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- PDB-4aan: MacA wild-type fully reduced -

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Basic information

Entry
Database: PDB / ID: 4aan
TitleMacA wild-type fully reduced
ComponentsCYTOCHROME C551 PEROXIDASE
KeywordsOXIDOREDUCTASE / MULTIHEME CYTOCHROMES / CONFORMATIONAL REARRANGEMENT
Function / homology
Function and homology information


cytochrome-c peroxidase activity / periplasmic space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Di-c-type haem protein, MauG/cytochrome c peroxidase / Di-haem cytochrome c peroxidase / Di-haem cytochrome c peroxidase / : / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily ...Di-c-type haem protein, MauG/cytochrome c peroxidase / Di-haem cytochrome c peroxidase / Di-haem cytochrome c peroxidase / : / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(R,R)-2,3-BUTANEDIOL / HEME C / Cytochrome c peroxidase
Similarity search - Component
Biological speciesGEOBACTER SULFURREDUCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsSeidel, J.
CitationJournal: Biochemistry / Year: 2012
Title: Maca is a Second Cytochrome C Peroxidase of Geobacter Sulfurreducens.
Authors: Seidel, J. / Hoffmann, M. / Ellis, K.E. / Seidel, A. / Spatzal, T. / Gerhardt, S. / Elliott, S.J. / Einsle, O.
History
DepositionDec 5, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2012Provider: 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 / 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_alt_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_alt_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 1.2Nov 20, 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: CYTOCHROME C551 PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4528
Polymers36,8151
Non-polymers1,6387
Water6,539363
1
A: CYTOCHROME C551 PEROXIDASE
hetero molecules

A: CYTOCHROME C551 PEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,90516
Polymers73,6302
Non-polymers3,27514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area10190 Å2
ΔGint-143.8 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.600, 46.970, 77.930
Angle α, β, γ (deg.)90.00, 90.94, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2055-

HOH

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Components

#1: Protein CYTOCHROME C551 PEROXIDASE / CYTOCHROME C PEROXIDASE


Mass: 36814.848 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-346
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACTER SULFURREDUCENS (bacteria) / Strain: PCA / Description: DSM / Plasmid: PETSN22 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q74FY6, cytochrome-c peroxidase
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.49 Å3/Da / Density % sol: 50.69 % / Description: NONE
Crystal growpH: 5.6
Details: 0.1 M SODIUM CITRATE PH 5.6, 1 M AMMONIUM PHOSPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→19.5 Å / Num. obs: 103844 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.4
Reflection shellResolution: 1.2→1.3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0113refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HQ6

3hq6


Resolution: 1.22→77.92 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.13 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
RfactorNum. reflection% reflectionSelection details
Rfree0.16624 5188 5 %RANDOM
Rwork0.1469 ---
obs0.14788 98594 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.268 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20.08 Å2
2--0.63 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.22→77.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2437 0 111 363 2911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.022796
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2982.0263864
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6575375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.423.925107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42915452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1351517
X-RAY DIFFRACTIONr_chiral_restr0.1570.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0222176
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.216→1.248 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 378 -
Rwork0.27 7055 -
obs--99.83 %
Refinement TLS params.Method: refined / Origin x: 3.2668 Å / Origin y: -24.5805 Å / Origin z: -22.0362 Å
111213212223313233
T0.0146 Å2-0.0019 Å2-0.0013 Å2-0.0044 Å2-0.0013 Å2--0.0138 Å2
L0.1235 °2-0.0257 °2-0.053 °2-0.0175 °20.0032 °2--0.1623 °2
S0.0041 Å °-0.0135 Å °0.0064 Å °0.0088 Å °0.0049 Å °-0.0087 Å °-0.0035 Å °0 Å °-0.009 Å °

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