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- PDB-2oyy: HTHP: a hexameric tyrosine-coordinated heme protein -

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Basic information

Entry
Database: PDB / ID: 2oyy
TitleHTHP: a hexameric tyrosine-coordinated heme protein
ComponentsHexameric cytochrome
KeywordsUNKNOWN FUNCTION / all helical
Function / homology
Function and homology information


Hexameric tyrosine-coordinated heme protein (HTHP) / Hexameric tyrosine-coordinated heme protein (HTHP) / HTHP domain superfamily / Hexameric tyrosine-coordinated heme protein (HTHP) / DNA polymerase; domain 1 / Helix non-globular / Special
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / IODIDE ION / Peroxidase
Similarity search - Component
Biological speciesSilicibacter pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.5 Å
AuthorsDobbek, H.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: HTHP: A Novel Class of Hexameric, Tyrosine-coordinated Heme Proteins
Authors: Jeoung, J.H. / Pippig, D.A. / Martins, B.M. / Wagener, N. / Dobbek, H.
History
DepositionFeb 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hexameric cytochrome
B: Hexameric cytochrome
C: Hexameric cytochrome
D: Hexameric cytochrome
E: Hexameric cytochrome
F: Hexameric cytochrome
G: Hexameric cytochrome
H: Hexameric cytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,41928
Polymers66,9648
Non-polymers6,45520
Water00
1
A: Hexameric cytochrome
B: Hexameric cytochrome
hetero molecules

A: Hexameric cytochrome
B: Hexameric cytochrome
hetero molecules

A: Hexameric cytochrome
B: Hexameric cytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,06421
Polymers50,2236
Non-polymers4,84115
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
2
C: Hexameric cytochrome
D: Hexameric cytochrome
E: Hexameric cytochrome
F: Hexameric cytochrome
G: Hexameric cytochrome
H: Hexameric cytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,06421
Polymers50,2236
Non-polymers4,84115
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22060 Å2
ΔGint-203 kcal/mol
Surface area16060 Å2
MethodPISA
3
A: Hexameric cytochrome
B: Hexameric cytochrome
hetero molecules

A: Hexameric cytochrome
B: Hexameric cytochrome
hetero molecules

A: Hexameric cytochrome
B: Hexameric cytochrome
hetero molecules

C: Hexameric cytochrome
D: Hexameric cytochrome
E: Hexameric cytochrome
F: Hexameric cytochrome
G: Hexameric cytochrome
H: Hexameric cytochrome
hetero molecules

C: Hexameric cytochrome
D: Hexameric cytochrome
E: Hexameric cytochrome
F: Hexameric cytochrome
G: Hexameric cytochrome
H: Hexameric cytochrome
hetero molecules

C: Hexameric cytochrome
D: Hexameric cytochrome
E: Hexameric cytochrome
F: Hexameric cytochrome
G: Hexameric cytochrome
H: Hexameric cytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,25684
Polymers200,89124
Non-polymers19,36460
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation4_455x-1/3,y+1/3,z+1/31
crystal symmetry operation5_455-y-1/3,x-y+1/3,z+1/31
crystal symmetry operation6_455-x+y-1/3,-x+1/3,z+1/31
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area89860 Å2
ΔGint-819 kcal/mol
Surface area63090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.710, 173.710, 45.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: 4 / Auth seq-ID: 1 - 71 / Label seq-ID: 4 - 74

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
DetailsHexameric structure with C6 symmetry

