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- PDB-6ds7: Crystal structure of MhuD R26S mutant with two hemes bound per ac... -

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Basic information

Entry
Database: PDB / ID: 6ds7
TitleCrystal structure of MhuD R26S mutant with two hemes 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
PROTOPORPHYRIN IX CONTAINING FE / Heme oxygenase (mycobilin-producing)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 hemes 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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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)23,6128
Polymers21,0762
Non-polymers2,5376
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-122 kcal/mol
Surface area9600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.210, 68.571, 74.090
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 39 or resid 41 through 55 or resid 57 through 100))
21(chain B and (resid 2 through 39 or resid 41 through 55 or resid 57 through 100))

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
11PROPROPHEPHE(chain A and (resid 2 through 39 or resid 41 through 55 or resid 57 through 100))AA2 - 391 - 38
12LEULEUTHRTHR(chain A and (resid 2 through 39 or resid 41 through 55 or resid 57 through 100))AA41 - 5540 - 54
13TRPTRPGLYGLY(chain A and (resid 2 through 39 or resid 41 through 55 or resid 57 through 100))AA57 - 10056 - 99
21PROPROPHEPHE(chain B and (resid 2 through 39 or resid 41 through 55 or resid 57 through 100))BB2 - 391 - 38
22LEULEUTHRTHR(chain B and (resid 2 through 39 or resid 41 through 55 or resid 57 through 100))BB41 - 5540 - 54
23TRPTRPGLYGLY(chain B and (resid 2 through 39 or resid 41 through 55 or resid 57 through 100))BB57 - 10056 - 99

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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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / 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.: 125 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.6 M ammonium sulfate, 0.1 M sodium acetate, pH 5.5, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50.325 Å / Num. obs: 29276 / % possible obs: 99.04 % / Redundancy: 2 % / Biso Wilson estimate: 21.39 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.02947 / Rpim(I) all: 0.02947 / Rrim(I) all: 0.04168 / Net I/σ(I): 12.23
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2111 / Mean I/σ(I) obs: 2.67 / Num. unique obs: 1514 / CC1/2: 0.738 / Rpim(I) all: 0.2111 / Rrim(I) all: 0.2985 / % possible all: 96.54

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Processing

Software
NameVersionClassification
BOSdata collection
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIX1.13_2998refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HX9

3hx9


Resolution: 1.9→50.325 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.99
RfactorNum. reflection% reflection
Rfree0.227 2939 10.04 %
Rwork0.1729 --
obs0.1783 29276 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.57 Å2 / Biso mean: 27.4027 Å2 / Biso min: 8.1 Å2
Refinement stepCycle: final / Resolution: 1.9→50.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1482 0 174 125 1781
Biso mean--25.69 35.26 -
Num. residues----198
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A572X-RAY DIFFRACTION9.251TORSIONAL
12B572X-RAY DIFFRACTION9.251TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9001-1.93130.50771520.4841118127092
1.9313-1.96460.30281440.29051237138199
1.9646-2.00030.25621380.231912761414100
2.0003-2.03880.21531270.19821279140699
2.0388-2.08040.35811490.25121211136097
2.0804-2.12560.23461420.17781291143399
2.1256-2.17510.24391100.185512651375100
2.1751-2.22950.27081470.21911264141199
2.2295-2.28980.39771330.26851181131495
2.2898-2.35710.24461520.204112721424100
2.3571-2.43320.26651350.180612741409100
2.4332-2.52020.2481300.16681281141199
2.5202-2.62110.22141330.164112561389100
2.6211-2.74040.23951440.167812801424100
2.7404-2.88480.20461450.157812591404100
2.8848-3.06550.20291400.143812461386100
3.0655-3.30220.22581430.15512581401100
3.3022-3.63440.19391400.143112841424100
3.6344-4.16010.16251490.134712651414100
4.1601-5.24040.14411390.116712821421100
5.2404-50.34280.21261470.162612581405100
Refinement TLS params.Method: refined / Origin x: -14.9314 Å / Origin y: -3.0651 Å / Origin z: 8.3786 Å
111213212223313233
T0.0722 Å2-0.0028 Å2-0.0005 Å2-0.0886 Å2-0.0147 Å2--0.0905 Å2
L0.2215 °20.1562 °2-0.1788 °2-0.3851 °20.0036 °2--0.7869 °2
S-0.0253 Å °0.0383 Å °-0.0175 Å °-0.0272 Å °0.04 Å °0.0203 Å °0.0516 Å °0.077 Å °0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 100
2X-RAY DIFFRACTION1allA201 - 203
3X-RAY DIFFRACTION1allB2 - 100
4X-RAY DIFFRACTION1allB201 - 203
5X-RAY DIFFRACTION1allS1 - 125

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