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- PDB-3rv4: Crystal structure of E.coli biotin carboxylase R16E mutant in com... -

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Basic information

Entry
Database: PDB / ID: 3rv4
TitleCrystal structure of E.coli biotin carboxylase R16E mutant in complex with Mg-ADP and bicarbonate
ComponentsBiotin carboxylase
KeywordsLIGASE
Function / homology
Function and homology information


biotin carboxylase / biotin carboxylase activity / acetyl-CoA carboxylase complex / 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 / biotin carboxylase activity / acetyl-CoA carboxylase complex / 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 / 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, A domain / 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
ADENOSINE-5'-DIPHOSPHATE / BICARBONATE ION / : / METHANOL / Biotin carboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsChou, C.Y. / Tong, L.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and biochemical studies on the regulation of biotin carboxylase by substrate inhibition and dimerization.
Authors: Chou, C.Y. / Tong, L.
History
DepositionMay 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,52711
Polymers49,6411
Non-polymers88610
Water6,575365
1
A: Biotin carboxylase
hetero molecules

A: Biotin carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,05522
Polymers99,2822
Non-polymers1,77320
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7180 Å2
ΔGint-209 kcal/mol
Surface area32970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.404, 51.171, 84.156
Angle α, β, γ (deg.)90.000, 119.750, 90.000
Int Tables number5
Space group name H-MC121
DetailsAUTHORS STATE THAT SOLUTION LIGHT SCATTERING AND AUC EXPERIMENTS INDICATED THE PROTEIN IS DIMERIC.

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 49640.848 Da / Num. of mol.: 1 / Mutation: R16E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: accC, fabG, b3256, JW3224 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P24182, biotin carboxylase, acetyl-CoA carboxylase

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Non-polymers , 9 types, 375 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cs
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-MOH / METHANOL / Methanol


Mass: 32.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG3350, CsCl, methanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 29337 / % possible obs: 94.3 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.075 / Χ2: 0.893 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.663.60.36244630.855176.1
1.66-1.724.50.30849630.884185.6
1.72-1.84.80.25152190.853189.3
1.8-1.94.60.22155000.858194.1
1.9-2.025.50.20657260.869198.4
2.02-2.175.50.15558080.985199.4
2.17-2.395.60.12158540.889199.9
2.39-2.745.70.09458740.9731100
2.74-3.455.70.0759130.9531100
3.45-305.60.03859990.767199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.2252 / WRfactor Rwork: 0.1838 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8459 / SU B: 4.173 / SU ML: 0.118 / SU R Cruickshank DPI: 0.203 / SU Rfree: 0.1666 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 1473 5 %RANDOM
Rwork0.1786 ---
obs0.1807 29337 95.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.43 Å2 / Biso mean: 21.3976 Å2 / Biso min: 6.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20.72 Å2
2---0.33 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.98→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3431 0 45 365 3841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223532
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.9774769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2245445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72323.758157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9515612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9431528
X-RAY DIFFRACTIONr_chiral_restr0.0810.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022667
X-RAY DIFFRACTIONr_nbd_refined0.1990.21725
X-RAY DIFFRACTIONr_nbtor_refined0.30.22417
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2309
X-RAY DIFFRACTIONr_metal_ion_refined0.4030.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.221
X-RAY DIFFRACTIONr_mcbond_it0.5581.52210
X-RAY DIFFRACTIONr_mcangle_it1.07323542
X-RAY DIFFRACTIONr_scbond_it1.86631322
X-RAY DIFFRACTIONr_scangle_it3.1944.51227
LS refinement shellResolution: 1.98→2.09 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.268 183 -
Rwork0.211 3853 -
all-4036 -
obs--90.59 %

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