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- PDB-6hih: Cytochrome c prime beta from Methylococcus capsulatus (Bath) -

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Basic information

Entry
Database: PDB / ID: 6hih
TitleCytochrome c prime beta from Methylococcus capsulatus (Bath)
ComponentsCytochrome c
KeywordsOXIDOREDUCTASE / cytochrome / NO / CO / methanotroph
Function / homologyCytochrome P460 / Cytochrome P460 superfamily / Cytochrome P460 / metal ion binding / HEME C / Cytochrome c
Function and homology information
Biological speciesMethylococcus capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsAdams, H. / Chicano, T.M. / Hough, M.A.
CitationJournal: Chem Sci / Year: 2019
Title: One fold, two functions: cytochrome P460 and cytochromec'-beta from the methanotrophMethylococcus capsulatus(Bath).
Authors: Adams, H.R. / Krewson, C. / Vardanega, J.E. / Fujii, S. / Moreno, T. / Sambongi, Y. / Svistunenko, D. / Paps, J. / Andrew, C.R. / Hough, M.A.
History
DepositionAug 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.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_asym_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_asym_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_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,3899
Polymers34,7412
Non-polymers1,6487
Water3,981221
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-104 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.960, 105.960, 105.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-202-

ZN

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cytochrome c


Mass: 17370.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath) (bacteria)
Strain: ATCC 33009 / NCIMB 11132 / Bath / Gene: ccp, MCA2394 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: G1UBD5

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Non-polymers , 5 types, 228 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.27 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15 mg/ml protein mixed with 10 mM ZnSO4, 35% PEG 550, 100 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.6→61.2 Å / Num. obs: 52377 / % possible obs: 99 % / Redundancy: 7.6 % / Biso Wilson estimate: 24.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.018 / Rrim(I) all: 0.051 / Net I/σ(I): 20.9
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 4 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3805 / CC1/2: 0.54 / Rpim(I) all: 0.51 / Rrim(I) all: 1.07 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
xia2data reduction
Aimless0.5.17data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→61.2 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.751 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.074 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20233 2657 5.1 %RANDOM
Rwork0.17663 ---
obs0.17798 49688 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.286 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.6→61.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2107 0 105 221 2433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0152341
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171950
X-RAY DIFFRACTIONr_angle_refined_deg2.1541.7653193
X-RAY DIFFRACTIONr_angle_other_deg1.0681.6964558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7685287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06721.231130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.22115333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2731517
X-RAY DIFFRACTIONr_chiral_restr0.0860.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022842
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02478
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_it2.3392.7271115
X-RAY DIFFRACTIONr_mcbond_other2.3322.7261114
X-RAY DIFFRACTIONr_mcangle_it3.1084.0761395
X-RAY DIFFRACTIONr_mcangle_other3.1074.0781396
X-RAY DIFFRACTIONr_scbond_it3.6482.9941226
X-RAY DIFFRACTIONr_scbond_other3.6462.9941226
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1294.3721793
X-RAY DIFFRACTIONr_long_range_B_refined6.02732.782562
X-RAY DIFFRACTIONr_long_range_B_other5.92532.4012524
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 188 -
Rwork0.305 3596 -
obs--99.34 %

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