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- PDB-4bm4: CRYSTAL STRUCTURE OF MANGANESE PEROXIDASE 4 FROM PLEUROTUS OSTREA... -

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Basic information

Entry
Database: PDB / ID: 4bm4
TitleCRYSTAL STRUCTURE OF MANGANESE PEROXIDASE 4 FROM PLEUROTUS OSTREATUS - CRYSTAL FORM IV
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: 2.3 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 16, 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)37,0474
Polymers36,3501
Non-polymers6973
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.870, 86.500, 41.400
Angle α, β, γ (deg.)90.00, 108.05, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.77 Å3/Da / Density % sol: 55.67 % / Description: NONE
Crystal growDetails: 0.1 M CAPS AT PH 10.5, 1.2 M NAH2PO4/0.8 M K2HPO4 & 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: 2.3→50 Å / Num. obs: 18317 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 26.14 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.2
Reflection shellResolution: 2.3→2.43 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 5.2 / % possible all: 92.5

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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: 2.3→43.25 Å / SU ML: 0.64 / σ(F): 1.34 / Phase error: 33.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2971 927 5.1 %
Rwork0.2249 --
obs0.2287 18254 98.67 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.884 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.2014 Å2-0 Å2-2.0542 Å2
2--1.0225 Å2-0 Å2
3----2.2599 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2536 0 45 207 2788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092648
X-RAY DIFFRACTIONf_angle_d1.2513597
X-RAY DIFFRACTIONf_dihedral_angle_d16.826971
X-RAY DIFFRACTIONf_chiral_restr0.079387
X-RAY DIFFRACTIONf_plane_restr0.005478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.42130.35091280.30072423X-RAY DIFFRACTION98
2.4213-2.5730.45261300.30362439X-RAY DIFFRACTION98
2.573-2.77160.35031340.30522476X-RAY DIFFRACTION98
2.7716-3.05040.37071290.26442457X-RAY DIFFRACTION99
3.0504-3.49170.29951280.24412492X-RAY DIFFRACTION99
3.4917-4.39850.27121350.18082491X-RAY DIFFRACTION99
4.3985-43.25760.20671430.16042549X-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)
10.1161-0.0231-0.13881.6370.53280.32240.2040.26-0.1141-0.0387-0.004-0.6479-0.02290.5099-0.03540.14050.0458-0.00470.68830.09420.3507165.1973-9.633719.2229
21.14570.00450.57121.6897-0.22081.3696-0.12850.1593-0.1939-0.2240.19920.04160.40410.018-0.06360.14280.0598-0.02190.205-0.00710.1809142.1795-9.712617.712
31.948-0.17330.22361.4389-0.16330.66620.13720.4538-0.2755-0.6136-0.0385-0.10670.19150.2798-0.010.18670.07110.02920.1436-0.09210.1216143.9038-18.477212.3749
40.829-0.28420.35951.3775-0.62440.6070.07780.1541-0.0562-0.009-0.0973-0.02960.02530.23370.01360.08970.0045-0.01050.13360.02660.0647142.1589-4.572915.0076
51.57670.70420.74621.1280.14790.88310.03690.8062-0.0807-0.09540.0004-0.1003-0.01090.00660.06910.1386-0.01120.0080.47970.04680.11132.73555.29010.8744
60.6813-0.35770.07151.1002-0.05690.0274-0.1119-0.09080.03330.2775-0.0926-0.1022-0.16740.25490.1190.0912-0.0437-0.06670.39830.06510.1425141.26434.490420.301
70.4114-0.66150.29251.3737-0.34790.2566-0.05950.23870.1130.0432-0.0785-0.3227-0.20320.05150.08750.2129-0.0607-0.06220.58010.18450.2928153.43879.113911.231
80.4426-0.1969-0.02380.64010.09310.34020.06990.19280.2921-0.1149-0.1297-0.4167-0.04470.2028-0.01750.2212-0.02650.04630.51670.18960.2744137.786915.82912.8097
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:28)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 29:70)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 71:101)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 102:201)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 202:235)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 236:285)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 286:303)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 304:337)

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