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- PDB-4czo: Crystal structure of the extralong fungal manganese peroxidase fr... -

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Basic information

Entry
Database: PDB / ID: 4czo
TitleCrystal structure of the extralong fungal manganese peroxidase from Ceriporiopsis subvermispora in complex with manganese
ComponentsEXTRALONG MANGANESE PEROXIDASE
KeywordsOXIDOREDUCTASE / CLASS II (FUNGAL) PEROXIDASES / PROTOPORPHYRIN IX / ELECTRON TRANSFER / LIGNIN PEROXIDASE / LIGNIN DEGRADATION / MANGANESE PEROXIDASE / MNII OXIDATION / PEROXIDASE / HYDROGEN PEROXIDE / IRON / MANGANESE / METAL-BINDING / SECRETED
Function / homologyPeroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Orthogonal Bundle / Mainly Alpha / PROTOPORPHYRIN IX CONTAINING FE / :
Function and homology information
Biological speciesCERIPORIOPSIS SUBVERMISPORA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.199 Å
AuthorsMedrano, F.J. / Romero, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural Implications of the C-Terminal Tail in the Catalytic and Stability Properties of Manganese Peroxidases from Ligninolytic Fungi
Authors: Fernandez-Fueyo, E. / Acebes, S. / Ruiz-Duenas, F.J. / Martinez, M.J. / Romero, A. / Medrano, F.J. / Guallar, V. / Martinez, A.T.
History
DepositionApr 21, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Dec 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 / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EXTRALONG MANGANESE PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5546
Polymers38,7471
Non-polymers8075
Water8,827490
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.450, 108.450, 68.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein EXTRALONG MANGANESE PEROXIDASE


Mass: 38747.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CERIPORIOPSIS SUBVERMISPORA (fungus) / Plasmid: PFLAG1-CSMNP6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 SUBSTR. W3110 / References: 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.5 Å3/Da / Density % sol: 50.77 % / Description: NONE
Crystal growpH: 4.6 / Details: 18% PEG 4000, 100MM NA-ACETATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.2→1.27 Å / Num. obs: 127081 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Biso Wilson estimate: 13.68 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.2
Reflection shellResolution: 1.2→1.27 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MQ5

3mq5
PDB Unreleased entry


Resolution: 1.199→33.461 Å / SU ML: 0.11 / σ(F): 1.34 / Phase error: 13.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1537 6344 5 %
Rwork0.1393 --
obs0.14 126815 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.8 Å2
Refinement stepCycle: LAST / Resolution: 1.199→33.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 47 490 3237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082832
X-RAY DIFFRACTIONf_angle_d1.3183877
X-RAY DIFFRACTIONf_dihedral_angle_d12.28996
X-RAY DIFFRACTIONf_chiral_restr0.075440
X-RAY DIFFRACTIONf_plane_restr0.007518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.199-1.21260.31161980.30823759X-RAY DIFFRACTION95
1.2126-1.22690.2712070.27423919X-RAY DIFFRACTION98
1.2269-1.24190.2822060.24733902X-RAY DIFFRACTION98
1.2419-1.25760.25792070.22733921X-RAY DIFFRACTION98
1.2576-1.27410.22632070.20663914X-RAY DIFFRACTION99
1.2741-1.29160.19862100.19153962X-RAY DIFFRACTION99
1.2916-1.310.19852090.1713966X-RAY DIFFRACTION100
1.31-1.32960.19272070.17053946X-RAY DIFFRACTION100
1.3296-1.35040.19652120.16324023X-RAY DIFFRACTION100
1.3504-1.37250.17342110.15044012X-RAY DIFFRACTION100
1.3725-1.39620.18192100.14093972X-RAY DIFFRACTION100
1.3962-1.42160.1572100.13434014X-RAY DIFFRACTION100
1.4216-1.44890.16282110.12694010X-RAY DIFFRACTION100
1.4489-1.47850.15982100.1183978X-RAY DIFFRACTION100
1.4785-1.51060.13232110.10974021X-RAY DIFFRACTION100
1.5106-1.54580.14132120.10384033X-RAY DIFFRACTION100
1.5458-1.58440.12462100.10334014X-RAY DIFFRACTION100
1.5844-1.62730.12672110.10134011X-RAY DIFFRACTION100
1.6273-1.67520.12362120.10324007X-RAY DIFFRACTION100
1.6752-1.72920.13992120.10674027X-RAY DIFFRACTION100
1.7292-1.7910.12982110.11264025X-RAY DIFFRACTION100
1.791-1.86270.13842130.1174049X-RAY DIFFRACTION100
1.8627-1.94750.14792140.11774044X-RAY DIFFRACTION100
1.9475-2.05020.13682130.11974058X-RAY DIFFRACTION100
2.0502-2.17860.1282130.11974057X-RAY DIFFRACTION100
2.1786-2.34680.13352140.11814072X-RAY DIFFRACTION100
2.3468-2.58280.13382170.13194112X-RAY DIFFRACTION100
2.5828-2.95640.15172170.14364120X-RAY DIFFRACTION100
2.9564-3.7240.15552200.15334160X-RAY DIFFRACTION100
3.724-33.47450.16452290.15724363X-RAY DIFFRACTION100

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