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- PDB-6erc: Peroxidase A from Dictyostelium discoideum (DdPoxA) -

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Basic information

Entry
Database: PDB / ID: 6erc
TitlePeroxidase A from Dictyostelium discoideum (DdPoxA)
ComponentsPeroxinectin A
KeywordsOXIDOREDUCTASE / Heme peroxidase / modified heme / halide oxidation / antibacterial activity / social amoeba
Function / homology
Function and homology information


Thyroxine biosynthesis / : / Events associated with phagocytolytic activity of PMN cells / iodide peroxidase activity / Neutrophil degranulation / thiocyanate peroxidase activity / peroxidase / hydrogen peroxide catabolic process / peroxidase activity / response to oxidative stress ...Thyroxine biosynthesis / : / Events associated with phagocytolytic activity of PMN cells / iodide peroxidase activity / Neutrophil degranulation / thiocyanate peroxidase activity / peroxidase / hydrogen peroxide catabolic process / peroxidase activity / response to oxidative stress / defense response to bacterium / immune response / heme binding / endoplasmic reticulum / extracellular region
Similarity search - Function
Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Haem peroxidase superfamily
Similarity search - Domain/homology
beta-D-mannopyranose / PROTOPORPHYRIN IX CONTAINING FE / Peroxinectin A
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.50001845399 Å
AuthorsNicolussi, A. / Mlynek, G. / Furtmueller, P.G. / Djinovic-Carugo, K. / Obinger, C.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundW1224 Austria
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Secreted heme peroxidase from Dictyostelium discoideum: Insights into catalysis, structure, and biological role.
Authors: Nicolussi, A. / Dunn, J.D. / Mlynek, G. / Bellei, M. / Zamocky, M. / Battistuzzi, G. / Djinovic-Carugo, K. / Furtmuller, P.G. / Soldati, T. / Obinger, C.
History
DepositionOct 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 7, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxinectin A
B: Peroxinectin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,88917
Polymers117,0752
Non-polymers2,81415
Water2,954164
1
A: Peroxinectin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,21410
Polymers58,5381
Non-polymers1,6779
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxinectin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6757
Polymers58,5381
Non-polymers1,1376
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.253, 128.253, 146.015
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Peroxinectin A


Mass: 58537.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: poxA, DDB_G0277275 / Production host: Komagataella pastoris (fungus) / Variant (production host): BG11 / References: UniProt: Q6TMK4, peroxidase

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Sugars , 2 types, 5 molecules

#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-BMA / beta-D-mannopyranose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 7 types, 174 molecules

#3: 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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M BIS-TRIS, pH 5.5, 0.2 M MgSO4, 23.2% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 25, 2017
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.5→48.672 Å / Num. obs: 48501 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 55.7108172641 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.3149 / Rpim(I) all: 0.1043 / Rrim(I) all: 0.3319 / Net I/σ(I): 7.64
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 9.7 % / Rmerge(I) obs: 4.14 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4813 / CC1/2: 0.298 / Rpim(I) all: 1.395 / Rrim(I) all: 4.372 / % possible all: 99.98

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.50001845399→48.6716666667 Å / SU ML: 0.508372546101 / Cross valid method: FREE R-VALUE / σ(F): 1.34082399034 / Phase error: 31.6616486608
RfactorNum. reflection% reflection
Rfree0.256737835507 1189 2.45265893808 %
Rwork0.228062798378 --
obs0.228760684094 48478 99.9525782974 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 71.3662475869 Å2
Refinement stepCycle: LAST / Resolution: 2.50001845399→48.6716666667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8240 0 182 164 8586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005508470305248669
X-RAY DIFFRACTIONf_angle_d0.54672412515311737
X-RAY DIFFRACTIONf_chiral_restr0.03964105915281219
X-RAY DIFFRACTIONf_plane_restr0.003385542898141552
X-RAY DIFFRACTIONf_dihedral_angle_d11.34510039435155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.61380.3724505805391430.3921542487715861X-RAY DIFFRACTION99.9666999667
2.6138-2.75160.3955508040521490.3623942766695804X-RAY DIFFRACTION99.9664147775
2.7516-2.9240.3612266053761480.3186451188365891X-RAY DIFFRACTION99.9338077114
2.924-3.14970.3403648011931450.2862986387415833X-RAY DIFFRACTION99.9331327315
3.1497-3.46660.2603242726031500.256295168795919X-RAY DIFFRACTION100
3.4666-3.9680.2489082124811480.2058425758335898X-RAY DIFFRACTION100
3.968-4.99850.2151365697231490.1802504346975944X-RAY DIFFRACTION99.9671862182
4.9985-48.68090.2030036597341570.183888277326139X-RAY DIFFRACTION99.8889417738
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)
11.011965648550.2789981869-0.1251193140941.249860482040.05009023404172.873952466990.01217134715590.003175001555820.03556185689090.0452933399303-0.06956287303750.0655765096214-0.0705372529929-0.2651174026890.05853735935940.3496885536690.02385709182440.001699020245240.3225355673390.004109020711320.35320148164555.108113358-21.6436281166-35.2060820281
22.40927428633-0.4122730145450.7378872555351.7419643595-0.0829807092662.59459085144-0.0158877141644-0.1762716014840.187359046769-0.04691300689490.0001006062148230.15306767313-0.366456989882-0.3327055208720.01517660475210.474400300758-0.0156321840382-0.01118592302030.446748205828-0.03192958727550.40246489245613.3224293384-34.8833071461-19.6537590087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 21 through 531)
2X-RAY DIFFRACTION2(chain 'B' and resid 21 through 531)

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