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- PDB-6ck0: Crystal Structure of Biotin Acetyl Coenzyme A Carboxylase Synthet... -

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Basic information

Entry
Database: PDB / ID: 6ck0
TitleCrystal Structure of Biotin Acetyl Coenzyme A Carboxylase Synthetase from Helicobacter pylori with bound Biotinylated ATP
ComponentsBiotin acetyl coenzyme A carboxylase synthetase
KeywordsLIGASE / SSGCID / biotin-[acetyl-CoA-carboxylase] ligase activity / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


biotin--[biotin carboxyl-carrier protein] ligase activity / protein modification process / 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
Chem-F5D / Biotin acetyl coenzyme A carboxylase synthetase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Co-crystal structure of Helicobacter pylori biotin protein ligase with biotinyl-5-ATP.
Authors: Ayanlade, J.P. / Davis, D.E. / Subramanian, S. / Dranow, D.M. / Lorimer, D.D. / Hammerson, B. / Myler, P.J. / Asojo, O.A.
History
DepositionFeb 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Revision 1.2Jan 15, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Biotin acetyl coenzyme A carboxylase synthetase
B: Biotin acetyl coenzyme A carboxylase synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,13312
Polymers50,0302
Non-polymers2,10410
Water2,072115
1
A: Biotin acetyl coenzyme A carboxylase synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9094
Polymers25,0151
Non-polymers8943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Biotin acetyl coenzyme A carboxylase synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2258
Polymers25,0151
Non-polymers1,2107
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.890, 57.080, 57.030
Angle α, β, γ (deg.)122.140, 94.730, 107.850
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Biotin acetyl coenzyme A carboxylase synthetase


Mass: 25014.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain G27) (bacteria)
Strain: G27 / Gene: HPG27_1085 / Plasmid: HepyC.19466.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B5Z8D8
#2: Chemical ChemComp-F5D / 5'-O-[(S)-({5-[(2R,3aS,4S,6aR)-2-hydroxyhexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}oxy){[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]adenosine


Mass: 735.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H32N7O15P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4
Details: HepyC.19466.a.B1.PS38345 at 23.36 mg/ml was incubated with 6 mM MgCl2, ATP, and biotin, then mixed 1:1 with JCSG+(b1): 0.1 M sodium citrate tribasic/ citric acid, pH=4.0, 0.8 M ammonium ...Details: HepyC.19466.a.B1.PS38345 at 23.36 mg/ml was incubated with 6 mM MgCl2, ATP, and biotin, then mixed 1:1 with JCSG+(b1): 0.1 M sodium citrate tribasic/ citric acid, pH=4.0, 0.8 M ammonium sulfate. Crystal cryoprotected with 25% ethylene glycol. Tray: 295125b1, puck: xga0-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 24, 2017 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→47.95 Å / Num. obs: 23767 / % possible obs: 97.1 % / Redundancy: 3.92 % / Biso Wilson estimate: 36.37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.055 / Χ2: 1.02 / Net I/σ(I): 18.29 / Num. measured all: 93167 / Scaling rejects: 580
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.25-2.313.9580.4523.436432181716250.9370.52389.4
2.31-2.373.9820.2744.996813176617110.9650.31696.9
2.37-2.443.9880.2355.856541168316400.9680.27297.4
2.44-2.523.9820.1996.776510167816350.9740.2397.4
2.52-2.63.9750.1787.666336164115940.9790.20697.1
2.6-2.693.9770.1349.756002154315090.9850.15597.8
2.69-2.793.9620.10612.075768148814560.9890.12397.8
2.79-2.93.9540.08714.415603145014170.9930.197.7
2.9-3.033.9410.0717.135372139213630.9960.08197.9
3.03-3.183.9210.05520.485117134013050.9970.06497.4
3.18-3.353.8960.04624.624854127112460.9980.05498
3.35-3.563.8840.03928.714606120511860.9980.04598.4
3.56-3.83.80.03830.324176112310990.9980.04497.9
3.8-4.113.8660.03334.493936103610180.9980.03898.3
4.11-4.53.8350.02936.2736059539400.9990.03498.6
4.5-5.033.8380.02838.4133128778630.9990.03298.4
5.03-5.813.790.02937.6528887777620.9990.03498.1
5.81-7.123.8170.02937.6324356506380.9980.03498.2
7.12-10.063.8290.02441.6618765024900.9990.02897.6
10.06-47.953.6480.02242.169852822700.9990.02695.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.13_2998)refinement
PDB_EXTRACT3.24data extraction
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L1A

3l1a


Resolution: 2.25→47.95 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.42
RfactorNum. reflection% reflection
Rfree0.2207 1978 8.33 %
Rwork0.1711 --
obs0.1752 23747 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.61 Å2 / Biso mean: 42.3463 Å2 / Biso min: 14.24 Å2
Refinement stepCycle: final / Resolution: 2.25→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3229 0 128 116 3473
Biso mean--56.76 44.84 -
Num. residues----419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2501-2.30630.431320.36981428156089
2.3063-2.36870.26121410.23291553169497
2.3687-2.43840.28261330.19981533166698
2.4384-2.51710.24991560.19351549170598
2.5171-2.6070.28321420.19871582172498
2.607-2.71140.31191340.20021561169598
2.7114-2.83480.29231370.1931562169998
2.8348-2.98420.24041480.19511578172698
2.9842-3.17120.23711570.18811536169399
3.1712-3.4160.22231340.1691582171699
3.416-3.75960.23381320.15931587171999
3.7596-4.30330.17031460.14321570171699
4.3033-5.42050.15321470.1321571171899
5.4205-47.96110.19191390.15481577171699
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)
15.4376-0.2381-0.77715.9168-2.37696.8051-0.10260.1681-0.1839-0.4528-0.0064-0.2020.3248-0.09180.0870.2647-0.01570.00840.2533-0.00330.23562.226618.695841.784
22.3422-0.77670.42733.5889-0.88923.4001-0.2012-0.1110.48410.63740.1053-0.6065-0.29030.05560.06220.29850.0064-0.09120.2407-0.03120.39427.81220.700756.1899
33.16791.7674-0.04613.7073-2.29077.1586-0.1238-0.2631-0.26780.05780.0151-0.50470.21670.22130.04280.33580.0423-0.07860.3145-0.03590.35212.48685.004564.2202
45.07520.24620.08077.59460.42975.11250.1576-0.03310.049-0.2511-0.1661-0.47730.05180.2162-0.04740.25070.02370.0060.2607-0.01040.232318.8607-14.717531.9413
52.8374-0.88580.60544.78260.80363.43940.0459-0.0074-0.0530.01840.15830.2077-0.1545-0.1175-0.17960.2314-0.02810.03250.21970.04760.22426.6562-7.476934.8298
65.2141-0.68552.46437.7241-1.5077.60970.1412-0.3469-0.41330.37630.26390.77181.092-0.2281-0.35990.4403-0.05630.0040.31530.12170.32331.8878-17.112638.2231
75.14562.89581.17347.98530.86792.9176-0.13490.01570.1548-0.55560.24450.4843-0.3433-0.2607-0.24630.35330.0907-0.00470.34520.07530.3638-0.16553.645526.2288
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 54 )A3 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 171 )A55 - 171
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 211 )A172 - 211
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 54 )B2 - 54
5X-RAY DIFFRACTION5chain 'B' and (resid 55 through 144 )B55 - 144
6X-RAY DIFFRACTION6chain 'B' and (resid 145 through 161 )B145 - 161
7X-RAY DIFFRACTION7chain 'B' and (resid 162 through 211 )B162 - 211

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