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- PDB-7u6i: HalB with glycine and succinate -

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Basic information

Entry
Database: PDB / ID: 7u6i
TitleHalB with glycine and succinate
ComponentsHalogenase B
KeywordsBIOSYNTHETIC PROTEIN
Function / homology: / Halogenase D / q2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta / GLYCINE / SUCCINIC ACID / ArpA protein
Function and homology information
Biological speciesStreptomyces wuyuanensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsNeugebauer, M.E. / Kissman, E.N. / Chang, M.C.Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Biocatalytic control of site-selectivity and chain length-selectivity in radical amino acid halogenases.
Authors: Kissman, E.N. / Neugebauer, M.E. / Sumida, K.H. / Swenson, C.V. / Sambold, N.A. / Marchand, J.A. / Millar, D.C. / Chang, M.C.Y.
History
DepositionMar 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
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
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Halogenase B
B: Halogenase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6686
Polymers57,2642
Non-polymers4034
Water7,909439
1
A: Halogenase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8253
Polymers28,6321
Non-polymers1932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Halogenase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8423
Polymers28,6321
Non-polymers2102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.480, 165.480, 105.332
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Halogenase B


Mass: 28632.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces wuyuanensis (bacteria) / Gene: SAMN05444921_127108 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1H0BKU7
#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.64 Å3/Da / Density % sol: 66.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: Equal volumes of protein solution (SwHalB (2.5 mg/ml), lysine (3 mM), alpha-ketoglutarate (3 mM, pH 7)) and reservoir solution (succinate phosphate glycine (SPG) buffer (100 mM, pH 5.2), 18% ...Details: Equal volumes of protein solution (SwHalB (2.5 mg/ml), lysine (3 mM), alpha-ketoglutarate (3 mM, pH 7)) and reservoir solution (succinate phosphate glycine (SPG) buffer (100 mM, pH 5.2), 18% (w/v) PEG 1500) were mixed

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Data collection

DiffractionMean temperature: 194 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 2.05→143.41 Å / Num. obs: 53826 / % possible obs: 99.8 % / Redundancy: 39.65 % / CC1/2: 1 / Net I/σ(I): 23.9
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3989 / CC1/2: 0.706 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
Aimless0.7.4data scaling
XDSJan 26, 2018data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NIE

6nie


Resolution: 2.05→82.74 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2231 2774 5.16 %
Rwork0.1973 50973 -
obs0.1986 53747 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.59 Å2 / Biso mean: 47.3102 Å2 / Biso min: 22.59 Å2
Refinement stepCycle: final / Resolution: 2.05→82.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3829 0 27 439 4295
Biso mean--58.05 56.56 -
Num. residues----481
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.080.50781170.38332410252796
2.08-2.120.35931440.335424902634100
2.12-2.160.35631560.295825042660100
2.16-2.20.3091270.270225272654100
2.2-2.250.28891160.257725422658100
2.25-2.30.28121520.248224952647100
2.3-2.360.29191330.241225252658100
2.36-2.430.30141660.242424872653100
2.43-2.50.29671240.237525362660100
2.5-2.580.27191260.236925522678100
2.58-2.670.25381590.219325072666100
2.67-2.780.23331630.218225222685100
2.78-2.90.27351170.208625542671100
2.9-3.060.24181370.204625542691100
3.06-3.250.22131400.202425592699100
3.25-3.50.20721400.181625772717100
3.5-3.850.20041300.174225902720100
3.85-4.410.17091280.155626082736100
4.41-5.550.16471440.144826482792100
5.55-82.740.1851550.189727862941100

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