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- PDB-6qkn: Structure of the azide-inhibited form of cytochrome c peroxidase ... -

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Basic information

Entry
Database: PDB / ID: 6qkn
TitleStructure of the azide-inhibited form of cytochrome c peroxidase from obligate human pathogenic bacterium Neisseria gonorrhoeae
ComponentsCytochrome-c peroxidaseCytochrome c peroxidase
KeywordsELECTRON TRANSPORT / Neisseria gonorrhoeae / bacterial peroxidase / ROS detoxification
Function / homology
Function and homology information


cytochrome-c peroxidase / cytochrome-c peroxidase activity / peroxidase activity / electron transfer activity / periplasmic space / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. ...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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
AZIDE ION / HEME C / Protein CcpR / Cytochrome C peroxidase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCarvalho, A.L. / Romao, M.J. / Pauleta, S. / Nobrega, C.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaRECI/BBB-BEP/0124/2012 Portugal
Fundacao para a Ciencia e a TecnologiaPTDC/BIA-BQM/29442/2017 Portugal
CitationJournal: To Be Published
Title: Structure of the mixed-valence, active form, of cytochrome c peroxidase from obligate human pathogenic bacterium Neisseria gonorrhoeae
Authors: Carvalho, A.L. / Romao, M.J. / Pauleta, S. / Nobrega, C.
History
DepositionJan 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / database_2 / entity / pdbx_audit_support / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / reflns_shell / software / struct_conf / struct_conn / struct_conn_type / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_site / struct_site_gen
Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] ..._atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.percent_reflns_obs / _reflns.d_resolution_low / _reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all / _software.version / _struct_mon_prot_cis.pdbx_omega_angle
Description: Ligand geometry
Details: A covalent LINK instruction was added to the coordinates file to bind the Type c hemes to the cysteine residues in the protein. A final refinement of the coordinates was performed.
Provider: author / Type: Coordinate replacement
Revision 2.1Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome-c peroxidase
B: Cytochrome-c peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,24410
Polymers72,6062
Non-polymers2,6388
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.120, 89.140, 94.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome-c peroxidase / Cytochrome c peroxidase / Protein CcpR


Mass: 36302.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: ccpA, E8M64_00570, ERS135259_00627, NCTC13484_01765 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1D3HIT0, UniProt: Q5F5Z9*PLUS, cytochrome-c peroxidase
#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 30 % 5/4 PO/OH and 0.1 M MES pH 6.0 in the presence of 2 mM CaCl2, 10 mM sodium ascorbate and 0.2 mM FMN

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→65 Å / Num. obs: 30270 / % possible obs: 97.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 9.2
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.723 / Num. unique obs: 2907

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FU3

6fu3


Resolution: 2.3→64.95 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 13.06 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.353 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21461 1466 4.9 %RANDOM
Rwork0.1712 ---
obs0.17336 28748 99.18 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.118 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---1.5 Å20 Å2
3---1.11 Å2
Refinement stepCycle: LAST / Resolution: 2.3→64.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5059 0 180 187 5426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0185410
X-RAY DIFFRACTIONr_bond_other_d0.0010.0194991
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.9197358
X-RAY DIFFRACTIONr_angle_other_deg1.1062.73711518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.055652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88823.773273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77915880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0761526
X-RAY DIFFRACTIONr_chiral_restr0.1080.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026224
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021232
X-RAY DIFFRACTIONr_mcbond_it1.5152.0112620
X-RAY DIFFRACTIONr_mcbond_other1.5012.0092611
X-RAY DIFFRACTIONr_mcangle_it2.3043.0063257
X-RAY DIFFRACTIONr_mcangle_other2.3043.0073258
X-RAY DIFFRACTIONr_scbond_it2.3152.2622790
X-RAY DIFFRACTIONr_scbond_other2.1972.262786
X-RAY DIFFRACTIONr_scangle_other3.2273.3114099
X-RAY DIFFRACTIONr_long_range_B_refined4.95224.2926288
X-RAY DIFFRACTIONr_long_range_B_other4.93424.2446272
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 99 -
Rwork0.251 2070 -
obs--98.19 %
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)
12.0828-1.05350.54852.4737-0.37581.30620.00220.1092-0.0375-0.15210.00340.4668-0.0354-0.1723-0.00570.0551-0.0292-0.04290.1327-0.00260.1813-26.983-2.47813.141
21.7628-1.1173-0.1033.1114-0.02420.82590.08830.1119-0.0073-0.1836-0.0613-0.1866-0.01390.0609-0.0270.0558-0.02120.01880.0485-0.0340.04789.354-4.15614.715
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 329
2X-RAY DIFFRACTION2B3 - 325

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