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- PDB-2cgh: crystal structure of biotin ligase from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 2cgh
Titlecrystal structure of biotin ligase from Mycobacterium tuberculosis
ComponentsBIOTIN LIGASE
KeywordsLIGASE / BIOTIN LIGASE / MYCOBACTERIUM TUBERCULOSIS
Function / homology
Function and homology information


: / biotin-[biotin carboxyl-carrier protein] ligase / biotin--[biotin carboxyl-carrier protein] ligase activity / small molecule binding / post-translational protein modification
Similarity search - Function
Biotin protein ligase, C-terminal / Biotin protein ligase C terminal domain / Biotin--acetyl-CoA-carboxylase ligase / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / 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. ...Biotin protein ligase, C-terminal / Biotin protein ligase C terminal domain / Biotin--acetyl-CoA-carboxylase ligase / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / 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
biotin--[biotin carboxyl-carrier protein] ligase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMa, Q. / Wilmanns, M.
CitationJournal: Protein Sci. / Year: 2014
Title: Active Site Conformational Changes Upon Reaction Intermediate Biotinyl-5'-AMP Binding in Biotin Protein Ligase from Mycobacterium Tuberculosis.
Authors: Ma, Q. / Akhter, Y. / Wilmanns, M. / Ehebauer, M.T.
History
DepositionMar 6, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 23, 2014Group: Database references / Derived calculations / Structure summary
Revision 1.3Jul 2, 2014Group: Database references
Revision 1.4Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.6Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.7Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BIOTIN LIGASE
B: BIOTIN LIGASE


Theoretical massNumber of molelcules
Total (without water)56,5022
Polymers56,5022
Non-polymers00
Water6,161342
1
A: BIOTIN LIGASE


Theoretical massNumber of molelcules
Total (without water)28,2511
Polymers28,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BIOTIN LIGASE


Theoretical massNumber of molelcules
Total (without water)28,2511
Polymers28,2511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.099, 81.007, 101.881
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BIOTIN LIGASE


Mass: 28251.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLySS
References: UniProt: P96884, biotin-[biotin carboxyl-carrier protein] ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsOWING TO PLASMID CONSTRUCTION, THE SECOND AMINO ACID IS CHANGED FROM THR TO ALA. AND GLY AND ALA ...OWING TO PLASMID CONSTRUCTION, THE SECOND AMINO ACID IS CHANGED FROM THR TO ALA. AND GLY AND ALA ARE ADDED TO THE N-TERMINAL OF THE PROTEIN.

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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: 2.3 Å3/Da / Density % sol: 45.4 %
Crystal growpH: 8.5
Details: 0.1M TRIS HCL PH8.5, 0.2M TRIMETHYLAMINE N-OXIDE, 20%(W/V) MPEG 2000, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9364
DetectorType: MARRESEARCH / Detector: CCD / Date: May 9, 2005 / Details: MIRROR
RadiationMonochromator: FOCUSING DOUBLE SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9364 Å / Relative weight: 1
ReflectionResolution: 1.8→39.38 Å / Num. obs: 48344 / % possible obs: 99.8 % / Redundancy: 16 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 36.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
CaspRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HXD

1hxd


Resolution: 1.8→39.37 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.069 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES WITH CLEAR ELECTRON DENSITY ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2326 4.8 %THIN SHELLS
Rwork0.185 ---
obs0.187 45951 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2--1.48 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3503 0 0 342 3845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223571
X-RAY DIFFRACTIONr_bond_other_d0.0010.023515
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.9724874
X-RAY DIFFRACTIONr_angle_other_deg0.90338047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.8365474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37723.05141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00515557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4921540
X-RAY DIFFRACTIONr_chiral_restr0.1070.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024026
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02688
X-RAY DIFFRACTIONr_nbd_refined0.2170.2671
X-RAY DIFFRACTIONr_nbd_other0.1970.23539
X-RAY DIFFRACTIONr_nbtor_refined0.170.21742
X-RAY DIFFRACTIONr_nbtor_other0.0870.22395
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2267
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3340.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1781.52525
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65923784
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5931287
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9374.51090
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.226 3532
Rfree-0
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.24340.09480.29761.8146-1.02583.50450.08740.071-0.0673-0.246-0.134-0.11460.24850.21730.0465-0.06370.0618-0.0099-0.07310.0197-0.08338.281371.888214.0874
22.31190.4551.13963.4396-2.09342.3949-0.070.2459-0.1021-0.26960.06040.05570.061-0.0890.0096-0.0192-0.0284-0.0072-0.0576-0.0151-0.077632.618355.123832.2716
32.08850.1076-0.55630.9064-0.36952.2059-0.0948-0.4103-0.15640.03920.02420.09350.1460.18620.0706-0.08630.040.0095-0.01790.033-0.058841.150155.611364.9394
41.32080.60740.51432.51210.08473.2685-0.13120.137-0.14140.02270.0403-0.1464-0.00590.07950.0909-0.01820.0120.0067-0.0807-0.0235-0.028642.254950.010541.1266
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 218
2X-RAY DIFFRACTION2A219 - 265
3X-RAY DIFFRACTION3B8 - 218
4X-RAY DIFFRACTION4B219 - 265

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