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- PDB-6ple: Crystal structure of MhuD R26S mutant in complex with biliverdin -

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Basic information

Entry
Database: PDB / ID: 6ple
TitleCrystal structure of MhuD R26S mutant in complex with biliverdin
ComponentsHeme oxygenase (mycobilin-producing)
KeywordsOXIDOREDUCTASE / Heme Oxygenase (decyclizing) Activity / Monooxygenase Activity / Oxidoreductase Activity / Heme Binding / Metal Ion Binding / Heme Catabolic Process / Oxidation Reduction Process / Cell Wall / Plasma Membrane / Biliverdin / Metal Binding Protein
Function / homology
Function and homology information


heme oxygenase (mycobilin-producing) / heme oxygenase (decyclizing) activity / heme catabolic process / peptidoglycan-based cell wall / heme binding / metal ion binding / plasma membrane
Similarity search - Function
ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / Heme oxygenase (mycobilin-producing)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChao, A. / Goulding, C.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE-1321846 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI095208 United States
CitationJournal: Biochemistry / Year: 2019
Title: Structure of aMycobacterium tuberculosisHeme-Degrading Protein, MhuD, Variant in Complex with Its Product.
Authors: Chao, A. / Burley, K.H. / Sieminski, P.J. / de Miranda, R. / Chen, X. / Mobley, D.L. / Goulding, C.W.
History
DepositionJun 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heme oxygenase (mycobilin-producing)
B: Heme oxygenase (mycobilin-producing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1597
Polymers26,2462
Non-polymers2,9135
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Assembly based on previous Rv3592 structures
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-81 kcal/mol
Surface area10360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.220, 113.610, 113.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Heme oxygenase (mycobilin-producing) / Mycobacterial heme utilization / degrader / MHUD


Mass: 13122.765 Da / Num. of mol.: 2 / Mutation: R26S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: mhuD, Rv3592 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WKH3, heme oxygenase (mycobilin-producing)
#2: Chemical
ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C33H34N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M HEPES pH 6.5, 4.6 M NaCl, 30 mM glycyl-glycyl-glycine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→80.35 Å / Num. obs: 8717 / % possible obs: 100 % / Redundancy: 13.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.026 / Rrim(I) all: 0.095 / Net I/σ(I): 22.5 / Num. measured all: 120788 / Scaling rejects: 122
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.592 / Num. measured all: 13587 / Num. unique obs: 943 / CC1/2: 0.986 / Rpim(I) all: 0.16 / Rrim(I) all: 0.613 / Net I/σ(I) obs: 8.9 / % possible all: 100

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Processing

Software
NameVersionClassification
BOSdata collection
pointlessdata scaling
MOSFLMdata reduction
PHENIXphasing
PHENIX(1.15.2_3472: ???)refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NL5

4nl5


Resolution: 2.5→40.174 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.52
RfactorNum. reflection% reflection
Rfree0.2847 1591 9.89 %
Rwork0.231 --
obs0.2367 16085 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→40.174 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 0 215 16 1661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091700
X-RAY DIFFRACTIONf_angle_d1.5162341
X-RAY DIFFRACTIONf_dihedral_angle_d12.761926
X-RAY DIFFRACTIONf_chiral_restr0.073218
X-RAY DIFFRACTIONf_plane_restr0.007298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58070.43241480.34871290X-RAY DIFFRACTION100
2.5807-2.67290.40261460.32081318X-RAY DIFFRACTION100
2.6729-2.77990.35721490.25171315X-RAY DIFFRACTION100
2.7799-2.90640.46751340.28161317X-RAY DIFFRACTION100
2.9064-3.05960.36731500.31353X-RAY DIFFRACTION100
3.0596-3.25120.31891420.26781297X-RAY DIFFRACTION100
3.2512-3.50210.27331340.23611324X-RAY DIFFRACTION100
3.5021-3.85420.31171510.21721306X-RAY DIFFRACTION100
3.8542-4.41140.19151540.1931320X-RAY DIFFRACTION100
4.4114-5.55550.22721490.18191308X-RAY DIFFRACTION100
5.5555-40.17940.23571340.21011346X-RAY DIFFRACTION100

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