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- PDB-2ejf: Crystal Structure Of The Biotin Protein Ligase (Mutations R48A an... -

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Basic information

Entry
Database: PDB / ID: 2ejf
TitleCrystal Structure Of The Biotin Protein Ligase (Mutations R48A and K111A) and Biotin Carboxyl Carrier Protein Complex From Pyrococcus Horikoshii OT3
Components
  • 149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain
  • 235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase
KeywordsLIGASE / Biotinylation / 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 / Biotin-binding site / Biotin-requiring enzymes attachment site. ...: / 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 / Biotin-binding site / Biotin-requiring enzymes attachment site. / SH3 type barrels. - #100 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / 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. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / BIOTIN / 235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase / 149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionMar 16, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase
B: 235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase
C: 149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain
D: 149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,24910
Polymers67,8904
Non-polymers1,3606
Water7,368409
1
A: 235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase
C: 149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7015
Polymers33,9452
Non-polymers7563
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase
D: 149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5485
Polymers33,9452
Non-polymers6043
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.849, 63.117, 75.636
Angle α, β, γ (deg.)90.00, 95.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein 235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase / BPL


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: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3)RIL / References: UniProt: O57883
#2: Protein 149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain / BCCP


Mass: 7985.457 Da / Num. of mol.: 2 / Fragment: residues 77-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: bccp / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3)RIL / References: UniProt: O59021

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Non-polymers , 4 types, 415 molecules

#3: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N2O3S
#4: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.96
Details: 10.5w/v(%) PEG 20000, 0.1M Acet, NaOH, pH 4.96, 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: Dec 12, 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: 2→37.62 Å / Num. obs: 42136 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.071 / Net I/σ(I): 8.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3935 / Rsym value: 0.298 / % possible all: 90

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2E64 AND 2D5D

2e64

2d5d


Resolution: 2→37.62 Å / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2090 -RANDOM
Rwork0.209 ---
obs0.209 42136 95.6 %-
all-44059 --
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.33 Å20 Å2-1.82 Å2
2---3.13 Å20 Å2
3----0.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→37.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4631 0 91 409 5131
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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