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- PDB-3efs: Biotin protein ligase from Aquifex aeolicus in complex with bioti... -

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Basic information

Entry
Database: PDB / ID: 3efs
TitleBiotin protein ligase from Aquifex aeolicus in complex with biotin and ATP
ComponentsBiotin [acetyl-CoA-carboxylase] ligase
KeywordsLIGASE / BPL ATP BIOTIN COMPLEX
Function / homology
Function and homology information


biotin-[biotin carboxyl-carrier protein] ligase / biotin--[biotin carboxyl-carrier protein] ligase activity / protein modification process / ATP 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 / 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) ...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 / 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
ADENOSINE-5'-TRIPHOSPHATE / BIOTIN / biotin--[biotin carboxyl-carrier protein] ligase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTron, C.M. / McNae, I.W. / Walkinshaw, M.D. / Baxter, R.L. / Campopiano, D.J.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural and functional studies of the biotin protein ligase from Aquifex aeolicus reveal a critical role for a conserved residue in target specificity.
Authors: Tron, C.M. / McNae, I.W. / Nutley, M. / Clarke, D.J. / Cooper, A. / Walkinshaw, M.D. / Baxter, R.L. / Campopiano, D.J.
History
DepositionSep 10, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _struct_ref_seq_dif.details
Revision 1.3Nov 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_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

Downloads & links

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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)55,2939
Polymers53,5022
Non-polymers1,7917
Water3,369187
1
A: Biotin [acetyl-CoA-carboxylase] ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6955
Polymers26,7511
Non-polymers9444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Biotin [acetyl-CoA-carboxylase] ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5994
Polymers26,7511
Non-polymers8483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.225, 81.695, 143.278
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 [acetyl-CoA-carboxylase] ligase / Biotin Protein Ligase


Mass: 26751.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: O66837, 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-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O3S
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 0.2M Ammonium Sulphate, 15% MPEG 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.284 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 18, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.284 Å / Relative weight: 1
ReflectionResolution: 2.3→39.618 Å / Num. obs: 22163 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 34.13 Å2 / Rsym value: 0.097 / Net I/σ(I): 10.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 3166 / Rsym value: 0.423 / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WPY

