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- PDB-3hdl: Crystal Structure of Highly Glycosylated Peroxidase from Royal Pa... -

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Basic information

Entry
Database: PDB / ID: 3hdl
TitleCrystal Structure of Highly Glycosylated Peroxidase from Royal Palm Tree
ComponentsRoyal Palm Tree Peroxidase
KeywordsOXIDOREDUCTASE / peroxidase / palm tree / Glycosylated
Function / homology
Function and homology information


peroxidase / hydrogen peroxide catabolic process / peroxidase activity / response to oxidative stress / heme binding / extracellular region / metal ion binding
Similarity search - Function
Plant peroxidase / Secretory peroxidase / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. ...Plant peroxidase / Secretory peroxidase / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / HYDROGEN PEROXIDE / Peroxidase
Similarity search - Component
Biological speciesRoystonea regia (Cuban royal palm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWatanabe, L. / Moura, P.R. / Bleicher, L. / Nascimento, A.S. / Zamorano, L.S. / Calvete, J.J. / Bursakov, S. / Roig, M.G. / Shnyrov, V.L. / Polikarpov, I.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia).
Authors: Watanabe, L. / de Moura, P.R. / Bleicher, L. / Nascimento, A.S. / Zamorano, L.S. / Calvete, J.J. / Sanz, L. / Perez, A. / Bursakov, S. / Roig, M.G. / Shnyrov, V.L. / Polikarpov, I.
History
DepositionMay 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_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: Royal Palm Tree Peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,93239
Polymers31,8751
Non-polymers8,05738
Water10,557586
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.821, 117.821, 93.447
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-621-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Royal Palm Tree Peroxidase


Mass: 31874.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Roystonea regia (Cuban royal palm)
References: UniProt: D1MPT2*PLUS, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases

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Sugars , 6 types, 9 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][beta-D-xylofuranose-(1-6)]alpha-D- ...alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][beta-D-xylofuranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1189.079 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2[DManpa1-3][DXylfb1-6]DManpa1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1a_1-5][a212h-1b_1-4]/1-2-1-3-3-3-4/a3-b1_a4-c1_c4-d1_d2-e1_d3-f1_d6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}[(3+1)][a-D-Manp]{}[(6+1)][b-D-Xylf]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1a_1-5]/1-2-1-3-3/a3-b1_a4-c1_c4-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2[DManpa1-3]DManpa1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1a_1-5]/1-2-1-3-3-3/a3-b1_a4-c1_c4-d1_d2-e1_d3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#13: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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

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Non-polymers , 7 types, 615 molecules

#7: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-PEO / HYDROGEN PEROXIDE / Hydrogen peroxide


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
#10: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#11: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#12: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#14: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 586 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5 and 2.6 M ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.42 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 1, 2006 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.42 Å / Relative weight: 1
ReflectionResolution: 1.85→44.78 Å / Num. all: 64103 / Num. obs: 64039 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.85→1.95 Å / % possible all: 100

