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- PDB-8iag: Crystal structure of rDcaUPO A161C mutant from Daldinia caldariorum -

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Basic information

Entry
Database: PDB / ID: 8iag
TitleCrystal structure of rDcaUPO A161C mutant from Daldinia caldariorum
ComponentsrDcaUPO
KeywordsOXIDOREDUCTASE / rDcaUPO / Daldinia caldariorum
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE
Function and homology information
Biological speciesDaldinia caldariorum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.50000155539 Å
AuthorsLi, T. / Wang, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chin.Chem.Lett. / Year: 2024
Title: A novel insight of enhancing the hydrogen peroxide tolerance of unspecific peroxygenase from Daldinia caldariorum based on structure
Authors: Li, T. / Jin, R. / Wu, B. / Lan, D. / Ma, Y. / Wang, Y.
History
DepositionFeb 8, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: 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.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: rDcaUPO
B: rDcaUPO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,64713
Polymers58,6362
Non-polymers2,01111
Water9,026501
1
B: rDcaUPO
hetero molecules

B: rDcaUPO
hetero molecules

A: rDcaUPO
hetero molecules

A: rDcaUPO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,29326
Polymers117,2724
Non-polymers4,02122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
crystal symmetry operation5_545x+1/2,y-1/2,z1
crystal symmetry operation7_544-x+1/2,y-1/2,-z-1/21
Buried area14030 Å2
ΔGint-283 kcal/mol
Surface area35130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.558, 107.52, 120.016
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein rDcaUPO


Mass: 29317.975 Da / Num. of mol.: 2 / Mutation: A161C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Daldinia caldariorum (fungus) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 512 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.05 Å3/Da / Density % sol: 40.03 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop
Details: 10% (w/v) PEG 3350, 100 mM Imidazole/Hydrochloric acid, pH 6.5, 200 mM Ammonium sulfate, 30% (v/v) 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9779 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 1.47→61.27 Å / Num. obs: 81310 / % possible obs: 99.8 % / Redundancy: 11.8 % / CC1/2: 0.999 / Net I/σ(I): 22.3
Reflection shellResolution: 1.47→1.55 Å / Num. unique obs: 11621 / CC1/2: 0.876

