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- PDB-6o0a: Crystal structure of flavohemoglobin from Malassezia yamatoensis ... -

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Basic information

Entry
Database: PDB / ID: 6o0a
TitleCrystal structure of flavohemoglobin from Malassezia yamatoensis with bound FAD and heme determined by iron SAD phasing
ComponentsFlavohemoglobin
KeywordsOXIDOREDUCTASE / SSGCID / FAD / heme / flavohemoglobin / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


nitric oxide dioxygenase / nitric oxide dioxygenase NAD(P)H activity / response to nitrosative stress / FAD binding / oxygen binding / heme binding
Similarity search - Function
Flavohemoprotein / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Globin/Protoglobin / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel ...Flavohemoprotein / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Globin/Protoglobin / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Globins / Globin domain profile. / Globin-like / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide dioxygenase
Similarity search - Component
Biological speciesMalassezia yamatoensis (fungus)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: HGT in the human and skin commensal Malassezia : A bacterially derived flavohemoglobin is required for NO resistance and host interaction.
Authors: Ianiri, G. / Coelho, M.A. / Ruchti, F. / Sparber, F. / McMahon, T.J. / Fu, C. / Bolejack, M. / Donovan, O. / Smutney, H. / Myler, P. / Dietrich, F. / Fox 3rd, D. / LeibundGut-Landmann, S. / Heitman, J.
History
DepositionFeb 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flavohemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7644
Polymers46,2441
Non-polymers1,5203
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-42 kcal/mol
Surface area17570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.010, 110.600, 39.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-746-

HOH

21A-920-

HOH

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Components

#1: Protein Flavohemoglobin


Mass: 46243.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Malassezia yamatoensis (fungus) / Plasmid: MayaA.00765.a.TH11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4V8H045*PLUS
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 19.93 mg/mL MayaA.00765.a.TH11.PD38344, 1:1 with Morpheus(b12) (12.5% w/v PEG1000, 12.5% w/v PEG3350, 12.5% MPD, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, 0.1 M ...Details: 19.93 mg/mL MayaA.00765.a.TH11.PD38344, 1:1 with Morpheus(b12) (12.5% w/v PEG1000, 12.5% w/v PEG3350, 12.5% MPD, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, 0.1 M bicine/Trizma base, pH 8.5), tray: 306177b12, puck: swh5-1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→47.26 Å / Num. obs: 44250 / % possible obs: 99.9 % / Redundancy: 9.509 % / Biso Wilson estimate: 26.385 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.06 / Χ2: 1.084 / Net I/σ(I): 24.66 / Num. measured all: 795009 / Scaling rejects: 103
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.744.4050.5462.4626757614660740.8250.61898.8
1.74-1.795.7670.5083.2134992607060680.8940.56100
1.79-1.846.0370.4194.0635505588458810.9240.4699.9
1.84-1.96.3360.3155.6336143570457040.9540.344100
1.9-1.966.590.2617.0336340551655140.9680.284100
1.96-2.036.9290.2079.3737174536553650.980.224100
2.03-2.117.2970.16412.3637173509450940.9880.177100
2.11-2.198.7740.13517.2443644497449740.9940.143100
2.19-2.299.7490.11421.3146784479947990.9960.12100
2.29-2.410.190.09924.0546356454945490.9970.105100
2.4-2.5310.8640.08527.9946726430143010.9980.089100
2.53-2.6911.8890.07233.8348663409340930.9990.075100
2.69-2.8713.9230.06340.1553393383538350.9990.065100
2.87-3.115.2080.05248.5754702359735970.9990.054100
3.1-3.415.2810.04355.9850106327932790.9990.044100
3.4-3.815.3410.03566.54461153006300610.037100
3.8-4.3915.3690.03272.31400822608260810.034100
4.39-5.3815.4290.03275.73339892203220310.033100
5.38-7.615.380.03769.87265761728172810.038100
7.6-47.2614.7790.03879.981378993593310.0499.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.7→47.26 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.07
RfactorNum. reflection% reflection
Rfree0.1977 2028 4.59 %
Rwork0.1674 --
obs0.1688 44179 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.56 Å2 / Biso mean: 25.3577 Å2 / Biso min: 8.28 Å2
Refinement stepCycle: final / Resolution: 1.7→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 0 104 428 3474
Biso mean--18.3 34.22 -
Num. residues----383
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7001-1.74260.27051320.24042901303398
1.7426-1.78970.27241480.221129853133100
1.7897-1.84240.24031490.201329463095100
1.8424-1.90180.21241490.188329793128100
1.9018-1.96980.21191590.182229433102100
1.9698-2.04870.22021440.182129863130100
2.0487-2.14190.20441380.171329863124100
2.1419-2.25480.20321330.168530023135100
2.2548-2.39610.19841450.16630133158100
2.3961-2.58110.19671520.171430003152100
2.5811-2.84080.21071430.170230263169100
2.8408-3.25180.19461550.163630513206100
3.2518-4.09650.19381310.140730853216100
4.0965-47.27790.15481500.157132483398100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3766-0.8088-0.62212.25471.00071.02860.0904-0.04340.1385-0.01880.0126-0.2833-0.12940.143-0.08480.1316-0.0113-0.02590.13110.00790.183614.454-2.490431.9909
21.79640.14630.64180.73380.09061.30110.02130.13840.0298-0.0673-0.0322-0.0697-0.06390.12250.00610.09240.01590.01510.1024-0.00220.076431.4251-24.726123.1526
31.387-0.27620.53173.9552-0.86732.2914-0.2166-0.03870.26540.25050.11270.0087-0.4722-0.03020.10550.1861-0.0226-0.02360.1607-0.01960.187843.9165-16.460936.3399
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 146 )A0 - 146
2X-RAY DIFFRACTION2chain 'A' and (resid 147 through 315 )A147 - 315
3X-RAY DIFFRACTION3chain 'A' and (resid 316 through 382 )A316 - 382

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