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- PDB-6fu3: Structure of the mixed-valence, active form, of cytochrome c pero... -

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Basic information

Entry
Database: PDB / ID: 6fu3
TitleStructure of the mixed-valence, active form, of cytochrome c peroxidase from obligate human pathogenic bacterium Neisseria gonorrhoeae
ComponentsProtein CcpR
KeywordsELECTRON TRANSPORT / Neisseria gonorrhoeae / bacterial peroxidase / ROS detoxification
Function / homology
Function and homology information


cytochrome-c peroxidase / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c551 peroxidase / Cytochrome C peroxidase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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/BBB-BQB/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
DepositionFeb 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: 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 / diffrn / 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_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / 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 / _diffrn.pdbx_serial_crystal_experiment / _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_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _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_d_res_low / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_solvent_vdw_probe_radii / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _reflns_shell.d_res_low / _reflns_shell.number_unique_obs / _software.version / _struct_conn_type.id / _struct_mon_prot_cis.pdbx_omega_angle
Description: Ligand geometry
Details: A LINK instruction was added to the coordinate file to assure covalent binding of the type c heme to the protein. A final refinement step was performed using PDB-REDO.
Provider: author / Type: Coordinate replacement
Revision 2.1Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein CcpR
B: Protein CcpR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7898
Polymers75,2352
Non-polymers2,5546
Water9,440524
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)78.942, 88.780, 93.122
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 Protein CcpR


Mass: 37617.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria)
Gene: ccpA, WHOF_00612, WHOF_02054, WHOG_00329, WHOG_02247C, WHOK_00254, WHOK_02247C, WHOL_00503, WHOL_01944C, WHOM_00704, WHOM_02256C, WHON_00634, WHON_02251C, WHOO_00344, WHOO_01926, WHOP_00646, ...Gene: ccpA, WHOF_00612, WHOF_02054, WHOG_00329, WHOG_02247C, WHOK_00254, WHOK_02247C, WHOL_00503, WHOL_01944C, WHOM_00704, WHOM_02256C, WHON_00634, WHON_02251C, WHOO_00344, WHOO_01926, WHOP_00646, WHOP_02256C, WHOU_00764, WHOU_02329C, WHOV_00550, WHOV_02317C, WHOW_00232, WHOW_02310C, WHOX_00887, WHOX_02246C, WHOY_00586, WHOY_02329C, WHOZ_00270, WHOZ_02318C
Production host: Escherichia coli (E. coli)
References: UniProt: A0A1D3HIT0, UniProt: Q5F5Z9*PLUS, cytochrome-c peroxidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 7.5
Details: 30% 5/4 PO/OH and 0.1M MES pH6.0 in the presence of 2mM CaCl2, 10mM sodium ascorbate and 0.2mM FMN, using a 20mg/mL protein solution previously incubated with calcium, sodium ascorbate and FMN.

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.5418 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Apr 4, 2016
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.79→64.3 Å / Num. obs: 61589 / % possible obs: 99.1 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.1565 / Net I/σ(I): 10.3
Reflection shellResolution: 1.79→1.82 Å / Rmerge(I) obs: 0.8398 / Num. unique obs: 2299

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PROTEUMdata reduction
SAINTdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VHD

2vhd


Resolution: 1.8→23.82 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.836 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.142 / 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
Rfree0.2436 2997 5 %RANDOM
Rwork0.20769 ---
obs0.20946 57511 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.856 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0 Å2
2--0.04 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.8→23.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5062 0 174 524 5760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0185424
X-RAY DIFFRACTIONr_bond_other_d0.0010.0195006
X-RAY DIFFRACTIONr_angle_refined_deg2.1981.9187383
X-RAY DIFFRACTIONr_angle_other_deg1.2282.73811554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1675657
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6223.841276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66315883
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0071526
X-RAY DIFFRACTIONr_chiral_restr0.1390.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026257
X-RAY DIFFRACTIONr_gen_planes_other0.010.021239
X-RAY DIFFRACTIONr_mcbond_it2.1180.9522628
X-RAY DIFFRACTIONr_mcbond_other2.1190.952619
X-RAY DIFFRACTIONr_mcangle_it2.761.4163268
X-RAY DIFFRACTIONr_mcangle_other2.761.4173269
X-RAY DIFFRACTIONr_scbond_it3.6671.2682796
X-RAY DIFFRACTIONr_scbond_other3.6631.2682794
X-RAY DIFFRACTIONr_scangle_other4.9051.764112
X-RAY DIFFRACTIONr_long_range_B_refined6.16712.6386548
X-RAY DIFFRACTIONr_long_range_B_other6.11412.1566423
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 230 -
Rwork0.394 4141 -
obs--98.07 %
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)
11.71980.73240.5651.47860.37690.72740.0117-0.0836-0.05580.05110.0087-0.20880.0120.0275-0.02040.02360.0184-0.00840.0436-0.00650.041527.16442.31233.58
21.25170.823-0.05632.2461-0.10480.38330.0211-0.0611-0.04420.0844-0.01110.1445-0.0132-0.0297-0.010.02350.01750.00820.03950.02060.0336-9.22440.50932.188
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 329
2X-RAY DIFFRACTION2B2 - 325

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