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- PDB-1x01: Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horiko... -

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Basic information

Entry
Database: PDB / ID: 1x01
TitleCrystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii Ot3 in complex with ATP
Componentsbiotin--[acetyl-CoA-carboxylase] ligase
KeywordsLIGASE / Biotin Protein Ligase / Dimer / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses
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
ACETIC ACID / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / 235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsBagautdinov, B. / 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
DepositionMar 11, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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)53,4978
Polymers52,2072
Non-polymers1,2896
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-12 kcal/mol
Surface area20100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.404, 82.828, 72.174
Angle α, β, γ (deg.)90.00, 102.78, 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: 26103.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / 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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 42.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: PEG20K, Acetate, NaOH, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 12, 2004 / 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: 2→40 Å / Num. all: 29087 / Num. obs: 29015 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2837 / % possible all: 94.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CNS1.1refinement
HKL-2000data reduction
CNS1.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1wq7

1wq7


Resolution: 2→32.39 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1457 -RANDOM
Rwork0.195 ---
all-29087 --
obs-29015 97.2 %-
Displacement parametersBiso mean: 35.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2---7.59 Å20 Å2
3---6.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→32.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3674 0 79 337 4090
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2-2.070.31570.2630.024283794.9
2.07-2.150.3161310.2460.028281594.7

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