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- PDB-6ohj: Crystal Structure of the Debrominase Bmp8 C82A in Complex with 2,... -

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Basic information

Entry
Database: PDB / ID: 6ohj
TitleCrystal Structure of the Debrominase Bmp8 C82A in Complex with 2,3,4-tribromopyrrole
ComponentsDebrominase Bmp8
KeywordsBIOSYNTHETIC PROTEIN / Debrominase
Function / homologyCarboxymuconolactone decarboxylase family / AhpD-like / 2,3,4-tribromo-1H-pyrrole / Carboxymuconolactone decarboxylase
Function and homology information
Biological speciesMarinomonas mediterranea MMB-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.19 Å
AuthorsChekan, J.R. / Moore, B.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Science Foundation (NSF, United States) United States
CitationJournal: Biochemistry / Year: 2019
Title: Bacterial Tetrabromopyrrole Debrominase Shares a Reductive Dehalogenation Strategy with Human Thyroid Deiodinase.
Authors: Chekan, J.R. / Lee, G.Y. / El Gamal, A. / Purdy, T.N. / Houk, K.N. / Moore, B.S.
History
DepositionApr 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Debrominase Bmp8
B: Debrominase Bmp8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5154
Polymers43,1152
Non-polymers4002
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-45 kcal/mol
Surface area14730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.817, 65.817, 288.848
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Components on special symmetry positions
IDModelComponents
11A-301-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPSERSER(chain 'A' and (resid 3 through 176 or resid 178 through 189))AA3 - 1756 - 178
12GLUGLUILEILE(chain 'A' and (resid 3 through 176 or resid 178 through 189))AA178 - 188181 - 191
23ASPASPSERSER(chain 'B' and (resid 3 through 176 or resid 178 through 189))BB3 - 1756 - 178
24GLUGLUILEILE(chain 'B' and (resid 3 through 176 or resid 178 through 189))BB178 - 188181 - 191

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Components

#1: Protein Debrominase Bmp8 / Carboxymuconolactone decarboxylase


Mass: 21557.393 Da / Num. of mol.: 2 / Mutation: C82A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinomonas mediterranea MMB-1 (bacteria)
Gene: Marme_4087 / Production host: Escherichia coli (E. coli) / References: UniProt: F2K073
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MKV / 2,3,4-tribromo-1H-pyrrole


Mass: 303.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H2Br3N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2.3 M ammonium sulfate, 0.1 M BisTris propane pH 9.0, 7 mg/mL Bmp8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.91 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 3.19→57 Å / Num. obs: 6726 / % possible obs: 98.5 % / Redundancy: 16.2 % / Biso Wilson estimate: 89.01 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.046 / Net I/σ(I): 15
Reflection shellResolution: 3.19→3.249 Å / Redundancy: 17.5 % / Rmerge(I) obs: 1.467 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 332 / CC1/2: 0.9 / Rpim(I) all: 0.24 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15rc3_3435refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.19→57 Å / SU ML: 0.3669 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.8843
RfactorNum. reflection% reflection
Rfree0.2824 320 4.76 %
Rwork0.2316 --
obs0.234 6716 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 95.33 Å2
Refinement stepCycle: LAST / Resolution: 3.19→57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 13 2 2917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00352988
X-RAY DIFFRACTIONf_angle_d0.54494051
X-RAY DIFFRACTIONf_chiral_restr0.0383442
X-RAY DIFFRACTIONf_plane_restr0.0046532
X-RAY DIFFRACTIONf_dihedral_angle_d1.77612115
LS refinement shellResolution: 3.19→3.249 Å
RfactorNum. reflection% reflection
Rfree0.3187 151 -
Rwork0.287 3028 -
obs--96.63 %

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