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- PDB-4bm1: CRYSTAL STRUCTURE OF MANGANESE PEROXIDASE 4 FROM PLEUROTUS OSTREA... -

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Basic information

Entry
Database: PDB / ID: 4bm1
TitleCRYSTAL STRUCTURE OF MANGANESE PEROXIDASE 4 FROM PLEUROTUS OSTREATUS - CRYSTAL FORM I
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 / 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 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site ...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 / 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
CITRIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Peroxidase
Similarity search - Component
Biological speciesPLEUROTUS OSTREATUS (oyster mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.098 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 1.1Jan 25, 2017Group: Atomic model / Other
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.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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MANGANESE PEROXIDASE 4
B: MANGANESE PEROXIDASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,49531
Polymers72,7002
Non-polymers3,79529
Water21,7441207
1
A: MANGANESE PEROXIDASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,19915
Polymers36,3501
Non-polymers1,84914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MANGANESE PEROXIDASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,29516
Polymers36,3501
Non-polymers1,94515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.990, 75.370, 75.610
Angle α, β, γ (deg.)69.75, 75.69, 75.82
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein MANGANESE PEROXIDASE 4 /


Mass: 36350.035 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: W5IDB6*PLUS, manganese peroxidase

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Non-polymers , 5 types, 1236 molecules

#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 / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1207 / 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

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.16 % / Description: NONE
Crystal growDetails: 0.1 M NA-CITRATE AT PH 5.5 & 2.0 M (NH4)2SO4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.891976
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Nov 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.891976 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 271193 / % possible obs: 83.9 % / Observed criterion σ(I): 2 / Redundancy: 13.5 % / Biso Wilson estimate: 8.92 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.5
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.9 / % possible all: 43

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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: 1.098→38.148 Å / SU ML: 0.09 / σ(F): 1.96 / Phase error: 13.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1473 13516 5 %
Rwork0.1312 --
obs0.132 271117 84.01 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.371 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1536 Å20.7786 Å21.2304 Å2
2---0.2204 Å21.2987 Å2
3---0.0668 Å2
Refinement stepCycle: LAST / Resolution: 1.098→38.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5086 0 221 1207 6514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0165437
X-RAY DIFFRACTIONf_angle_d1.717396
X-RAY DIFFRACTIONf_dihedral_angle_d13.9421974
X-RAY DIFFRACTIONf_chiral_restr0.107776
X-RAY DIFFRACTIONf_plane_restr0.011969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.098-1.11050.29091380.26982798X-RAY DIFFRACTION27
1.1105-1.12350.26221970.2293763X-RAY DIFFRACTION37
1.1235-1.13720.21432260.21324496X-RAY DIFFRACTION44
1.1372-1.15160.2272660.20485138X-RAY DIFFRACTION51
1.1516-1.16680.18683250.19266222X-RAY DIFFRACTION61
1.1668-1.18280.19544130.18127873X-RAY DIFFRACTION77
1.1828-1.19970.21334540.17528445X-RAY DIFFRACTION83
1.1997-1.21760.19824150.16468653X-RAY DIFFRACTION84
1.2176-1.23660.19484720.15948879X-RAY DIFFRACTION87
1.2366-1.25690.19234760.15418902X-RAY DIFFRACTION87
1.2569-1.27850.15954770.14549084X-RAY DIFFRACTION89
1.2785-1.30180.16374770.14479288X-RAY DIFFRACTION91
1.3018-1.32680.15285020.13819387X-RAY DIFFRACTION92
1.3268-1.35390.15624920.13459423X-RAY DIFFRACTION92
1.3539-1.38340.16245020.12939532X-RAY DIFFRACTION93
1.3834-1.41550.14595020.12399459X-RAY DIFFRACTION93
1.4155-1.45090.14255110.11599518X-RAY DIFFRACTION93
1.4509-1.49020.13824990.10679669X-RAY DIFFRACTION94
1.4902-1.5340.13465360.10949585X-RAY DIFFRACTION94
1.534-1.58350.12854850.10929620X-RAY DIFFRACTION94
1.5835-1.64010.13054890.10979685X-RAY DIFFRACTION95
1.6401-1.70580.14065270.11189684X-RAY DIFFRACTION95
1.7058-1.78340.1365180.10929655X-RAY DIFFRACTION95
1.7834-1.87750.12765130.11429765X-RAY DIFFRACTION95
1.8775-1.99510.12895090.11469848X-RAY DIFFRACTION96
1.9951-2.14910.12275190.11199777X-RAY DIFFRACTION96
2.1491-2.36530.12575220.1169882X-RAY DIFFRACTION96
2.3653-2.70750.15295240.13519816X-RAY DIFFRACTION96
2.7075-3.41090.14695110.14219691X-RAY DIFFRACTION95
3.4109-38.17150.14815190.140310064X-RAY DIFFRACTION98

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