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- PDB-6ohi: Crystal Structure of the Debrominase Bmp8 (Apo) -

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Basic information

Entry
Database: PDB / ID: 6ohi
TitleCrystal Structure of the Debrominase Bmp8 (Apo)
ComponentsDebrominase Bmp8
KeywordsBIOSYNTHETIC PROTEIN / Debrominase
Function / homologyCarboxymuconolactone decarboxylase family / AhpD-like / Carboxymuconolactone decarboxylase
Function and homology information
Biological speciesMarinomonas mediterranea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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)43,2753
Polymers43,1792
Non-polymers961
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-47 kcal/mol
Surface area14590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.459, 65.459, 288.707
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 4 - 188 / Label seq-ID: 7 - 191

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Debrominase Bmp8 / Carboxymuconolactone decarboxylase


Mass: 21589.459 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinomonas mediterranea (strain ATCC 700492 / JCM 21426 / NBRC 103028 / MMB-1) (bacteria)
Strain: ATCC 700492 / JCM 21426 / NBRC 103028 / MMB-1 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.16 Å3/Da / Density % sol: 43.11 %
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: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→144.4 Å / Num. obs: 17455 / % possible obs: 97.8 % / Redundancy: 21.9 % / CC1/2: 0.99 / Rpim(I) all: 0.032 / Rsym value: 0.145 / Net I/σ(I): 17.1
Reflection shellResolution: 2.272→2.312 Å / Redundancy: 23.7 % / Rmerge(I) obs: 1.522 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 873 / CC1/2: 0.801 / Rpim(I) all: 0.317 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→56.69 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.988 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.365 / ESU R Free: 0.232 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23538 886 5.1 %RANDOM
Rwork0.19757 ---
obs0.19952 16569 97.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.712 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.33 Å20 Å2
2--0.67 Å2-0 Å2
3----2.16 Å2
Refinement stepCycle: 1 / Resolution: 2.27→56.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 0 5 59 2960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0142968
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172612
X-RAY DIFFRACTIONr_angle_refined_deg0.9811.6464019
X-RAY DIFFRACTIONr_angle_other_deg0.8411.6326108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4795371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.83522.739157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13915477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1931516
X-RAY DIFFRACTIONr_chiral_restr0.0490.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023375
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02581
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3964.8611490
X-RAY DIFFRACTIONr_mcbond_other2.3954.8591489
X-RAY DIFFRACTIONr_mcangle_it3.7127.2861859
X-RAY DIFFRACTIONr_mcangle_other3.7117.2881860
X-RAY DIFFRACTIONr_scbond_it2.7425.221478
X-RAY DIFFRACTIONr_scbond_other2.7185.2091472
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3057.692154
X-RAY DIFFRACTIONr_long_range_B_refined6.45658.3483459
X-RAY DIFFRACTIONr_long_range_B_other6.45558.3613456
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6139 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.272→2.331 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 61 -
Rwork0.283 1230 -
obs--100 %

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