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- PDB-6vdy: Crystal Structure of Dehaloperoxidase B wild type in Complex with... -

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Basic information

Entry
Database: PDB / ID: 6vdy
TitleCrystal Structure of Dehaloperoxidase B wild type in Complex with Substrate Trichlorophenol
ComponentsDehaloperoxidase B
KeywordsOXIDOREDUCTASE / heme peroxidase / peroxygenase / heme cofactor / oxygen binding
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / metal ion binding
Similarity search - Function
Myoglobin-like, M family globin domain / Globin/Protoglobin / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 2,4,6-trichlorophenol / Dehaloperoxidase B
Similarity search - Component
Biological speciesAmphitrite ornata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGhiladi, R.A. / de Serrano, V.S. / McGuire, A. / Malewschik, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: Nonnative Heme Incorporation into Multifunctional Globin Increases Peroxygenase Activity an Order and Magnitude Compared to Native Enzyme
Authors: McGuire, A.H. / Petit, A.R. / Kang, J. / Malewschik, T. / de Serrano, V. / Carey, L.M. / Ghiladi, R.A.
History
DepositionDec 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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

Downloads & links

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Assembly

Deposited unit
A: Dehaloperoxidase B
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,89712
Polymers30,8292
Non-polymers2,06810
Water2,990166
1
A: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4836
Polymers15,4141
Non-polymers1,0685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dehaloperoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4156
Polymers15,4141
Non-polymers1,0005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.227, 67.457, 68.132
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dehaloperoxidase B


Mass: 15414.462 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphitrite ornata (invertebrata) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): Gold(DE3)pLysS / References: UniProt: Q9NAV7

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Non-polymers , 5 types, 176 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-T6C / 2,4,6-trichlorophenol


Mass: 197.446 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H3Cl3O
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.2 M Ammonium Sulphate MPEG 2000 29-33%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→37.26 Å / Num. obs: 30258 / % possible obs: 98.79 % / Redundancy: 4.9 % / Biso Wilson estimate: 23.12 Å2 / CC1/2: 0.998 / Net I/σ(I): 35.5
Reflection shellResolution: 1.7→1.745 Å / Num. unique obs: 2098 / CC1/2: 0.848

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Processing

Software
NameVersionClassification
PHENIXdev_3714refinement
PHENIXdev_3714refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IXF