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Processing

Software
NameClassification
MAR345dtbdata collection
MOLREPphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→44.779 Å / SU ML: 0.29 / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.187 3241 5.07 %random
Rwork0.1765 ---
obs0.177 63971 99.82 %-
all-64086 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.685 Å2 / ksol: 0.359 e/Å3
Refinement stepCycle: LAST / Resolution: 1.85→44.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 520 586 3335
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_deg0.946
X-RAY DIFFRACTIONf_dihedral_angle_d18.969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8780.23611530.23732613X-RAY DIFFRACTION99
1.878-1.90740.21271480.22012602X-RAY DIFFRACTION100
1.9074-1.93860.24721380.21382602X-RAY DIFFRACTION100
1.9386-1.97210.25231260.20332628X-RAY DIFFRACTION100
1.9721-2.00790.18771400.19022636X-RAY DIFFRACTION100
2.0079-2.04660.19971480.17232590X-RAY DIFFRACTION100
2.0466-2.08830.19461530.17032623X-RAY DIFFRACTION100
2.0883-2.13370.17621610.16682570X-RAY DIFFRACTION100
2.1337-2.18340.2081290.16642676X-RAY DIFFRACTION100
2.1834-2.2380.19151280.16962598X-RAY DIFFRACTION100
2.238-2.29850.22071310.16722630X-RAY DIFFRACTION100
2.2985-2.36610.17921370.16872644X-RAY DIFFRACTION100
2.3661-2.44250.20871320.16342647X-RAY DIFFRACTION100
2.4425-2.52980.15771550.16852610X-RAY DIFFRACTION100
2.5298-2.6310.18691300.16462657X-RAY DIFFRACTION100
2.631-2.75080.17581420.17072639X-RAY DIFFRACTION100
2.7508-2.89580.19591350.18022658X-RAY DIFFRACTION100
2.8958-3.07720.181430.18052661X-RAY DIFFRACTION100
3.0772-3.31470.17691500.16382625X-RAY DIFFRACTION100
3.3147-3.64810.1711530.15522659X-RAY DIFFRACTION100
3.6481-4.17570.13251420.13492702X-RAY DIFFRACTION100
4.1757-5.25960.14621420.15192695X-RAY DIFFRACTION100
5.2596-44.79210.21331250.19542765X-RAY DIFFRACTION98
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)
10.5280.25820.8540.6843-0.20150.6484-0.12330.02990.04110.06680.1148-0.114-0.04590.1743-0.02890.24080.0456-0.00150.3231-0.04240.23175.857453.673618.3251
20.2033-0.0664-0.4348-0.4010.13170.8352-0.35350.21830.1364-0.12480.06660.156-0.57570.10950.13180.4398-0.0793-0.08560.33920.0460.4071.795771.84867.1326
30.6250.07560.41450.0103-0.00410.732-0.2051-0.00310.22180.04160.14440.0035-0.19880.12310.03630.2858-0.0096-0.02590.2937-0.0210.26340.878862.458915.602
4-0.24520.057-0.02970.040.04730.0709-0.02860.07450.7409-0.2307-0.18210.2031-0.01440.14690.10260.2377-0.0078-0.01880.3769-0.04680.376815.459161.896819.7687
51.2940.22920.28110.43540.22760.0637-0.10210.1249-0.0756-0.05840.1045-0.10220.1060.2006-0.00490.25050.01630.01160.3122-0.03010.22732.215550.90339.967
61.1595-0.57780.63952.0725-0.54880.870.19030.2318-0.188-0.2019-0.0598-0.11880.12270.3315-0.07440.3195-0.0130.080.3972-0.10840.30063.630145.7302-0.1345
71.18840.7295-0.14840.59360.16960.3883-0.07330.1329-0.077-0.1280.11970.05210.00120.0007-0.04450.242300.00910.22960.00420.2357-17.093745.42358.6431
80.29130.03860.1389-0.2378-0.0610.58240.04580.1523-0.6766-0.01030.1759-0.25080.18610.20030.01970.40670.02910.01180.2778-0.19730.4248-7.924832.12130.206
91.6518-1.05330.64060.1294-0.58561.509-0.0151-0.0495-0.6534-0.08310.1098-0.04910.33320.2087-0.09110.28010.07240.01260.2641-0.04850.3773-1.014835.591613.2072
100.17850.03980.31320.2364-0.12470.211-0.21590.30580.0398-0.03110.107-0.1454-0.11070.32560.1260.2623-0.0599-0.01030.388-0.02630.325113.025261.285510.7078
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:54)A1 - 54
2X-RAY DIFFRACTION2(chain A and resid 55:60)A55 - 60
3X-RAY DIFFRACTION3(chain A and resid 61:91)A61 - 91
4X-RAY DIFFRACTION4(chain A and resid 92:97)A92 - 97
5X-RAY DIFFRACTION5(chain A and resid 98:151)A98 - 151
6X-RAY DIFFRACTION6(chain A and resid 152:156)A152 - 156
7X-RAY DIFFRACTION7(chain A and resid 157:253)A157 - 253
8X-RAY DIFFRACTION8(chain A and resid 254:259)A254 - 259
9X-RAY DIFFRACTION9(chain A and resid 260:283)A260 - 283
10X-RAY DIFFRACTION10(chain A and resid 284:304)A284 - 304

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