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- PDB-7dbs: Crystal Structure Of Biotin Protein Ligase From Leishmania Major ... -

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Basic information

Entry
Database: PDB / ID: 7dbs
TitleCrystal Structure Of Biotin Protein Ligase From Leishmania Major in complex with Biotin
ComponentsBiotin/lipoate protein ligase-like protein
KeywordsLIGASE / Biotin protein ligase / Enzyme
Function / homology
Function and homology information


biotin-[biotin carboxyl-carrier protein] ligase / biotin--[biotin carboxyl-carrier protein] ligase activity / cytoplasm
Similarity search - Function
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 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Similarity search - Domain/homology
BIOTIN / Biotin/lipoate protein ligase-like protein
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsRajak, M. / Sundd, M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Leishmania major biotin protein ligase forms a unique cross-handshake dimer.
Authors: Rajak, M.K. / Bhatnagar, S. / Pandey, S. / Kumar, S. / Verma, S. / Patel, A.K. / Sundd, M.
History
DepositionOct 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Biotin/lipoate protein ligase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8042
Polymers30,5601
Non-polymers2441
Water97354
1
A: Biotin/lipoate protein ligase-like protein
hetero molecules

A: Biotin/lipoate protein ligase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6094
Polymers61,1202
Non-polymers4892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area5160 Å2
ΔGint-16 kcal/mol
Surface area22030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.918, 44.700, 54.472
Angle α, β, γ (deg.)90.000, 104.072, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Biotin/lipoate protein ligase-like protein


Mass: 30560.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_31_1070 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q4Q6F6, biotin-[biotin carboxyl-carrier protein] ligase
#2: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 19.5% PEG 3350, 200 mM Ammonium sulfate

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Data collection

DiffractionMean temperature: 277.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979507 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979507 Å / Relative weight: 1
ReflectionResolution: 2.33→52.84 Å / Num. obs: 11509 / % possible obs: 98.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 64.68 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.027 / Net I/σ(I): 13.2
Reflection shellResolution: 2.332→2.372 Å / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 567 / CC1/2: 0.949 / Rpim(I) all: 0.258 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimlessdata scaling
PHENIXphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JHU

6jhu


Resolution: 2.33→52.84 Å / SU ML: 0.3804 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 39.9543
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2416 558 4.87 %
Rwork0.2167 10903 -
obs0.2179 11461 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.59 Å2
Refinement stepCycle: LAST / Resolution: 2.33→52.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 16 56 1885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00261865
X-RAY DIFFRACTIONf_angle_d0.66792542
X-RAY DIFFRACTIONf_chiral_restr0.0457305
X-RAY DIFFRACTIONf_plane_restr0.0043323
X-RAY DIFFRACTIONf_dihedral_angle_d19.7371272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.570.40981470.33872712X-RAY DIFFRACTION99.1
2.57-2.940.32051510.27272756X-RAY DIFFRACTION99.35
2.94-3.70.28471270.25572647X-RAY DIFFRACTION94.71
3.7-52.840.19981330.18382788X-RAY DIFFRACTION97.43
Refinement TLS params.Method: refined / Origin x: 36.135690271 Å / Origin y: 0.685091776768 Å / Origin z: 38.7954802389 Å
111213212223313233
T0.487627570302 Å20.00323023214131 Å2-0.0211671123617 Å2-0.354343109149 Å2-0.00405204601738 Å2--0.475212434607 Å2
L5.27473292097 °20.201153315991 °2-0.780908731581 °2-1.77161155864 °2-0.908675195863 °2--4.28018404069 °2
S-0.0764174123609 Å °0.0402874168852 Å °0.351540234294 Å °0.0170829082367 Å °0.159920198307 Å °0.0245834913603 Å °0.0279293154016 Å °-0.326780866652 Å °-0.0816601671371 Å °
Refinement TLS groupSelection details: all

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