3ixf


Resolution: 1.7→37.26 Å / SU ML: 0.1786 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.5092
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2141 1453 4.8 %
Rwork0.1788 28805 -
obs0.1805 30258 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.06 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 124 167 2413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01562650
X-RAY DIFFRACTIONf_angle_d1.44353659
X-RAY DIFFRACTIONf_chiral_restr0.0781366
X-RAY DIFFRACTIONf_plane_restr0.0083489
X-RAY DIFFRACTIONf_dihedral_angle_d21.8712395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.760.26541430.21582827X-RAY DIFFRACTION99.17
1.76-1.830.27681310.20542894X-RAY DIFFRACTION99.93
1.83-1.920.26621450.20332867X-RAY DIFFRACTION99.74
1.92-2.020.2391500.19182843X-RAY DIFFRACTION99.44
2.02-2.140.24311410.18262876X-RAY DIFFRACTION99.02
2.14-2.310.22031420.17582864X-RAY DIFFRACTION98.75
2.31-2.540.20591640.16992852X-RAY DIFFRACTION98.89
2.54-2.910.2021250.18032920X-RAY DIFFRACTION98.7
2.91-3.660.20921440.17372898X-RAY DIFFRACTION98.35
3.66-37.260.19621680.17222964X-RAY DIFFRACTION96.19
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)
13.7703198877-1.827539156191.15314408742.41685431829-1.246314235783.87956312105-0.0987075044439-0.243689224103-0.2821454078370.07722765157450.1160804597790.2128880673720.010352661108-0.298950036028-0.006891490954480.138308087615-0.0136380253783-0.0007717521102450.1552398016970.005339156387290.155971971239-0.187988519743-2.07507639542-23.7953955257
28.30094851505-1.164480443164.104235592789.116413106353.737756975618.96245543097-0.432182516679-0.4700448086570.6171732205660.4982999987340.156282833594-0.195719971909-0.1728153766840.6935659693540.279282828980.1516434318330.009116967360380.004762838306770.34344787890.06903850387470.26320212541116.7603899068-3.98985874127-15.1311478072
33.634569990914.809564594313.108162230158.990376673442.385663148273.960222784610.0690716647006-0.0207656283610.5623878179190.496722013912-0.17951787116-0.164819890384-0.6120450643650.6048123006820.06011942165680.5363850032-0.170656704120.05986247754530.621231438554-0.1379886039220.67137419457111.4914973359-1.1440065839-7.55431471872
42.34717584111-2.726526603610.1477321062048.59962613173-1.102500924861.82846159553-0.537185427231-0.557200315033-0.3648952224680.9956189087170.386524607630.543942313440.159057728251-0.01920463105410.1394547398090.3219597318770.06012261521250.1029779719270.2680020309570.04370665572220.2420151819772.45631450926-5.3986657711-10.7300520936
52.384922652180.600972547566-1.291315712621.07898843346-0.1348694944290.7477104557390.347403918742-0.3331277599680.2921997715740.44651309912-0.2405388517480.144122994155-0.799982472060.496929812823-0.06878237936440.364851251088-0.0592303764024-0.02050031736810.22544118824-0.04237851853720.2099197168221.6735870746812.4721358153-25.6485439221
61.634771919581.8024493847-2.400924195727.19302847706-0.6150351728069.330649839030.145476265688-0.355109464748-0.1432740152860.939879614987-0.2675612515020.02580940283260.2559220085540.149755760940.0466468975551.28952924272-0.522062856568-0.1753614974080.920553584409-0.1134415834180.7493771398048.9791480479912.6861362947-12.0830350526
72.69677367318-2.8383026825-1.735577203745.462464081890.06861798471788.66994826031-0.273271957303-0.4099996950520.7978827179450.988852179146-0.173951597122-0.957647245663-1.355847864330.9173610974220.3028466229240.509651589757-0.152363515626-0.2005289729310.3700238842820.1246631761640.47295793148115.56614421635.56941173839-19.956306446
88.928385354620.7811790384861.011372131697.686786917552.14646031892.42156340162-0.07129181829580.484025681762-0.639169602294-0.0211778869379-0.397716797425-0.04725604444460.3012694119050.3213790531430.3820596522830.2018752168770.04059696211720.03248788260670.1900785124160.01653660066510.237850234168.26458761133-4.46843897489-29.0573636345
98.391466886444.479983586071.703617413249.005224399323.329678653086.942212114950.01300503707410.412475214424-0.4448497073810.00724085569265-0.167634665455-0.67565040992-0.1976657759610.4065000445690.1225582929790.1244313073950.00916774022501-0.03469976097960.1608431330140.06610338154120.2007858093476.883301088622.53811934704-32.6595334006
101.015404884931.32529052079-0.2175861973152.335063868770.2120693580160.451417808483-0.0204060564791-0.0703800005318-0.04448720340540.238380270664-0.0525389060968-0.2879195772450.05109873223690.09584303534750.01064011075720.814209459732-0.592334170289-0.4306704727350.2008980544940.212773879040.55476800002514.946925062615.3179227915-21.868758448