1wpy


Resolution: 2.3→39.618 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.38 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.22 / Stereochemistry target values: ML / Details: TLS was used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1135 5.12 %RANDOM'
Rwork0.23 21028 --
obs0.232 21993 99.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.623 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso max: 185.07 Å2 / Biso mean: 44.491 Å2 / Biso min: 10.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20 Å2
2--0.046 Å20 Å2
3---0.574 Å2
Refine analyzeLuzzati sigma a obs: 0.335 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3754 0 109 187 4050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023924
X-RAY DIFFRACTIONf_angle_d0.6885272
X-RAY DIFFRACTIONf_chiral_restr0.037582
X-RAY DIFFRACTIONf_plane_restr0.003642
X-RAY DIFFRACTIONf_dihedral_angle_d13.4141530
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.4050.2931260.2422585271199
2.405-2.5320.3371390.2642566270599
2.532-2.690.3151410.2782567270899
2.69-2.8980.311370.2612600273799
2.898-3.1890.2741570.2522600275799
3.189-3.6510.2291400.20226302770100
3.651-4.5980.2181630.19626592822100
4.598-39.6240.2471320.21428212953100
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)
10.89480.8579-0.63661.2075-0.75552.45740.3005-0.35580.23931.0392-0.34310.18680.42440.29040.17450.4381-0.01030.03280.2067-0.07510.1755-12.4395-5.913130.2869
22.22450.5624-0.12661.6582-0.26982.88810.3585-0.29360.3139-0.102-0.31810.5574-0.53380.1250.18570.32980.0969-0.09740.2327-0.0370.1993-12.0567-2.233124.3709
31.9653-0.7937-1.93921.281.74921.9910.0533-0.28370.1421-0.12790.1663-0.0027-0.28680.0650.39380.09440.0319-0.03180.06510.02630.1443-3.0052-12.342921.109
48.16962.5935-3.35141.8366-1.01451.8544-0.26190.2375-0.5836-0.1947-0.0172-0.25640.3001-0.225-0.18150.14430.0138-0.00530.0979-0.02590.1709-10.3457-17.494613.9857
51.0915-0.553-0.38070.6494-0.44460.71030.15720.1193-0.2812-0.059-0.0808-0.01140.20460.1162-0.05190.14060.03490.02150.1655-0.03370.0911-15.2673-11.927710.986
69.0901-1.45230.21240.89990.17591.35040.3374-0.05411.22910.0425-0.1101-0.125-0.31350.1524-0.09740.1285-0.00110.05710.0723-0.02570.1008-9.0731-7.637122.0202
72.25730.14170.58960.67621.8393.4303-0.1663-0.17790.41170.08140.05630.0173-0.3661-0.6003-0.06720.13370.0650.04170.22060.02890.2727-25.7033-8.251816.6852
81.16350.0256-0.22970.32191.14153.4701-0.0887-0.0136-0.1244-0.14240.2058-0.05120.3422-0.0537-0.00970.39660.07440.02970.1167-0.02730.1556-6.7207-17.37837.2518
90.5985-0.7045-0.4533.0894-4.71699.701-0.3087-0.19920.0978-0.158-0.2033-0.43880.53220.811-0.3680.34190.11710.06470.0974-0.05320.1372-1.5745-14.7058-3.9191
100.8724-1.8071.12414.41752.56113.42670.05420.61660.94170.06860.3777-0.79640.19760.50610.2620.3201-0.0227-0.01460.04060.07950.1814-3.5406-7.8502-0.438
111.6744-0.43690.82840.4272-0.18852.7846-0.25420.2751-0.2748-0.2625-0.04410.3572-0.42150.06210.1450.37340.0795-0.04250.23750.01160.1397-12.86845.4803-29.383
122.2566-0.57080.40561.85770.78773.37340.0607-0.0587-0.1474-0.3927-0.49120.12170.39180.53650.16180.17820.05640.05140.29340.06740.1018-11.5452.2842-23.3806
131.2826-0.8183-3.04291.1957-0.64176.53370.2291-0.4880.2861-0.3061-0.07290.0279-0.85931.1659-0.80880.1188-0.03410.09760.20110.01960.1731-6.810714.5048-21.0905
143.48960.1541.94331.73120.95270.99770.0638-0.618-0.0156-0.38410.11190.0481-0.38480.0932-0.18790.1799-0.08440.04250.1818-0.03160.1249-14.453117.4578-13.2278
151.45940.68880.30261.84060.05051.77440.2917-0.28580.15770.3412-0.1095-0.123-0.09970.1792-0.08170.1506-0.0366-0.04370.1119-0.00780.0984-15.877910.6587-13.0735
162.4220.59020.4781.23522.11854.20460.21310.0415-0.0687-0.2405-0.17480.16090.7258-0.5434-0.05050.1806-0.0394-0.01720.2153-0.01630.1981-26.32415.6349-17.1431
172.168-1.28590.2028-1.35692.13922.99030.25310.05330.8731-0.30530.2634-0.2059-0.7761-0.0087-0.03380.3668-0.05720.04260.20950.02010.2871-12.864623.7964-11.2298
180.7971-0.2896-0.2924-0.2173-0.01871.3675-0.25890.5614-0.3106-0.1555-0.06880.30461.0926-0.468-0.00890.49890.0560.05690.11010.04570.359-9.39118.83025.6589
190.82011.04630.47271.29310.19771.43280.1127-0.1015-0.33880.4491-0.0204-0.5486-0.51990.39-0.02590.1328-0.0363-0.03850.1186-0.06120.1826-7.508418.14534.9732
20-1.6624-0.15440.69582.85891.8376.36410.42880.1157-0.2105-0.27630.5276-0.40630.29090.85270.36770.13660.0701-0.04070.020.02250.3386-7.178410.92441.7369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:18)
2X-RAY DIFFRACTION2(chain A and resid 19:51)
3X-RAY DIFFRACTION3(chain A and resid 52:67)
4X-RAY DIFFRACTION4(chain A and resid 68:81)
5X-RAY DIFFRACTION5(chain A and resid 82:112)
6X-RAY DIFFRACTION6(chain A and resid 113:125)
7X-RAY DIFFRACTION7(chain A and resid 126:157)
8X-RAY DIFFRACTION8(chain A and resid 158:202)
9X-RAY DIFFRACTION9(chain A and resid 203:218)
10X-RAY DIFFRACTION10(chain A and resid 219:233)
11X-RAY DIFFRACTION11(chain B and resid 2:18)
12X-RAY DIFFRACTION12(chain B and resid 19:50)
13X-RAY DIFFRACTION13(chain B and resid 51:66)
14X-RAY DIFFRACTION14(chain B and resid 67:81)
15X-RAY DIFFRACTION15(chain B and resid 82:123)
16X-RAY DIFFRACTION16(chain B and resid 124:160)
17X-RAY DIFFRACTION17(chain B and resid 161:186)
18X-RAY DIFFRACTION18(chain B and resid 187:202)
19X-RAY DIFFRACTION19(chain B and resid 203:218)
20X-RAY DIFFRACTION20(chain B and resid 219:233)

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