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- PDB-1dv1: STRUCTURE OF BIOTIN CARBOXYLASE (APO) -

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Basic information

Entry
Database: PDB / ID: 1dv1
TitleSTRUCTURE OF BIOTIN CARBOXYLASE (APO)
ComponentsBIOTIN CARBOXYLASE
KeywordsLIGASE / ATP-grasp / carboxylase / biotin-dependent
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
PHOSPHATE ION / Biotin carboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsThoden, J.B. / Blanchard, C.Z. / Holden, H.M. / Waldrop, G.L.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Movement of the biotin carboxylase B-domain as a result of ATP binding.
Authors: Thoden, J.B. / Blanchard, C.Z. / Holden, H.M. / Waldrop, G.L.
History
DepositionJan 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: BIOTIN CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9634
Polymers98,7732
Non-polymers1902
Water9,800544
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.700, 95.800, 180.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailshe biological assembly is a homodimer constructed from chain A and chain B

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Components

#1: Protein BIOTIN CARBOXYLASE /


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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 9

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 298 K / Method: microdialysis / pH: 7
Details: 10mM potassium phosphate 1mM EDTA 2mM DTT, pH 7.0, MICRODIALYSIS, temperature 298.0K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein11
210 mMpotassium phosphate12
31 mMEDTA12
42 mMdithiothreitol12
51 mM12NaN3

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 78489 / Num. obs: 78489 / % possible obs: 92.1 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.7
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.219 / Num. unique all: 7871 / % possible all: 71.9
Reflection
*PLUS
Num. measured all: 235595
Reflection shell
*PLUS
% possible obs: 71.9 % / Num. unique obs: 7871 / Num. measured obs: 11472 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
FRAMBOdata collection
SAINTdata scaling
RefinementResolution: 1.9→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 7850 10 %RANDOM
Rwork0.18 ---
all0.182 78489 --
obs0.182 78489 92.1 %-
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6624 0 10 544 7178
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.38
X-RAY DIFFRACTIONt_bond_d0.014
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.5
X-RAY DIFFRACTIONt_plane_restr0.013

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