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- PDB-4bm2: CRYSTAL STRUCTURE OF MANGANESE PEROXIDASE 4 FROM PLEUROTUS OSTREA... -

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Basic information

Entry
Database: PDB / ID: 4bm2
TitleCRYSTAL STRUCTURE OF MANGANESE PEROXIDASE 4 FROM PLEUROTUS OSTREATUS - CRYSTAL FORM II
ComponentsMANGANESE PEROXIDASE 4
KeywordsOXIDOREDUCTASE / CLASS II (FUNGAL) PEROXIDASES / PROTOPORPHYRIN IX / 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: 1.391 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 1.2Oct 23, 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)37,4318
Polymers36,3501
Non-polymers1,0817
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.670, 86.560, 40.030
Angle α, β, γ (deg.)90.00, 107.64, 90.00
Int Tables number5
Space group name H-MC121

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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.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.87 Å3/Da / Density % sol: 54.22 % / Description: NONE
Crystal growDetails: 0.1 M NA-ACETATE AT PH 4.6 & 2.0 M (NH4)2SO4.

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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: 1.4→50 Å / Num. obs: 78216 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 10.95 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.5
Reflection shellResolution: 1.4→1.47 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.2 / % possible all: 87.4

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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: 1.391→43.28 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 25.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2445 3884 5 %
Rwork0.221 --
obs0.2221 78113 97.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.391→43.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 65 485 3093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082677
X-RAY DIFFRACTIONf_angle_d1.2563638
X-RAY DIFFRACTIONf_dihedral_angle_d14.097979
X-RAY DIFFRACTIONf_chiral_restr0.079388
X-RAY DIFFRACTIONf_plane_restr0.006481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3909-1.40790.4121800.41371480X-RAY DIFFRACTION54
1.4079-1.42570.26871370.27222712X-RAY DIFFRACTION97
1.4257-1.44450.30241400.24862621X-RAY DIFFRACTION97
1.4445-1.46430.2741290.24012652X-RAY DIFFRACTION97
1.4643-1.48520.28851370.23942665X-RAY DIFFRACTION98
1.4852-1.50740.28681420.24042647X-RAY DIFFRACTION98
1.5074-1.53090.26811430.22342646X-RAY DIFFRACTION98
1.5309-1.5560.27861340.22622674X-RAY DIFFRACTION98
1.556-1.58290.27051370.22072660X-RAY DIFFRACTION98
1.5829-1.61160.25691380.21852690X-RAY DIFFRACTION98
1.6116-1.64260.26521490.21922674X-RAY DIFFRACTION98
1.6426-1.67620.24871450.22262686X-RAY DIFFRACTION98
1.6762-1.71260.30351430.22932640X-RAY DIFFRACTION98
1.7126-1.75250.23981420.22292687X-RAY DIFFRACTION99
1.7525-1.79630.24591370.21592695X-RAY DIFFRACTION99
1.7963-1.84490.26861380.22992725X-RAY DIFFRACTION99
1.8449-1.89910.25391430.22042697X-RAY DIFFRACTION99
1.8991-1.96040.25431370.22812652X-RAY DIFFRACTION99
1.9604-2.03050.26281450.22332737X-RAY DIFFRACTION99
2.0305-2.11180.26931440.21662715X-RAY DIFFRACTION99
2.1118-2.20790.2471470.20862695X-RAY DIFFRACTION99
2.2079-2.32430.24741460.21322705X-RAY DIFFRACTION99
2.3243-2.46990.23511360.21382715X-RAY DIFFRACTION99
2.4699-2.66060.23561490.21232732X-RAY DIFFRACTION99
2.6606-2.92830.22351410.22182726X-RAY DIFFRACTION100
2.9283-3.35190.23811430.21062760X-RAY DIFFRACTION100
3.3519-4.22250.21121370.20052745X-RAY DIFFRACTION100
4.2225-43.30090.2091450.23372796X-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)
10.8445-0.34510.33290.883-0.13620.6854-0.03150.010.0367-0.0446-0.1332-0.2595-0.01780.24440.06140.08210.0047-0.01370.14710.00370.155542.1161-10.835518.2498
20.99260.0159-0.34761.1098-0.210.8293-0.0379-0.0064-0.038-0.01330.04390.06280.08810.0001-0.02770.08820.0141-0.00110.0766-0.00480.089518.876-10.010116.5463
30.47490.0985-0.19770.6388-0.1470.3769-0.04380.0902-0.0734-0.13580.01310.04870.1165-0.03240.02330.12770.0060.00270.0958-0.00350.091923.2609-16.364713.3626
40.2254-0.15150.25070.2326-0.09020.3628-0.0185-0.00940.0056-0.02930.01350.08350.03370.01740.01170.09640.01050.02330.0806-0.00390.076726.8722-9.076520.9715
50.4069-0.1052-0.18160.3277-0.19290.3105-0.00990.0247-0.03310.05480.00990.01550.0324-0.0434-0.01970.0742-0.0063-0.00040.08840.00410.071310.5694-2.745714.5659
60.3742-0.05480.02140.3195-0.02390.32680.02860.0229-0.0130.0082-0.02030.03080.0285-0.048-0.01320.05710.0021-0.00050.08670.00320.067211.31126.47895.15
70.2634-0.07590.00660.7977-0.31080.3056-0.029-0.0363-0.00390.1380.02680.0846-0.0070.0522-0.00210.121-0.0010.00810.09930.00110.089724.9451-0.753924.1563
80.5825-0.14190.17480.6898-0.41330.43660.03060.03320.09460.0124-0.0274-0.0506-0.01610.06870.00310.101-0.0132-0.01050.0954-0.0250.084920.15613.5768.7103
90.59180.19230.01120.32490.12360.7197-0.03430.04450.0010.09910.01310.0082-0.04880.19860.03810.1717-0.00940.04090.12550.02870.091519.927411.7709-3.3062
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2 THROUGH 27 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 28 THROUGH 70 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 71 THROUGH 120 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 121 THROUGH 140 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 141 THROUGH 188 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 189 THROUGH 257 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 258 THROUGH 285 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 286 THROUGH 319 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 320 THROUGH 338 )

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