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- PDB-7de4: Hybrid cluster protein (HCP) from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 7de4
TitleHybrid cluster protein (HCP) from Escherichia coli
ComponentsHydroxylamine reductase
KeywordsOXIDOREDUCTASE / Hybrid cluster / iron-sulfur cluster / METAL BINDING PROTEIN
Function / homology
Function and homology information


hydroxylamine reductase / nitric oxide catabolic process / hydroxylamine reductase activity / peroxidase activity / response to hydrogen peroxide / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / metal ion binding / cytoplasm
Similarity search - Function
Hydroxylamine reductase / Prismane, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily
Similarity search - Domain/homology
FE-S-O HYBRID CLUSTER / IRON/SULFUR CLUSTER / Hydroxylamine reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.61 Å
AuthorsFujishiro, T. / Ooi, M. / Takaoka, K. / Takahashi, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K14510 Japan
CitationJournal: Febs J. / Year: 2021
Title: Crystal structure of Escherichia coli class II hybrid cluster protein, HCP, reveals a [4Fe-4S] cluster at the N-terminal protrusion.
Authors: Fujishiro, T. / Ooi, M. / Takaoka, K.
History
DepositionNov 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Derived calculations / Category: citation / database_2 / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 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: Hydroxylamine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9113
Polymers61,2241
Non-polymers6872
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-44 kcal/mol
Surface area20290 Å2
Unit cell
Length a, b, c (Å)142.540, 142.540, 117.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Hydroxylamine reductase / Hybrid-cluster protein / HCP / Prismane protein


Mass: 61223.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: hcp, ybjW, b0873, JW0857 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P75825, hydroxylamine reductase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FS2 / FE-S-O HYBRID CLUSTER


Mass: 335.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4O3S2 / Feature type: SUBJECT OF INVESTIGATION
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: 4.86 Å3/Da / Density % sol: 74.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2.0M Sodium formate, 0.1M Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 27, 2018
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.61→46.29 Å / Num. obs: 14324 / % possible obs: 99.5 % / Redundancy: 11.48 % / Biso Wilson estimate: 95.64 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 14.16
Reflection shellResolution: 3.61→3.71 Å / Redundancy: 11.98 % / Rmerge(I) obs: 0.975 / Mean I/σ(I) obs: 3.01 / Num. unique obs: 13606 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W9M

1w9m


Resolution: 3.61→46.29 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.864 / SU B: 62.727 / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.57 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.278 717 5 %RANDOM
Rwork0.203 ---
obs0.207 13606 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 129.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20 Å2
2---0.51 Å20 Å2
3---1.01 Å2
Refinement stepCycle: LAST / Resolution: 3.61→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4220 0 17 0 4237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124344
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.3781.6335909
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1575549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27523.033211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.05715708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.6261522
X-RAY DIFFRACTIONr_chiral_restr0.1960.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023265
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.61→3.7 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 52 -
Rwork0.408 976 -
obs--99.71 %
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)
19.1353-7.03720.31825.4658-0.18770.1458-0.2178-0.7795-0.5880.11560.51110.3624-0.00270.0384-0.29330.20920.1217-0.07820.7585-0.13390.5709-29.9808-18.6734-0.2851
21.2324-0.158-1.26791.87151.00211.71280.0295-0.41170.3444-0.20480.475-0.2452-0.08140.6313-0.50460.131-0.0058-0.01010.7352-0.07760.2988-23.34161.8041-9.2945
30.7102-0.3967-0.34852.264-0.28880.29720.0368-0.25580.45250.0240.2064-0.21160.02360.1244-0.24310.2973-0.0477-0.01280.5897-0.10260.3008-34.81961.38170.16
42.6183-0.1688-0.21871.20220.5380.84210.19040.26260.05530.0621-0.199-0.16950.0375-0.10190.00860.41150.0449-0.00250.42320.0520.0378-48.9851-11.2881-23.0882
52.1026-0.28-0.03030.32420.26551.1177-0.2235-0.08930.07380.24580.010.0030.30670.00970.21350.55020.07150.05170.36230.13260.0985-53.6344-11.52843.9579
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 15
2X-RAY DIFFRACTION2A16 - 137
3X-RAY DIFFRACTION3A138 - 225
4X-RAY DIFFRACTION4A226 - 374
5X-RAY DIFFRACTION5A375 - 550

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