179426.57078.275
47.01041.19623.34714.01490.03112.6216-0.42780.34730.359-0.71850.27640.6126-0.2154-0.39110.15140.4620.01070.02930.3967-0.0090.43496.976126.53111.164
52.31191.1072-0.61913.4618-0.11110.62380.0719-0.3920.29110.43180.07010.2586-0.1091-0.0613-0.14190.13960.0290.03980.1947-0.00710.05326.43158.04359.0178
62.49960.26360.65111.65-0.31861.9874-0.0490.19310.4539-0.18950.0359-0.0685-0.15030.0790.01320.08720.00660.00770.07540.03670.104837.432113.3938-9.4816
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION2A6 - 114
3X-RAY DIFFRACTION3A115 - 178
4X-RAY DIFFRACTION4A179 - 206
5X-RAY DIFFRACTION5A207 - 331
6X-RAY DIFFRACTION6A332 - 445

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