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- PDB-1dv2: The structure of biotin carboxylase, mutant E288K, complexed with ATP -

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Basic information

Entry
Database: PDB / ID: 1dv2
TitleThe structure of biotin carboxylase, mutant E288K, complexed with ATP
ComponentsBIOTIN CARBOXYLASE
KeywordsLIGASE / ATP-grasp biotin-dependent carboxylase
Function / homologyBiotin carboxylase, C-terminal / ATP-grasp fold / Biotin carboxylation domain profile. / ATP-grasp fold profile. / Carbamoyl-phosphate synthase subdomain signature 2. / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin carboxylase C-terminal domain / Biotin carboxylase, N-terminal domain / Pre-ATP-grasp domain superfamily ...Biotin carboxylase, C-terminal / ATP-grasp fold / Biotin carboxylation domain profile. / ATP-grasp fold profile. / Carbamoyl-phosphate synthase subdomain signature 2. / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin carboxylase C-terminal domain / Biotin carboxylase, N-terminal domain / Pre-ATP-grasp domain superfamily / ATP-grasp fold, subdomain 1 / Acetyl-CoA carboxylase, biotin carboxylase / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Biotin carboxylase-like, N-terminal domain / Biotin carboxylation domain / Rudiment single hybrid motif / biotin carboxylase / biotin carboxylase activity / acetyl-CoA carboxylase / malonyl-CoA biosynthetic process / negative regulation of fatty acid biosynthetic process / acetyl-CoA carboxylase activity / fatty acid biosynthetic process / ATP binding / metal ion binding / cytosol / cytoplasm / Biotin carboxylase
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / 2.5 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 19, 2000 / Release: Jun 9, 2000
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jun 9, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Oct 4, 2017Structure modelRefinement descriptionsoftware
1.4Mar 14, 2018Structure modelDatabase referencesstruct_ref_seq_dif_struct_ref_seq_dif.details

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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)100,3524
Polyers99,3382
Non-polymers1,0142
Water2,342130
1
A: BIOTIN CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1762
Polyers49,6691
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BIOTIN CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1762
Polyers49,6691
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)81.300, 115.500, 122.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

#1: Protein/peptide BIOTIN CARBOXYLASE /


Mass: 49668.996 Da / Num. of mol.: 2 / Fragment: BIOTIN CARBOXYLASE / Mutation: E288K / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P24182, biotin carboxylase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Formula: H2O / Water

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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: 2.89 / Density percent sol: 57.46 %
Crystal growTemp: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG-8000 ATP magnesium chloride HEPPS potassium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temp: 4 ℃ / pH: 7 / Method: microdialysis
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
110 mg/mlprotein11
210 mMpotassium phosphate12
31 mMEDTA12
42 mMdithiothreitol12
51 mM12NaN3

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Data collection

DiffractionMean temperature: 273 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Collection date: Oct 7, 1999
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 2.5 Å / D resolution low: 3 Å / Number all: 37574 / Number obs: 37574 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.072 / NetI over sigmaI: 9.6 / Redundancy: 2.2 % / Percent possible obs: 92.6
Reflection shellRmerge I obs: 0.297 / Highest resolution: 2.5 Å / Lowest resolution: 2.61 Å / Number unique all: 3543 / Redundancy: 1.3 % / Percent possible all: 73.1
Reflection
*PLUS
Number measured all: 82537
Reflection shell
*PLUS
Number unique obs: 3543 / Number measured obs: 4686 / Percent possible obs: 73.1 / MeanI over sigI obs: 1.9

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Processing

Software
NameVersionClassification
FRAMBOdata collection
SAINTdata reduction
AMoREphasing
TNT5Erefinement
SAINTdata scaling
RefineR Free selection details: RANDOM / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.203 / R factor R work: 0.171 / R factor all: 0.172 / R factor obs: 0.172 / Highest resolution: 2.5 Å / Lowest resolution: 3 Å / Number reflection R free: 3760 / Number reflection all: 37574 / Number reflection obs: 37574 / Percent reflection obs: 92.6
Refine hist #LASTHighest resolution: 2.5 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 6921 / Nucleic acid: 0 / Ligand: 62 / Solvent: 130 / Total: 7113
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.35
X-RAY DIFFRACTIONt_bond_d0.012

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