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- PDB-7e0l: Class III hybrid cluster protein (HCP) from Methanothermobacter m... -

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Basic information

Entry
Database: PDB / ID: 7e0l
TitleClass III hybrid cluster protein (HCP) from Methanothermobacter marburgensis
ComponentsHydroxylamine reductase
KeywordsOXIDOREDUCTASE / Hybrid cluster / iron-sulfur cluster / rubredoxin / METAL BINDING PROTEIN / hydroxylamine reductase
Function / homology
Function and homology information


hydroxylamine reductase / hydroxylamine reductase activity / peroxidase activity / response to hydrogen peroxide / 4 iron, 4 sulfur cluster binding / iron ion binding / cytoplasm
Similarity search - Function
Hydroxylamine reductase / Prismane, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / 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 speciesMethanothermobacter marburgensis str. Marburg (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsFujishiro, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K14510 Japan
CitationJournal: Nat Commun / Year: 2023
Title: Class III hybrid cluster protein homodimeric architecture shows evolutionary relationship with Ni, Fe-carbon monoxide dehydrogenases
Authors: Fujishiro, T. / Takaoka, K.
History
DepositionJan 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 2.0Oct 19, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_src_gen / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / reflns_shell / software / struct / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _entity.pdbx_number_of_molecules / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity.pdbx_number_of_molecules / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _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.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _reflns.d_resolution_low / _reflns.pdbx_number_measured_all / _reflns.pdbx_scaling_rejects / _reflns_shell.d_res_low / _reflns_shell.number_measured_obs / _reflns_shell.number_possible / _software.name / _software.version / _struct.title / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet.number_strands / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sense / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id
Description: Polymer geometry
Details: Conformations such as rotamers have been improved by re-refinement with several cycles, as per request from a reviewer in the manuscript revision.
Provider: author / Type: Coordinate replacement
Revision 2.1Sep 20, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.3Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.4Oct 16, 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
B: Hydroxylamine reductase
K: Hydroxylamine reductase
M: Hydroxylamine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,85016
Polymers225,8784
Non-polymers2,97212
Water72140
1
A: Hydroxylamine reductase
B: Hydroxylamine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,4258
Polymers112,9392
Non-polymers1,4866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-125 kcal/mol
Surface area36720 Å2
MethodPISA
2
K: Hydroxylamine reductase
M: Hydroxylamine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,4258
Polymers112,9392
Non-polymers1,4866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-128 kcal/mol
Surface area36260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.950, 67.950, 469.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 56469.410 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter marburgensis str. Marburg (archaea)
Strain: ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg
Gene: hcp, MTBMA_c00390 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: D9PYV4, hydroxylamine reductase
#2: Chemical
ChemComp-FS2 / FE-S-O HYBRID CLUSTER


Mass: 335.508 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4O3S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30 % (w/v) Polyethylene glycol 4000, 100 mM Tris-HCl, 200 mM Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.73937 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 20, 2020
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.73937 Å / Relative weight: 1
ReflectionResolution: 2.82→48.05 Å / Num. obs: 50758 / % possible obs: 100 % / Redundancy: 12.401 % / Biso Wilson estimate: 63.225 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.185 / Rrim(I) all: 0.193 / Χ2: 0.899 / Net I/σ(I): 9.91
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.82-2.9211.8550.9532.250170.7340.996100
2.92-3.112.2250.6713.1875520.8610.7100
3.1-3.512.1490.45.63115920.9440.418100
3.5-412.2910.25110.4188280.9750.262100
4-4.513.4760.17216.0652420.9850.179100
4.5-612.6970.15317.1272450.9890.159100
6-1012.1720.11318.7441440.9950.117100
10-48.0513.4020.08821.8611380.9820.09298.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W9M

