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- PDB-2e41: Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horiko... -

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Basic information

Entry
Database: PDB / ID: 2.0E+41
TitleCrystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii Complexed with the Reaction Product Analog Biotinol-5'-AMP, Mutations R48A and K111A
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
Chem-BTX / 235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsBagautdinov, B. / Matsuura, Y. / Bagautdinova, S. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate
Authors: Bagautdinov, B. / Matsuura, Y. / Bagautdinova, S. / Kunishima, N.
History
DepositionDec 1, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0384
Polymers51,9192
Non-polymers1,1192
Water9,026501
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-20 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.248, 82.825, 72.711
Angle α, β, γ (deg.)90.00, 101.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 25959.305 Da / Num. of mol.: 2 / Mutation: R48A, K111A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / 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: Chemical ChemComp-BTX / ((2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHYL 5-((3AS,4S,6AR)-2-OXO-HEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL)PENTYL HYDROGEN PHOSPHATE / BIOTINOL-5-AMP


Mass: 559.533 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H30N7O8PS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.2
Details: PEG20K, Acetate, NaOH, biotinol-5'-AMP, 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: Oct 4, 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: 1.75→41.41 Å / Num. all: 44656 / Num. obs: 42972 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 18.16 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.058 / Net I/σ(I): 9.8
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3565 / Rsym value: 0.275 / % possible all: 84.6

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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: 1wqw

1wqw


Resolution: 1.75→37.47 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2122 -RANDOM
Rwork0.183 ---
obs0.183 42972 96.2 %-
all-44656 --
Displacement parametersBiso mean: 21.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å21.62 Å2
2---7.31 Å20 Å2
3---8.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.75→37.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3623 0 74 501 4198
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 1.75→1.81 Å / Rfactor Rfree error: 0.019
RfactorNum. reflection% reflection
Rfree0.281 210 -
Rwork0.287 --
obs-3859 86.5 %

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