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- PDB-3rir: Crystal Strucrture of Biotin Protein Ligase from S. aureus -

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Basic information

Entry
Database: PDB / ID: 3rir
TitleCrystal Strucrture of Biotin Protein Ligase from S. aureus
ComponentsBiotin-[acetyl-CoA-carboxylase] ligase
KeywordsLIGASE / Biotin protein ligase / Transcriptional repression / BCCP and DNA
Function / homology
Function and homology information


SH3 type barrels. - #100 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / SH3 type barrels. / Arc Repressor Mutant, subunit A / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta ...SH3 type barrels. - #100 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / SH3 type barrels. / Arc Repressor Mutant, subunit A / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWilce, M.C.J.
CitationJournal: To be published
Title: Crystal Strucrture of Biotin Protein Ligase from S. aureus
Authors: Pendini, N. / Yap, M. / Polyak, S. / Cowieson, N. / Daouda, T. / Booker, G. / Wallace, J. / Wilce, M.C.J.
History
DepositionApr 14, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Biotin-[acetyl-CoA-carboxylase] ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7602
Polymers37,1871
Non-polymers5741
Water54030
1
A: Biotin-[acetyl-CoA-carboxylase] ligase
hetero molecules

A: Biotin-[acetyl-CoA-carboxylase] ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5214
Polymers74,3742
Non-polymers1,1472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area2000 Å2
ΔGint-11 kcal/mol
Surface area28490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.564, 93.564, 130.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Biotin-[acetyl-CoA-carboxylase] ligase


Mass: 37186.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: ECT-R 2 / Gene: ECTR2_1310 / Production host: Escherichia coli (E. coli)
References: UniProt: E5R5T0, biotin-[biotin carboxyl-carrier protein] ligase
#2: Chemical ChemComp-BT5 / BIOTINYL-5-AMP


Type: RNA linking / Mass: 573.517 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28N7O9PS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.85 Å3/Da / Density % sol: 68.04 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→35 Å / Num. obs: 18098 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 35.2 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 7.1

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WQ7

1wq7


Resolution: 2.6→19.925 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2852 920 5.08 %RANDOM
Rwork0.2053 ---
all0.2088 ---
obs0.2091 17599 98.25 %-
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.863 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 35.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.0346 Å20 Å2-0 Å2
2--3.0346 Å20 Å2
3----6.0691 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2602 0 38 30 2670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0212694
X-RAY DIFFRACTIONf_angle_d1.9973639
X-RAY DIFFRACTIONf_dihedral_angle_d23.8061029
X-RAY DIFFRACTIONf_chiral_restr0.103395
X-RAY DIFFRACTIONf_plane_restr0.016465
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6002-2.73690.40991250.3393232695
2.7369-2.90790.35141240.2695240998
2.9079-3.13170.29631440.2297242599
3.1317-3.44540.30581280.2166245699
3.4454-3.94060.32691440.2136245799
3.9406-4.95210.2531180.15752532100
4.9521-19.92520.23411370.1946257397
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)
10.0964-0.0226-0.10320.12890.13370.425-0.0326-0.02330.3232-0.02070.0461-0.4573-0.072-0.4919-0.06930.26010.14260.07630.43610.0930.423424.442324.433246.354
21.53510.5966-0.60081.72150.22281.3270.08010.0824-0.0129-0.02620.20130.0754-0.1012-0.1643-0.20980.11410.04420.04680.24270.0780.187540.742917.290221.4038
31.2455-0.0909-0.61620.8271-0.8661.45970.42180.32220.1199-0.2997-0.0844-0.1801-0.4802-0.3469-0.2330.5573-0.04360.00420.47430.02840.326850.029718.17310.6827
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1RESSEQ 2:62
2X-RAY DIFFRACTION2RESSEQ 69:261
3X-RAY DIFFRACTION3RESSEQ 264:323

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