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- PDB-7u6j: HalB with lysine and succinate -

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Basic information

Entry
Database: PDB / ID: 7u6j
TitleHalB with lysine and succinate
ComponentsHalogenase B
KeywordsBIOSYNTHETIC PROTEIN
Function / homology: / Halogenase D / LYSINE / SUCCINIC ACID / ArpA protein
Function and homology information
Biological speciesStreptomyces wuyuanensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSumida, K.H. / Neugebauer, 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
C: Halogenase B
D: Halogenase B
E: Halogenase B
F: Halogenase B
G: Halogenase B
H: Halogenase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,18024
Polymers229,0588
Non-polymers2,12216
Water42,1192338
1
A: Halogenase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8983
Polymers28,6321
Non-polymers2652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Halogenase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8983
Polymers28,6321
Non-polymers2652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Halogenase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8983
Polymers28,6321
Non-polymers2652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Halogenase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8983
Polymers28,6321
Non-polymers2652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Halogenase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8983
Polymers28,6321
Non-polymers2652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Halogenase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8983
Polymers28,6321
Non-polymers2652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Halogenase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8983
Polymers28,6321
Non-polymers2652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Halogenase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8983
Polymers28,6321
Non-polymers2652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.241, 136.079, 116.240
Angle α, β, γ (deg.)90.000, 100.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Halogenase B


Mass: 28632.223 Da / Num. of mol.: 8
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.: 8 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2338 / 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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Equal volumes of protein solution (SwHalB (3 mg/mL), lysine (3 mM), aKG (3 mM, pH 7)) and reservoir solution (succinate phosphate lysine (SPL) buffer (100 mM), 20% (w/v) PEG 1500, pH 5.5) 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 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.9→87.6 Å / Num. obs: 168084 / % possible obs: 99.6 % / Redundancy: 6.9 % / CC1/2: 0.997 / Net I/σ(I): 8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 8185 / CC1/2: 0.449 / % possible all: 98.8

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Processing

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

6nie


Resolution: 1.9→69.17 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2112 8336 4.96 %
Rwork0.1618 159698 -
obs0.1642 168034 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.64 Å2 / Biso mean: 28.043 Å2 / Biso min: 11.09 Å2
Refinement stepCycle: final / Resolution: 1.9→69.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15778 0 144 2338 18260
Biso mean--25.95 35.75 -
Num. residues----1978
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 (%)
1.9-1.920.33662850.28425208549399
1.92-1.940.33012830.28145290557399
1.94-1.970.2862740.25935241551599
1.97-1.990.27422860.24255264555099
1.99-2.020.27422860.23635274556099
2.02-2.050.29832850.22925274555999
2.05-2.080.29182730.22585329560299
2.08-2.110.27492530.21285271552499
2.11-2.140.26762520.20165327557999
2.14-2.170.25032950.19385292558799
2.17-2.210.25692930.18955308560199
2.21-2.250.23723220.18435244556699
2.25-2.30.24912760.17935287556399
2.3-2.340.2562820.172353535635100
2.34-2.390.22722710.176253245595100
2.39-2.450.25532710.170153075578100
2.45-2.510.23922870.17453665653100
2.51-2.580.24833030.172352575560100
2.58-2.650.21842620.158353435605100
2.65-2.740.20862780.155153345612100
2.74-2.840.22442620.160553955657100
2.84-2.950.23012860.162953125598100
2.95-3.090.21892470.165653815628100
3.09-3.250.19372580.153253925650100
3.25-3.450.19392630.147953375600100
3.45-3.720.18942990.144753685667100
3.72-4.090.17172540.128453865640100
4.09-4.690.15492650.110754155680100
4.69-5.90.15263010.129853655666100
5.9-69.170.15252840.141454545738100

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