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- PDB-4bm3: CRYSTAL STRUCTURE OF MANGANESE PEROXIDASE 4 FROM PLEUROTUS OSTREA... -

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Basic information

Entry
Database: PDB / ID: 4bm3
TitleCRYSTAL STRUCTURE OF MANGANESE PEROXIDASE 4 FROM PLEUROTUS OSTREATUS - CRYSTAL FORM III
ComponentsMANGANESE PEROXIDASE 4
KeywordsOXIDOREDUCTASE / CLASS II (FUNGAL) PEROXIDASES / ELECTRON T LIGNIN PEROXIDASE / LIGNIN DEGRADATION
Function / homology
Function and homology information


Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / 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 / Peroxidase
Similarity search - Component
Biological speciesPLEUROTUS OSTREATUS (oyster mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / 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: _atom_site.occupancy / _citation.country ..._atom_site.occupancy / _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 2.1Nov 13, 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: MANGANESE PEROXIDASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3357
Polymers36,3501
Non-polymers9856
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.250, 86.530, 40.300
Angle α, β, γ (deg.)90.00, 107.82, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2260-

HOH

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Components

#1: Protein MANGANESE PEROXIDASE 4


Mass: 36350.035 Da / Num. of mol.: 1
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: W5IDB6*PLUS, manganese peroxidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.71 Å3/Da / Density % sol: 54.67 % / Description: NONE
Crystal growDetails: 0.1 M TRIS-HCL AT PH 7.0, 2.0 M (NH4)2SO4 & 0.2 M LI2SO4.

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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: 1.65→50 Å / Num. obs: 48575 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 17.78 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.5
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2 / % possible all: 97.6

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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: 1.65→38.366 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 26.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2422 2415 5 %
Rwork0.2104 --
obs0.212 48527 99.55 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.198 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.6551 Å20 Å2-4.7022 Å2
2---7.7933 Å20 Å2
3---4.1383 Å2
Refinement stepCycle: LAST / Resolution: 1.65→38.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 60 398 3001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172668
X-RAY DIFFRACTIONf_angle_d1.6883626
X-RAY DIFFRACTIONf_dihedral_angle_d15.185975
X-RAY DIFFRACTIONf_chiral_restr0.116388
X-RAY DIFFRACTIONf_plane_restr0.009480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6502-1.68380.3461340.33062557X-RAY DIFFRACTION94
1.6838-1.72050.36031420.27982697X-RAY DIFFRACTION100
1.7205-1.76050.33371430.26522713X-RAY DIFFRACTION100
1.7605-1.80450.26661420.23942705X-RAY DIFFRACTION100
1.8045-1.85330.29821420.22442718X-RAY DIFFRACTION100
1.8533-1.90780.27681390.21392743X-RAY DIFFRACTION100
1.9078-1.96940.27821410.20192673X-RAY DIFFRACTION100
1.9694-2.03980.21731480.20312739X-RAY DIFFRACTION100
2.0398-2.12150.24931350.19682748X-RAY DIFFRACTION100
2.1215-2.2180.27541440.20392703X-RAY DIFFRACTION100
2.218-2.33490.21771410.19182683X-RAY DIFFRACTION100
2.3349-2.48120.26261430.19082738X-RAY DIFFRACTION100
2.4812-2.67270.24591410.20172726X-RAY DIFFRACTION100
2.6727-2.94160.24011390.20262717X-RAY DIFFRACTION100
2.9416-3.3670.19931470.19712739X-RAY DIFFRACTION100
3.367-4.24120.18541450.18912733X-RAY DIFFRACTION100
4.2412-38.3760.25631490.23322780X-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)
10.9028-0.14090.28870.32090.12670.20850.0465-0.02730.0257-0.0065-0.1306-0.2527-0.0661-0.00330.00640.12740.0113-0.04310.14280.03350.409742.1036-10.597617.9266
20.0652-0.03360.05450.1323-0.06760.05910.00810.1702-0.0174-0.1385-0.0383-00.17370.027200.14960.0260.01140.1424-0.00280.164724.966-7.77378.5448
30.39080.21910.6780.14330.45261.44640.0180.0581-0.05850.0140.0144-0.0388-0.05980.16510.1360.11950.02470.0180.06080.04430.149910.7143-13.364528.3206
40.9814-0.04080.16090.019-0.0720.27910.1450.0716-0.5379-0.32860.03720.01630.33070.11190.00310.23330.0114-0.04590.1335-0.02550.203514.654-18.623313.5033
50.1397-0.0248-0.05760.14010.11530.1060.05140.0527-0.1517-0.2033-0.1328-0.22750.22070.0691-0.00040.18970.02570.0110.1430.01210.250428.6191-14.528813.4132
60.1771-0.1098-0.03070.0989-0.05150.1468-0.0388-0.0163-0.0887-0.08570.07190.02910.1632-0.013-00.15750.005-0.01410.14670.02610.162326.3678-9.260921.2853
70.0891-0.13860.11670.2089-0.17190.13770.04380.1148-0.067-0.0158-0.00360.00890.0244-0.083800.1311-0.0080.00150.1632-0.00540.103710.4677-2.863614.306
80.07220.06290.0370.28350.06720.02160.02590.1826-0.0021-0.1484-0.04460.0839-0.05010.0154-0.08010.13740.0250.01520.1889-0.00070.088114.71275.95541.6897
90.08720.03910.10990.261-0.11740.22720.01540.12140.0434-0.03680.01340.05960.0530.02010.00140.09470.00110.01830.167-0.00070.0938.87196.98928.2445
100.10610.0069-0.06140.10520.03690.04920.0241-0.0148-0.08930.1786-0.0589-0.1973-0.02550.1226-0.00010.1851-0.0121-0.02250.16940.01620.167125.221-0.892324.3717
110.2140.20940.15050.39380.06370.1332-0.0499-0.10650.09480.0622-0.0162-0.1921-0.08670.04460.03190.1272-0.0039-0.01770.13720.01030.1719.801713.89668.8368
120.37330.0844-0.38060.0720.01890.82510.0028-0.05230.02790.06340.0384-0.0267-0.16840.12730.34270.2664-0.00860.06810.21030.02490.099620.19210.6595-3.4132
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:27)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 28:50)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 51:70)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 71:88)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 89:120)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 121:140)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 141:188)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 189:219)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 220:257)
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 258:285)
11X-RAY DIFFRACTION11CHAIN A AND (RESSEQ 286:319)
12X-RAY DIFFRACTION12CHAIN A AND (RESSEQ 320:338)

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