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- PDB-4blz: CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS... -

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Basic information

Entry
Database: PDB / ID: 4blz
TitleCRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS OSTREATUS - CRYSTAL FORM VI
ComponentsVERSATILE PEROXIDASE I
KeywordsOXIDOREDUCTASE / CLASS II FUNGAL PEROXIDASES
Function / homology
Function and homology information


versatile peroxidase / reactive-black-5:hydrogen-peroxide oxidoreductase activity / manganese peroxidase activity / lignin catabolic process / response to reactive oxygen species / hydrogen peroxide catabolic process / cellular response to oxidative stress / heme binding / extracellular region / metal ion binding
Similarity search - Function
Fungal ligninase / Fungal ligninase, C-terminal / Fungal peroxidase extension region / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. ...Fungal ligninase / Fungal ligninase, C-terminal / Fungal peroxidase extension region / Heme-binding peroxidase Ccp1-like / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidase; domain 1 / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Versatile peroxidase VPL1
Similarity search - Component
Biological speciesPLEUROTUS OSTREATUS (oyster mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMedrano, F.J. / Romero, A.
CitationJournal: Biotechnol.Biofuels / Year: 2014
Title: Ligninolytic Peroxidase Genes in the Oyster Mushroom Genome: Heterologous Expression, Molecular Structure, Catalytic and Stability Properties, and Lignin-Degrading Ability.
Authors: Fernandez-Fueyo, E. / Ruiz-Duenas, F.J. / Martinez, M.J. / Romero, A. / Hammel, K.E. / Medrano, F.J. / Martinez, A.T.
History
DepositionMay 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VERSATILE PEROXIDASE I
B: VERSATILE PEROXIDASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9838
Polymers69,5902
Non-polymers1,3936
Water12,484693
1
A: VERSATILE PEROXIDASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4924
Polymers34,7951
Non-polymers6973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: VERSATILE PEROXIDASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4924
Polymers34,7951
Non-polymers6973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.540, 38.620, 98.190
Angle α, β, γ (deg.)90.00, 91.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein VERSATILE PEROXIDASE I


Mass: 34794.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLEUROTUS OSTREATUS (oyster mushroom) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): W3110 / References: UniProt: Q9UR19*PLUS, versatile peroxidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 49.93 % / Description: NONE
Crystal growDetails: 0.1 M IMIDAZOLE AT PH 8.0, 1.0 M K/NA TARTRATE & 0.2 M NACL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Nov 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 48950 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 17.56 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.27
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.3 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FMU

3fmu


Resolution: 2→49.085 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2718 2366 5 %
Rwork0.2231 --
obs0.2255 47201 96.88 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.433 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.5776 Å20 Å2-1.5291 Å2
2---5.7326 Å20 Å2
3---1.155 Å2
Refinement stepCycle: LAST / Resolution: 2→49.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4852 0 90 693 5635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055082
X-RAY DIFFRACTIONf_angle_d0.9986962
X-RAY DIFFRACTIONf_dihedral_angle_d13.5651796
X-RAY DIFFRACTIONf_chiral_restr0.061770
X-RAY DIFFRACTIONf_plane_restr0.005936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.04090.2991290.24522699X-RAY DIFFRACTION100
2.0409-2.08530.31411480.24612668X-RAY DIFFRACTION100
2.0853-2.13380.28171320.23352737X-RAY DIFFRACTION100
2.1338-2.18720.26951520.242649X-RAY DIFFRACTION100
2.1872-2.24630.63271110.52019X-RAY DIFFRACTION75
2.2463-2.31240.49361070.37822128X-RAY DIFFRACTION79
2.3124-2.3870.26051390.21552709X-RAY DIFFRACTION100
2.387-2.47230.27381490.22152683X-RAY DIFFRACTION100
2.4723-2.57130.25861430.20862733X-RAY DIFFRACTION100
2.5713-2.68830.24271360.21352681X-RAY DIFFRACTION100
2.6883-2.83010.2661540.20182703X-RAY DIFFRACTION100
2.8301-3.00730.26361410.20512741X-RAY DIFFRACTION100
3.0073-3.23950.26321490.20282726X-RAY DIFFRACTION100
3.2395-3.56540.221360.19872724X-RAY DIFFRACTION100
3.5654-4.08110.27961400.21182601X-RAY DIFFRACTION94
4.0811-5.14090.19121430.17172754X-RAY DIFFRACTION100
5.1409-49.09980.19421570.18722880X-RAY DIFFRACTION100
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)
11.4678-0.23640.67950.24560.00780.74950.05550.194-0.2634-0.01420.00250.10180.05550.0691-0.03540.1223-0.0177-0.04260.1405-0.01890.0917-14.9158-1.6441-28.8724
20.55260.04760.49810.2586-0.16610.8697-0.02220.046-0.0331-0.11020.03030.07120.0133-0.05410.00160.0917-0.0153-0.0190.0239-0.00920.0188-12.1143-0.0721-9.9724
30.23770.0570.40111.22141.14441.5863-0.12910.0773-0.36390.54090.28050.3590.7534-0.532-0.09070.5141-0.07910.11710.33420.09540.5819-20.278-7.78180.6443
41.19920.483-0.41351.6616-0.90830.9207-0.08720.32390.0008-0.108-0.02720.15610.18330.1490.11860.15840.0320.04760.31680.05560.1952-12.513711.7626-81.191
51.52790.0112-0.0711.3556-0.15092.29580.0750.093-0.3893-0.17060.1008-0.10580.4978-0.021-0.00220.17320.01490.02310.07880.00580.2504-23.69042.0599-68.1457
60.83670.0429-0.35030.6601-0.10290.9902-0.08190.0007-0.04060.2180.0111-0.21830.20.07310.07850.14380.01050.00340.26430.00390.2212-14.82063.9163-53.9474
71.1441-0.70280.45210.8810.08270.75940.0135-0.0309-0.1632-0.1311-0.0727-0.12140.16530.20590.04260.19120.05750.09420.18770.03730.2737-14.87983.6581-69.4964
80.4435-0.15790.11480.3598-0.18230.3742-0.0607-0.01990.098-0.0285-0.0098-0.05740.05930.0720.06320.12210.00150.02120.12650.02420.1067-22.202710.674-56.2402
90.61490.0422-0.32090.6631-0.39260.3822-0.00850.0893-0.071-0.1106-0.0360.04890.06530.01730.04180.10340.01590.01990.0874-0.00740.1347-39.00394.0954-58.7377
100.5774-0.1742-0.49480.3167-0.01130.66010.09160.12090.12820.02280.0456-0.03890.03540.0406-0.09860.16370.01880.03520.14690.02820.1805-26.756616.0131-68.5701
111.3209-0.0595-0.03910.5634-0.10520.8162-0.00210.1417-0.2113-0.41680.0610.09330.084-0.0426-0.05220.26290.0083-0.02260.1481-0.00590.2271-49.84656.5131-63.1794
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:159)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 160:313)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 314:330)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 2:28)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 29:50)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 51:82)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 83:114)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 115:159)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 160:251)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 252:297)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 298:330)

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