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- PDB-7wwf: Crystal structure of BioH3 from Mycolicibacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 7wwf
TitleCrystal structure of BioH3 from Mycolicibacterium smegmatis
ComponentsEsterase
KeywordsBIOSYNTHETIC PROTEIN / Mycolicibacterium smegmatis / BioH3 / crystal
Function / homologyAlpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER / Esterase
Function and homology information
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.27 Å
AuthorsYang, J. / Xu, Y.C. / Gan, J.H. / Feng, Y.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171197 China
CitationJournal: Plos Pathog. / Year: 2022
Title: Three enigmatic BioH isoenzymes are programmed in the early stage of mycobacterial biotin synthesis, an attractive anti-TB drug target.
Authors: Xu, Y. / Yang, J. / Li, W. / Song, S. / Shi, Y. / Wu, L. / Sun, J. / Hou, M. / Wang, J. / Jia, X. / Zhang, H. / Huang, M. / Lu, T. / Gan, J. / Feng, Y.
History
DepositionFeb 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Esterase
B: Esterase
C: Esterase
D: Esterase
E: Esterase
F: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,71015
Polymers181,7066
Non-polymers1,0039
Water4,342241
1
A: Esterase
B: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9035
Polymers60,5692
Non-polymers3343
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-19 kcal/mol
Surface area19160 Å2
MethodPISA
2
C: Esterase
D: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9035
Polymers60,5692
Non-polymers3343
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-16 kcal/mol
Surface area19270 Å2
MethodPISA
3
E: Esterase
F: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9035
Polymers60,5692
Non-polymers3343
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-25 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.668, 65.830, 172.809
Angle α, β, γ (deg.)90.000, 97.760, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Esterase


Mass: 30284.396 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: NCTC7017_02293 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8B4QLS5
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 56 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.8 / Details: PEG 3350, Citric acid / PH range: 8.7-8.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Sep 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.27→90.83 Å / Num. obs: 93409 / % possible obs: 98.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 38.42 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.054 / Rrim(I) all: 0.101 / Net I/σ(I): 11.9 / Num. measured all: 319239 / Scaling rejects: 219
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.27-2.393.60.57349137137250.8250.3510.6742.3100
7.18-90.833.40.0411056430870.9970.0260.04932.897.4

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.27→45.63 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2221 4490 4.81 %
Rwork0.189 88808 -
obs0.1906 93298 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.08 Å2 / Biso mean: 41.7663 Å2 / Biso min: 22.73 Å2
Refinement stepCycle: final / Resolution: 2.27→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12372 0 52 241 12665
Biso mean--53.47 40.21 -
Num. residues----1654
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.27-2.30.3241580.274629603118100
2.3-2.320.2691480.27129533101100
2.32-2.350.34141510.264630333184100
2.35-2.380.27651430.249929283071100
2.38-2.410.29491610.253630083169100
2.41-2.450.29231690.242829583127100
2.45-2.480.30481520.237429733125100
2.48-2.520.28711540.234629823136100
2.52-2.560.28111600.244829823142100
2.56-2.60.27841360.240729803116100
2.6-2.640.30951390.249730503189100
2.64-2.690.29291100.2461993210368
2.69-2.740.2831510.232630263177100
2.74-2.80.28061620.223429633125100
2.8-2.860.24111570.218829993156100
2.86-2.930.26261470.222529613108100
2.93-30.24231390.23130163155100
3-3.080.25971480.22430103158100
3.08-3.170.28321560.230229833139100
3.17-3.270.25751330.223032316599
3.27-3.390.25511600.20972969312999
3.39-3.530.25021440.1933008315299
3.53-3.690.2331460.18992998314499
3.69-3.880.20711400.1673016315699
3.88-4.120.17411480.15352978312699
4.12-4.440.14371520.13282993314599
4.44-4.890.15051650.13822976314198
4.89-5.60.1631540.14733014316899
5.6-7.040.18061530.16283013316698
7.05-45.630.17951540.1413053320796
Refinement TLS params.Method: refined / Origin x: 75.0405 Å / Origin y: -13.4704 Å / Origin z: 135.5625 Å
111213212223313233
T0.2772 Å2-0.0453 Å20.0178 Å2-0.2497 Å20.0288 Å2--0.2256 Å2
L0.1165 °2-0.018 °20.0003 °2-0.1381 °20.0136 °2--0.1981 °2
S-0.0364 Å °0.0085 Å °-0.0331 Å °0.0107 Å °-0.0083 Å °0.01 Å °0.0291 Å °0.016 Å °0.0441 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 282
2X-RAY DIFFRACTION1allB8 - 282
3X-RAY DIFFRACTION1allC6 - 282
4X-RAY DIFFRACTION1allD8 - 282
5X-RAY DIFFRACTION1allE8 - 282
6X-RAY DIFFRACTION1allF8 - 282
7X-RAY DIFFRACTION1allH1 - 6
8X-RAY DIFFRACTION1allI1 - 3
9X-RAY DIFFRACTION1allS1 - 277

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