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- PDB-4zid: Dimeric Hydrogenobacter thermophilus cytochrome c552 obtained fro... -

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Basic information

Entry
Database: PDB / ID: 4zid
TitleDimeric Hydrogenobacter thermophilus cytochrome c552 obtained from Escherichia coli
ComponentsCytochrome c-552
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c, class ID / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / Cytochrome c-552
Similarity search - Component
Biological speciesHydrogenobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHayashi, Y. / Yamanaka, M. / Nagao, S. / Komori, H. / Higuchi, Y. / Hirota, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceNo. 26288080 Japan
Japan Society for the Promotion of ScienceNo. 15K13744 Japan
CitationJournal: Sci Rep / Year: 2016
Title: Domain swapping oligomerization of thermostable c-type cytochrome in E. coli cells
Authors: Hayashi, Y. / Yamanaka, M. / Nagao, S. / Komori, H. / Higuchi, Y. / Hirota, S.
History
DepositionApr 28, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2052
Polymers8,5861
Non-polymers6191
Water52229
1
A: Cytochrome c-552
hetero molecules

A: Cytochrome c-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4094
Polymers17,1722
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area5440 Å2
ΔGint-64 kcal/mol
Surface area9290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.808, 45.808, 78.304
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Cytochrome c-552 / Cytochrome c552


Mass: 8586.015 Da / Num. of mol.: 1 / Fragment: UNP residues 19-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6) (bacteria)
Strain: DSM 6534 / IAM 12695 / TK-6 / Gene: HTH_0988, Hydth_0984 / Plasmid: pKO2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JCB387 / References: UniProt: P15452
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6 M sodium citrate buffer / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 9242 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 37.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 2.2 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
REFMAC5.8.0107data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VYM

3vym


Resolution: 1.8→39.67 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.982 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2035 440 4.8 %RANDOM
Rwork0.16709 ---
obs0.1688 8721 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.799 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20.69 Å20 Å2
2--1.37 Å2-0 Å2
3----4.45 Å2
Refinement stepCycle: 1 / Resolution: 1.8→39.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms601 0 43 29 673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.02662
X-RAY DIFFRACTIONr_bond_other_d0.0060.02650
X-RAY DIFFRACTIONr_angle_refined_deg2.8472.176904
X-RAY DIFFRACTIONr_angle_other_deg1.27831501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.136579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82926.1921
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75715116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.048151
X-RAY DIFFRACTIONr_chiral_restr0.1770.287
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.021742
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02125
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_it2.1072.11319
X-RAY DIFFRACTIONr_mcbond_other2.0922.104318
X-RAY DIFFRACTIONr_mcangle_it2.783.142397
X-RAY DIFFRACTIONr_mcangle_other2.7853.147398
X-RAY DIFFRACTIONr_scbond_it3.1132.427341
X-RAY DIFFRACTIONr_scbond_other3.0882.425337
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4763.512505
X-RAY DIFFRACTIONr_long_range_B_refined6.12718.303794
X-RAY DIFFRACTIONr_long_range_B_other6.13518.268793
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 30 -
Rwork0.256 586 -
obs--91.94 %
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)
111.0560.1797-1.13260.84330.51984.44260.0904-0.6666-0.79680.08570.10170.21860.4272-0.1897-0.19210.0756-0.0326-0.00640.0910.09280.2188-51.113316.72674.4051
27.2283-1.0484-0.13496.9424-1.966310.1763-0.09150.14960.2014-0.10620.1350.2758-0.4208-0.4194-0.04350.1080.034-0.04150.0949-0.02560.1573-29.651915.5012-5.1844
30.05170.311-0.3482.857-6.233424.3935-0.05630.04690.0405-0.02080.0060.0342-1.40310.13430.05030.2151-0.0776-0.00770.23160.14260.4166-17.392518.009-11.3817
415.44061.04898.36968.9280.634433.0388-0.0861-0.04750.41410.0569-0.062-0.4791-0.47390.62920.14810.0749-0.01330.01110.0948-0.00060.1275-15.653711.2765-1.9889
52.5075-1.86091.98964.79121.10226.0555-0.12850.0020.02070.09940.1468-0.0726-0.08750.3892-0.01830.0703-0.03590.01940.07770.00150.1335-19.564111.02060.034
610.6222-0.4295-1.65798.2166-2.68899.74070.07790.5726-0.1079-0.3288-0.06870.28810.26010.0664-0.00920.1081-0.00410.01140.1223-0.04010.0636-25.10519.1245-12.4622
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 18
2X-RAY DIFFRACTION2A19 - 33
3X-RAY DIFFRACTION3A34 - 42
4X-RAY DIFFRACTION4A43 - 48
5X-RAY DIFFRACTION5A49 - 70
6X-RAY DIFFRACTION6A71 - 80

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