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- PDB-2e65: Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horiko... -

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Basic information

Entry
Database: PDB / ID: 2.0E+65
TitleCrystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii OT3, Mutation D104A
Componentsbiotin--[acetyl-CoA-carboxylase] ligase
KeywordsLIGASE / Biotin Biosynthesis / Dimer / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


biotin--[biotin carboxyl-carrier protein] ligase activity / protein modification process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Biotin protein ligase, C-terminal / Biotin protein ligase C terminal domain / Biotin--acetyl-CoA-carboxylase ligase / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile. / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / Transcriptional repressor, C-terminal / SH3 type barrels. - #100 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 ...Biotin protein ligase, C-terminal / Biotin protein ligase C terminal domain / Biotin--acetyl-CoA-carboxylase ligase / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile. / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / Transcriptional repressor, C-terminal / SH3 type barrels. - #100 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / SH3 type barrels. / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 Å
AuthorsBagautdinov, B. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Ligand Structures Of Biotin Protein Ligase From Pyrococcus Horikoshii Ot3
Authors: Bagautdinov, B. / Kunishima, N.
History
DepositionDec 25, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: biotin--[acetyl-CoA-carboxylase] ligase
B: biotin--[acetyl-CoA-carboxylase] ligase


Theoretical massNumber of molelcules
Total (without water)52,1192
Polymers52,1192
Non-polymers00
Water9,116506
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-10 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.365, 82.596, 72.579
Angle α, β, γ (deg.)90.00, 102.96, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a dimer and identical to the asymmetric unit

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Components

#1: Protein biotin--[acetyl-CoA-carboxylase] ligase / Biotin Protein Ligase


Mass: 26059.514 Da / Num. of mol.: 2 / Mutation: D104A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: bpl / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3)RIL
References: UniProt: O57883, biotin-[biotin carboxyl-carrier protein] ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.2
Details: PEG20K, Acetate, NaOH, pH 5.2, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 25, 2006 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→41.3 Å / Num. all: 52629 / Num. obs: 50943 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.058 / Net I/σ(I): 12.5
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4713 / Rsym value: 0.258 / % possible all: 90.7

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2DXT

2dxt


Resolution: 1.65→36.62 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2541 -RANDOM
Rwork0.2 ---
obs0.2 50943 96.6 %-
all-52629 --
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å21.73 Å2
2---6.67 Å20 Å2
3---5.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.65→36.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3499 0 0 506 4005
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 1.65→1.71 Å / Rfactor Rfree error: 0.021
RfactorNum. reflection% reflection
Rfree0.316 237 -
Rwork0.295 --
obs-4572 87.5 %

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