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- PDB-6ds8: Crystal structure of MhuD R26S mutant with two Manganese protopor... -

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Basic information

Entry
Database: PDB / ID: 6ds8
TitleCrystal structure of MhuD R26S mutant with two Manganese protoporphyrin IX bound per active site
ComponentsHeme-degrading monooxygenase HmoB
KeywordsOXIDOREDUCTASE / Heme Oxygenase (decyclizing) Activity / Monooxygenase Activity / Oxidoreductase Activity / Heme Binding / Metal Ion Binding / Heme Catabolic Process / Oxidation Reduction Process / Cell Wall / Plasma Membrane
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
MANGANESE PROTOPORPHYRIN IX / Heme oxygenase (mycobilin-producing)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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: To Be Published
Title: Crystal structure of MhuD R26S mutant with two Manganese protoporphyrin IX bound per active site
Authors: Chao, A. / Goulding, C.W.
History
DepositionJun 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Heme-degrading monooxygenase HmoB
B: Heme-degrading monooxygenase HmoB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6098
Polymers21,0762
Non-polymers2,5336
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-120 kcal/mol
Surface area9680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.020, 68.701, 74.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 2 through 100)
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 2 - 100 / Label seq-ID: 1 - 99

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 2 through 100)AA
2chain BBB

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Components

#1: Protein Heme-degrading monooxygenase HmoB / Heme oxygenase / Mycobacterial heme utilization degrader / MHUD


Mass: 10537.784 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 (biliverdin-producing)
#2: Chemical
ChemComp-MNH / MANGANESE PROTOPORPHYRIN IX


Mass: 615.580 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32MnN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M ammonium sulfate, 0.1 M HEPES pH 7.5, 25% (w/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50.502 Å / Num. obs: 7868 / % possible obs: 95.06 % / Redundancy: 2 % / Biso Wilson estimate: 30.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.01736 / Rpim(I) all: 0.01736 / Rrim(I) all: 0.02455 / Net I/σ(I): 26.25
Reflection shellResolution: 2.4→2.486 Å / Rmerge(I) obs: 0.08277 / Mean I/σ(I) obs: 7.58 / Num. unique obs: 760 / CC1/2: 0.98 / Rpim(I) all: 0.08277 / Rrim(I) all: 0.1171 / % possible all: 93.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOSFLMdata reduction
pointlessdata scaling
Aimlessdata scaling
PHENIXphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HX9

3hx9


Resolution: 2.4→50.502 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.25
RfactorNum. reflection% reflection
Rfree0.242 776 9.87 %
Rwork0.1806 --
obs0.1866 7864 95.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.26 Å2 / Biso mean: 30.6722 Å2 / Biso min: 10.77 Å2
Refinement stepCycle: final / Resolution: 2.4→50.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1494 0 174 24 1692
Biso mean--28.77 28.41 -
Num. residues----198
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A884X-RAY DIFFRACTION13.241TORSIONAL
12B884X-RAY DIFFRACTION13.241TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4001-2.55050.28141240.22261149127394
2.5505-2.74740.30591320.21041148128095
2.7474-3.02390.29261300.21671162129295
3.0239-3.46130.2511220.19811173129595
3.4613-4.36050.22851320.16651197132995
4.3605-50.51280.19091360.14541259139595

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