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- PDB-5fnn: Iron and Selenomethionine containing Iron sulfur cluster repair p... -

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Basic information

Entry
Database: PDB / ID: 5fnn
TitleIron and Selenomethionine containing Iron sulfur cluster repair protein YtfE
ComponentsIRON-SULFUR CLUSTER REPAIR PROTEIN YTFE
KeywordsOXIDOREDUCTASE / NITRIC OXIDE / IRON-SULFUR CLUSTER REPAIR / DI-FE CENTER.
Function / homology
Function and homology information


response to nitrosative stress / protein repair / nitrite reductase activity / response to oxidative stress / iron ion binding / cytosol
Similarity search - Function
Repair of iron centres family / Iron-sulfur cluster repair protein YftE / Domain of Unknown function (DUF542) / Hemerythrin-like / Hemerythrin HHE cation binding domain
Similarity search - Domain/homology
: / : / OXYGEN ATOM / Iron-sulfur cluster repair protein YtfE
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å
AuthorsLo, F.-C. / Hsieh, C.-C. / Maestre-Reyna, M. / Chen, C.-Y. / Ko, T.-P. / Horng, Y.-C. / Lai, Y.-C. / Chiang, Y.-W. / Chou, C.-M. / Chiang, C.-H. ...Lo, F.-C. / Hsieh, C.-C. / Maestre-Reyna, M. / Chen, C.-Y. / Ko, T.-P. / Horng, Y.-C. / Lai, Y.-C. / Chiang, Y.-W. / Chou, C.-M. / Chiang, C.-H. / Huang, W.-N. / Liaw, W.-F.
CitationJournal: Chemistry / Year: 2016
Title: Crystal Structure of the Repair of Iron Centers Protein Ytfe and its Interaction with No
Authors: Lo, F.-C. / Hsieh, C.-C. / Maestre-Reyna, M. / Chen, C.-Y. / Ko, T.-P. / Horng, Y.-C. / Lai, Y.-C. / Chiang, Y.-W. / Chou, C.-M. / Chiang, C.-H. / Huang, W.-N. / Liaw, W.-F.
History
DepositionNov 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Jul 13, 2016Group: Database references
Revision 1.3Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_label_seq_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: IRON-SULFUR CLUSTER REPAIR PROTEIN YTFE
B: IRON-SULFUR CLUSTER REPAIR PROTEIN YTFE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,06110
Polymers50,7352
Non-polymers3268
Water1,35175
1
A: IRON-SULFUR CLUSTER REPAIR PROTEIN YTFE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5305
Polymers25,3671
Non-polymers1634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: IRON-SULFUR CLUSTER REPAIR PROTEIN YTFE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5305
Polymers25,3671
Non-polymers1634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.620, 98.620, 125.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein IRON-SULFUR CLUSTER REPAIR PROTEIN YTFE / REGULATOR OF CELL MORPHOGENESIS AND NO SIGNALING / RCMNS / YTFE


Mass: 25367.357 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P69506, nitric oxide reductase (cytochrome c)

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Non-polymers , 5 types, 83 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsOXO GROUP (OXO): U-OXO BRIDGE IN THE DIIRON CLUSTER
Sequence detailsOUR CONSTRUCT INCLUDED MUTATIONS ON C30 AND C31 TO A

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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: 3.09 Å3/Da / Density % sol: 60.23 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M TRISCL PH8.5, 21% PEG4000, 0.2 M MGCL2, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2014 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.1→27.9 Å / Num. obs: 34895 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.37
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.67 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.09→77.58 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.346 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2305 1657 4.7 %RANDOM
Rwork0.21106 ---
obs0.21201 33238 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.091 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20 Å2
2--1.54 Å20 Å2
3----3.08 Å2
Refinement stepCycle: LAST / Resolution: 2.09→77.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3179 0 8 75 3262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193278
X-RAY DIFFRACTIONr_bond_other_d0.0040.023029
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9924465
X-RAY DIFFRACTIONr_angle_other_deg1.18536963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6945434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.12924.737133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8715454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5291516
X-RAY DIFFRACTIONr_chiral_restr0.0870.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213760
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02684
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_it2.0244.6611718
X-RAY DIFFRACTIONr_mcbond_other2.0244.6611717
X-RAY DIFFRACTIONr_mcangle_it3.1156.9692146
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0814.6831559
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: 2.095→2.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 114 -
Rwork0.312 2216 -
obs--90.52 %
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)
10.7057-0.1848-0.07771.1428-0.40421.51050.00830.02280.11380.0138-0.2169-0.1047-0.15110.00610.20860.19810.04120.00120.15670.01540.0697112.07696.674.183
20.89040.13-1.05310.6710.04863.9028-0.1486-0.047-0.0519-0.09510.1195-0.0019-0.0173-0.51620.02910.17380.00090.01530.27760.01780.004398.18880.437-39.304
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 220
2X-RAY DIFFRACTION2B2 - 220

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