1w9m


Resolution: 2.82→48.05 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2593 2554 5.03 %RANDOM
Rwork0.234 ---
obs0.2353 50757 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.82→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15241 0 72 40 15353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415667
X-RAY DIFFRACTIONf_angle_d0.83421313
X-RAY DIFFRACTIONf_dihedral_angle_d15.6465805
X-RAY DIFFRACTIONf_chiral_restr0.0512377
X-RAY DIFFRACTIONf_plane_restr0.0052747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-2.870.34231490.33762606X-RAY DIFFRACTION100
2.87-2.930.33261430.31272707X-RAY DIFFRACTION100
2.93-30.36291400.30622666X-RAY DIFFRACTION100
3-3.070.29391460.28342685X-RAY DIFFRACTION100
3.07-3.140.30391390.29182646X-RAY DIFFRACTION100
3.14-3.230.32631550.28372716X-RAY DIFFRACTION100
3.23-3.320.29161370.2792647X-RAY DIFFRACTION100
3.32-3.430.30211480.29222700X-RAY DIFFRACTION100
3.43-3.550.29131410.27152685X-RAY DIFFRACTION100
3.55-3.690.25761430.26042665X-RAY DIFFRACTION100
3.69-3.860.28841230.24342670X-RAY DIFFRACTION100
3.86-4.070.28321380.2312675X-RAY DIFFRACTION100
4.07-4.320.2411290.20812712X-RAY DIFFRACTION100
4.32-4.650.24131340.20042677X-RAY DIFFRACTION100
4.65-5.120.22481460.20292692X-RAY DIFFRACTION100
5.12-5.860.2131540.21672665X-RAY DIFFRACTION100
5.86-7.370.24511330.21162724X-RAY DIFFRACTION100
7.38-48.050.21941560.19032665X-RAY DIFFRACTION100
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)
10.01220.05810.03990.1393-0.15980.0095-0.0018-0.0570.0826-0.06280.0108-0.22470.08450.0922-00.60460.092-0.13810.30660.03190.5111-34.7213-2.5769-3.0082
2-0.02880.24910.12540.40370.01860.28330.02440.02140.06070.01870.0418-0.14470.1282-0.050800.50450.1587-0.1370.3607-0.07460.4378-20.149336.871313.4004
30.02840.0222-0.0101-0.0127-0.0041-0.0039-0.05480.13290.11260.0460.06790.08240.0464-0.0701-01.20210.4149-0.45912.59930.2212.6834-33.264111.275434.9104
40.0219-0.03440.04080.09880.08330.039-0.7397-0.5830.1632-0.4110.33980.20670.51220.2498-00.68210.2304-0.03190.67180.07270.4078-34.514415.097220.1552
50.4628-0.0746-0.1086-0.06760.09480.1631-0.06630.00550.00840.02710.0623-0.00650.02060.000700.46710.0079-0.07780.1999-0.00330.3945-42.578421.5514-20.3759
60.26430.0914-0.07460.11580.16370.09210.025-0.04910.0114-0.05290.01430.09280.1508-0.017400.5540.0275-0.03580.27390.03390.3773-57.237321.7457-7.0784
7-0.0247-0.0328-0.02510.10310.037-0.01540.11160.04660.0358-0.0162-0.01990.0943-0.067-0.029-00.35870.1064-0.03470.6540.10670.4261-36.4003-2.169368.6888
80.0646-0.18330.0429-0.03480.07280.04490.1142-0.12870.1086-0.089-0.0329-0.055-0.01540.023100.4290.09390.05770.50910.11610.46025.59585.484153.8474
90.0624-0.04360.02750.0280.03650.0205-0.24370.1738-0.47110.21930.2855-0.1797-0.2699-0.016300.55210.09620.05360.75390.00790.583210.2779-4.151340.6701
100.0864-0.1065-0.11910.05780.04350.02360.16560.11050.0875-0.2402-0.1111-0.4084-0.009-0.020100.66540.14560.06690.68510.19270.70713.808326.156144.8877
11-0.07980.2290.0426-0.0081-0.11770.13130.30460.0630.299-0.081-0.3547-0.0291-0.0331-0.070600.38490.11420.04810.57350.20520.4188-6.155823.565756.1284
120.0008-0.01210.00250.02030.00030.01310.24090.1735-0.1584-0.10080.0872-0.1642-0.1243-0.041901.32260.4801-0.41491.5888-0.28471.1755-20.1571-1.434831.2223
130.0299-0.01650.01350.0018-0.02630.03580.1569-0.1518-0.1538-0.21660.0867-0.04960.3347-0.176600.53150.1111-0.06050.74870.10060.5781-17.8302-0.755250.2094
14-0.18650.0823-0.02760.4329-0.1360.48430.00790.02550.0340.0145-0.02110.02030.03290.0422-00.25990.00370.00290.47960.07180.3525-11.1381-3.582584.3361
150.1870.02330.0610.12710.3110.4340.0552-0.0654-0.0794-0.08410.08070.0199-0.0251-0.024100.2404-0.0042-0.03620.48560.07560.3992-13.2868-26.311483.6315
160.09430.0580.0127-0.0049-0.05140.11710.0161-0.28670.1932-0.37640.00460.27320.0580.090100.35640.086-0.02080.63190.06310.3772-15.6757-23.729567.558
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 88 )
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 491 )
3X-RAY DIFFRACTION3chain 'B' and (resid 3 through 31 )
4X-RAY DIFFRACTION4chain 'B' and (resid 32 through 88 )
5X-RAY DIFFRACTION5chain 'B' and (resid 89 through 399 )
6X-RAY DIFFRACTION6chain 'B' and (resid 400 through 493 )
7X-RAY DIFFRACTION7chain 'K' and (resid 1 through 88 )
8X-RAY DIFFRACTION8chain 'K' and (resid 89 through 266 )
9X-RAY DIFFRACTION9chain 'K' and (resid 267 through 318 )
10X-RAY DIFFRACTION10chain 'K' and (resid 319 through 399 )
11X-RAY DIFFRACTION11chain 'K' and (resid 400 through 493 )
12X-RAY DIFFRACTION12chain 'M' and (resid 2 through 50 )
13X-RAY DIFFRACTION13chain 'M' and (resid 51 through 88 )
14X-RAY DIFFRACTION14chain 'M' and (resid 89 through 318 )
15X-RAY DIFFRACTION15chain 'M' and (resid 319 through 434 )
16X-RAY DIFFRACTION16chain 'M' and (resid 435 through 493 )

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