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Components

#1: Protein
Hexameric cytochrome


Mass: 8370.478 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi (bacteria) / Gene: spoa0176 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: Q5LL55
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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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: 1.99 Å3/Da / Density % sol: 38.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 19-20 % PEG 3350, 0.1-0.5 M NH4I, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5817 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 12, 2005
RadiationMonochromator: Osmic mirror system / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5817 Å / Relative weight: 1
ReflectionResolution: 2.5→86.71 Å / Num. all: 35734 / Num. obs: 35356 / % possible obs: 98.1 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.5→2.6 Å / Mean I/σ(I) obs: 3.8 / % possible all: 98.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHARPphasing
REFMAC5.2refinement
MAR345345DTBdata collection
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→86.71 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.87 / SU B: 25.16 / SU ML: 0.29 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26867 911 5.1 %RANDOM
Rwork0.23421 ---
all0.23599 17867 --
obs0.23599 16942 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 3.796 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0.23 Å20 Å2
2---0.46 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.5→86.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 356 0 4732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224864
X-RAY DIFFRACTIONr_angle_refined_deg1.3172.1526776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0575560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00324.348184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.33515688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1891524
X-RAY DIFFRACTIONr_chiral_restr0.0790.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023672
X-RAY DIFFRACTIONr_nbd_refined0.2520.23075
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23398
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2153
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.28
X-RAY DIFFRACTIONr_mcbond_it0.2541.52850
X-RAY DIFFRACTIONr_mcangle_it0.48924600
X-RAY DIFFRACTIONr_scbond_it0.92432304
X-RAY DIFFRACTIONr_scangle_it1.4974.52160
Refine LS restraints NCS

Ens-ID: 1 / Number: 548 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.20.5
2Bmedium positional0.220.5
3Cmedium positional0.20.5
4Dmedium positional0.220.5
5Emedium positional0.190.5
6Fmedium positional0.220.5
7Gmedium positional0.220.5
8Hmedium positional0.210.5
1Amedium thermal0.342
2Bmedium thermal0.352
3Cmedium thermal0.32
4Dmedium thermal0.282
5Emedium thermal0.282
6Fmedium thermal0.322
7Gmedium thermal0.272
8Hmedium thermal0.292
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 66 -
Rwork0.315 1283 -
obs--100 %
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)
10.60370.51120.64791.83480.43131.1490.00950.13050.0748-0.0897-0.05950.4479-0.0767-0.30770.05-0.1020.019-0.0314-0.07190.0291-0.1146-12.28449.66982.2425
20.763-0.08030.9651.0106-0.48493.77250.09330.1758-0.2259-0.2252-0.08420.29540.0584-0.2477-0.0091-0.1545-0.0224-0.0424-0.0406-0.0423-0.1627-14.4346-5.74172.1969
32.79391.01690.01690.9326-0.02121.44140.1644-0.0118-0.08790.02590.0225-0.3669-0.08530.127-0.1869-0.08830.01620.0023-0.103-0.0616-0.1155-30.459716.7363-10.4426
41.5-0.0253-0.09090.0726-0.38752.10290.0118-0.01370.4325-0.0064-0.0708-0.32570.01360.13970.059-0.10140.02660.0743-0.03380.0130.0706-29.850831.8954-13.7999
51.7133-1.06880.36621.4450.96481.90760.06450.0991-0.26660.0683-0.15360.4716-0.0736-0.02640.0892-0.1054-0.03440.0145-0.0585-0.0315-0.0503-57.352918.243-8.909
60.7063-0.29560.15081.84770.36221.72550.0784-0.0979-0.47210.17180.02670.15230.17020.2066-0.105-0.09520.00830.0393-0.04360.016-0.0579-44.26649.8987-8.0049
71.14260.0287-0.39420.83850.68330.90490.01720.23590.5938-0.1746-0.11-0.0624-0.0703-0.03480.0928-0.01160.04680.0724-0.07450.05480.0478-42.976640.184-14.7379
82-0.5793-0.250.9937-0.46871.6540.28580.0670.23850.0489-0.12470.1360.0472-0.2437-0.1611-0.09640.0460.0235-0.0498-0.0014-0.0213-56.703233.466-12.2637
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 714 - 74
2X-RAY DIFFRACTION2BB1 - 714 - 74
3X-RAY DIFFRACTION3CC1 - 714 - 74
4X-RAY DIFFRACTION4DD1 - 714 - 74
5X-RAY DIFFRACTION5EE1 - 714 - 74
6X-RAY DIFFRACTION6FF1 - 714 - 74
7X-RAY DIFFRACTION7GG1 - 714 - 74
8X-RAY DIFFRACTION8HH1 - 714 - 74

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