111.421655189530.349976692382-0.8617975045463.0555950795-0.8265730221682.03514150899-0.0672650171723-0.144852650781-0.1092614947970.1075610496150.0804574965677-0.27711793143-0.009898498484310.0792518830015-0.006705436362240.1549634266-0.0103213437019-0.03399142899910.18712690922-0.02461659635020.13653397753-17.01048780536.1720109955-14.5263426078
124.46888445088-2.664484115851.260879361512.21568161911-2.473151376355.234946007840.1019563924350.877643652856-0.804052929537-0.9467938695480.05526284894981.196251185490.440761730624-0.0849098542504-0.1181145698760.305176940051-0.014114688306-0.0504183377640.378956552345-0.09828013722310.361765514588-26.9535861437-8.04889057236-13.0703389156
134.955331392941.74425003589-4.840863056642.848006869-2.292489885934.8866831734-0.155389189997-0.53121671016-0.616154173615-0.0934991549653-0.500510433467-0.6026432426450.7558414528541.035700990620.7066610338080.2749291257570.05006602711580.02771944746770.3923877907480.09980636833120.273984082379-18.0755619413-6.92013398943-5.48637001968
142.95038198277-3.155152368980.558809121879.78552729142-5.720664863814.19423043011-0.2355768204210.092185618805-0.312559026709-0.3005775516460.0680671528139-0.1469363994690.530120402260.05682862306050.2562765664930.21576771573-0.01451834845640.03843418921190.219197066763-0.01060094246160.230422019237-14.9213506955-2.99925402411-17.5738135305
153.58108655594-2.796168255041.707262028798.30263705477-4.889700618674.576706409260.2674627770510.2269458890730.0170151881307-0.295434767175-0.191895241983-0.0254701408755-0.1705765252270.363625318606-0.09944592087320.217557118156-0.0225905963120.02361912585970.190786580864-0.02703351903270.135325448506-17.046894356710.5463813721-28.8726798388
161.72092241658-0.02799287504921.210023413310.1357524192340.5492949863823.243361795610.644558845618-0.149905488995-0.8858317773370.251868751818-0.054701691371-0.1574085967021.17127759762-0.129185939894-0.6012916765110.7641518940640.0580597520448-0.481784384630.358878118944-0.0858794800490.57567097869-22.99037138580.202342453798-33.2220817586
175.93284180813-4.68616500013-3.32681178587.230991406423.107273056122.339226418210.1319604572680.691618076248-1.481525672910.109251000896-0.1505833534020.5238424105390.873077767988-0.05812475858270.2236380724050.989841047067-0.178160083991-0.09052578299110.564613124362-0.1678865942410.875636394076-28.2730826219-3.56641454189-26.4243430904
188.472686991495.537649158864.184745530848.402311134384.879132203023.05902546211-0.176686768117-0.3259399702010.1530156010810.0008617810153770.255424464080.355739368984-0.0504023800856-0.145185015967-0.06652450411580.21214208834-0.01621508788650.00422491144830.2015017667880.0363588641040.131058617468-25.32264029529.61073919047-15.0943231411
199.149635874112.956756899356.35117721625.413517588643.735827451736.51870165272-0.0452308854126-0.3710761747090.348618004607-0.0328006365423-0.01733894076820.188304690205-0.0961797861218-0.47889770320.03597032519020.189808530989-0.03720107250440.02834394687690.1933419130240.009496887225140.139792015665-22.348542102216.2953695736-20.3017410628
204.87048830669-0.3526008132412.872035050363.922045355674.96043731178.930183634330.670930225993-0.420054847598-0.6558455216740.495891844425-0.5925306818420.5243398165381.1240027078-1.51242346580.01396232080060.531198151575-0.163500716272-0.143402819590.5018848181770.01011202471450.298004103585-30.86739160255.64378418562-31.9178937932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:26)
2X-RAY DIFFRACTION2(chain A and resid 27:33)
3X-RAY DIFFRACTION3(chain A and resid 34:37)
4X-RAY DIFFRACTION4(chain A and resid 38:60)
5X-RAY DIFFRACTION5(chain A and resid 61:83)
6X-RAY DIFFRACTION6(chain A and resid 84:90)
7X-RAY DIFFRACTION7(chain A and resid 91:99)
8X-RAY DIFFRACTION8(chain A and resid 100:111)
9X-RAY DIFFRACTION9(chain A and resid 112:128)
10X-RAY DIFFRACTION10(chain A and resid 129:137)
11X-RAY DIFFRACTION11(chain B and resid 1:30)
12X-RAY DIFFRACTION12(chain B and resid 31:39)
13X-RAY DIFFRACTION13(chain B and resid 40:50)
14X-RAY DIFFRACTION14(chain B and resid 51:60)
15X-RAY DIFFRACTION15(chain B and resid 61:77)
16X-RAY DIFFRACTION16(chain B and resid 78:86)
17X-RAY DIFFRACTION17(chain B and resid 87:94)
18X-RAY DIFFRACTION18(chain B and resid 95:111)
19X-RAY DIFFRACTION19(chain B and resid 112:128)
20X-RAY DIFFRACTION20(chain B and resid 129:137)

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