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- PDB-2dz9: Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horiko... -

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Basic information

Entry
Database: PDB / ID: 2dz9
TitleCrystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii Complexed with biotinyl-5'-AMP, 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
BIOTINYL-5-AMP / 235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.84 Å
AuthorsBagautdinov, B. / Matsuura, Y. / 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. / Matsuura, Y. / Kunishima, N.
History
DepositionSep 26, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 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 / 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)53,2664
Polymers52,1192
Non-polymers1,1472
Water8,161453
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-18 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.082, 82.560, 72.240
Angle α, β, γ (deg.)90.00, 100.44, 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: birA / 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-BT5 / BIOTINYL-5-AMP


Type: RNA linking / Mass: 573.517 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28N7O9PS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.14 Å3/Da / Density % sol: 42.58 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.2
Details: PEG20K, Acetate, NaOH, ATP, Biotin, pH 5.2, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 23, 2006 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. all: 38110 / Num. obs: 37434 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.057 / Net I/σ(I): 14.3
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3364 / Rsym value: 0.369 / % possible all: 93.3

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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: PDB ENTRY 2DXT

2dxt


Resolution: 1.84→28.48 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1849 -RANDOM
Rwork0.192 ---
all0.192 38110 --
obs0.192 37434 98.2 %-
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å23.07 Å2
2---8.84 Å20 Å2
3---9.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.84→28.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 76 453 4197
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 1.84→1.91 Å / Rfactor Rfree error: 0.024
RfactorNum. reflection% reflection
Rfree0.313 167 -
Rwork0.287 --
obs-3531 92.2 %

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