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.50000155539→40.0414080291 Å / SU ML: 0.103251825928 / Cross valid method: FREE R-VALUE / σ(F): 1.34757518298 / Phase error: 14.4042926241
RfactorNum. reflection% reflection
Rfree0.155127258182 1899 2.46089649721 %
Rwork0.142565893195 75268 -
obs0.142880751083 77167 99.9041959581 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.3084746591 Å2
Refinement stepCycle: LAST / Resolution: 1.50000155539→40.0414080291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3481 0 138 501 4120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008106661007073717
X-RAY DIFFRACTIONf_angle_d1.210161906355092
X-RAY DIFFRACTIONf_chiral_restr0.0491181895878546
X-RAY DIFFRACTIONf_plane_restr0.00628106404882654
X-RAY DIFFRACTIONf_dihedral_angle_d15.62312100631311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.500005-1.53750.1967252415921330.1932135557625277X-RAY DIFFRACTION98.9935956084
1.5375-1.57910.1802663093791340.1640843239835303X-RAY DIFFRACTION99.8530762167
1.5791-1.62560.1926737982151350.1485344002025359X-RAY DIFFRACTION99.9636098981
1.6256-1.6780.1446202302171350.1444153338155344X-RAY DIFFRACTION99.9817518248
1.678-1.7380.1778026204791340.1512276507295291X-RAY DIFFRACTION99.9631472268
1.738-1.80760.1520708137741340.1523599954735337X-RAY DIFFRACTION100
1.8076-1.88980.14409935041350.1421677101615361X-RAY DIFFRACTION100
1.8898-1.98950.1326404175091350.1315960131445366X-RAY DIFFRACTION99.981824791
1.9895-2.11410.1623777436181360.1357152057565373X-RAY DIFFRACTION100
2.1141-2.27730.1412624498821360.1386679722125381X-RAY DIFFRACTION100
2.2773-2.50650.1643211233881360.1423437087245376X-RAY DIFFRACTION100
2.5065-2.86910.1694295799641370.1457053399335420X-RAY DIFFRACTION99.9820079165
2.8691-3.61440.1577174101361370.135992016245454X-RAY DIFFRACTION100
3.6144-40.040.1414272580241420.1417569802285626X-RAY DIFFRACTION99.9480159418
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)
11.63512958201-0.28845695190.4009240563312.30067179042-0.1484929231892.226333304560.0577044543047-0.100115216518-0.1196204405410.1166203298010.01798770468950.08877695752810.178508855411-0.0808542684471-0.06228516298180.150321341011-0.0133859170998-0.005306125371510.1111123972710.01763832681660.13750663271519.9512524691-3.47701336501-13.3957812757
22.386273684982.365202178982.173491374576.602876325483.408386649255.347492915950.07678862554860.179945654086-0.174808283804-0.08263865969070.135473512704-0.4150639340740.2700120993470.283276941812-0.2029098089580.166551455370.04872820771270.007617517460160.1985343803720.02229997441990.18794112318632.4919823169-2.4617734475-20.5151154743
30.42537834961-0.1772291200740.5709639504230.880826187337-0.3722644989121.737945361640.01076078075780.03210363784460.0024701185838-0.0194364884662-0.01254726786-0.0495470285741-0.007411732745590.06730872985320.01106124037020.1133450934040.008561201784740.009981772066570.132909515287-0.003585966634780.13864340373521.480492472311.4254167691-24.7744512298
42.131093822070.00334318099540.2165106579811.60471389059-0.1696581058662.447741239590.1412008132850.0462183261198-0.178871435478-0.1935567333690.01607091340270.1258982500850.266918786951-0.178521164573-0.1246020988170.19138830979-0.0237992171526-0.05077130258350.1148838017620.01336441994640.1924623635412.3141294742-3.80619432449-27.3065529926
53.00753634883-2.682199715371.44890338637.19055139059-3.170737633564.225935566550.05714618577630.2219639846650.271571227633-0.197106022734-0.329782984352-0.565077412617-0.1509797422180.3901296518420.2164860436210.2484407943740.02783833461520.03048469907850.250115577623-0.0116986648410.20888503673426.40678753657.06353336972-37.7854091359
61.22787071545-0.289984628926-0.202956190092.411456536610.4217714634881.57483153255-0.0115009586778-0.09157750555810.03259220564850.08658780650080.0534910957752-0.165083772202-0.007742083158480.250561904419-0.0371383765850.1081921252880.00282253306752-0.01362276784840.160246979819-0.02178301317420.11257375812736.476334944-22.11243693641.85992760493
70.4354690067220.1853763116980.3680521883731.651081329830.7385759775741.873182465850.00375903524791-0.02590113253740.0864036085939-0.0239506964445-0.09384141819110.165864937452-0.106434939976-0.1651634527910.09881753951110.1273551995750.02359866490070.004179463311120.156931896688-0.01444411776810.14379247770224.6540698813-18.2378428198-5.59507012864
85.16072120792-1.460799872640.1305598059751.924522065410.9679338609332.75203122979-0.0566466125621-0.0507005354887-0.2223344873650.155061781410.05604521161020.1949842894920.346716624796-0.06721286432190.01553977370360.193328751126-0.01699025513450.01277596819710.126907147841-0.0008260952943160.14468580842524.0319090456-38.8164770988-12.4785957211
91.580736555020.07251417702640.3765041900271.120051024860.2991637954461.40197535134-0.0347020108909-0.05015598427230.0873724642503-0.07215592163770.0085346989370.0501940058317-0.0661349366412-0.02900237852120.02076267523230.1198069728260.005060492519960.008159352112390.12153706603-0.01034661873120.1176439476727.9479365985-28.3836379817-17.424409475
102.124664069810.324595930823-0.7791505578212.001134129570.3925049445762.2580799992-0.0384930386418-0.0527889938932-0.09460809804890.1524315372020.0477791538164-0.1432707175060.243296036080.1898387222610.002198582845050.1629285354230.0496010346379-0.01974027654470.1622924152150.01165046872510.14114387605838.1019027564-36.9039508158-4.66971418948
116.830168363611.762141054173.259597144222.757084814021.579321147214.43268792401-0.2841588481630.3560140568950.321351669822-0.2959156089240.128406011490.0827383375292-0.3993393019370.147001685320.1800078104320.212159800338-0.004214903533790.02189663556310.1606332706820.0255782140910.17052823128535.2548099619-26.7492998854-23.2263175816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 166 )
4X-RAY DIFFRACTION4chain 'A' and (resid 167 through 202 )
5X-RAY DIFFRACTION5chain 'A' and (resid 203 through 224 )
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 66 )
7X-RAY DIFFRACTION7chain 'B' and (resid 67 through 106 )
8X-RAY DIFFRACTION8chain 'B' and (resid 107 through 120 )
9X-RAY DIFFRACTION9chain 'B' and (resid 121 through 166 )
10X-RAY DIFFRACTION10chain 'B' and (resid 167 through 202 )
11X-RAY DIFFRACTION11chain 'B' and (resid 203 through 226 )

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