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- PDB-5fnp: High resolution Zn containing Iron sulfur cluster repair protein YtfE -

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Basic information

Entry
Database: PDB / ID: 5fnp
TitleHigh resolution Zn 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_dist_value / _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_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
Revision 1.4Nov 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: IRON-SULFUR CLUSTER REPAIR PROTEIN YTFE
B: IRON-SULFUR CLUSTER REPAIR PROTEIN YTFE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,06810
Polymers49,7032
Non-polymers3658
Water7,891438
1
A: IRON-SULFUR CLUSTER REPAIR PROTEIN YTFE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0345
Polymers24,8521
Non-polymers1824
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)25,0345
Polymers24,8521
Non-polymers1824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.454, 98.454, 126.138
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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


Mass: 24851.516 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)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-O / OXYGEN ATOM


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


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsOXO GROUP (OXO): U-OXO BRIDGE IN THE METAL 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: 60.25 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.1 M TRIS/HCL PH 8.5 20% PEG8000 0.2 M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
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: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→25.9 Å / Num. obs: 51147 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 18.11
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.42 / % possible all: 74

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FNN

5fnn


Resolution: 1.8→25.87 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.418 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 2561 5 %RANDOM
Rwork0.18594 ---
obs0.18728 48586 92.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.525 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å2-0 Å2-0 Å2
2--1.84 Å2-0 Å2
3----3.67 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 8 438 3728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193390
X-RAY DIFFRACTIONr_bond_other_d0.0050.023192
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.984601
X-RAY DIFFRACTIONr_angle_other_deg1.17437374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1865436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.03124.895143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71215586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1571517
X-RAY DIFFRACTIONr_chiral_restr0.0830.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213807
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02686
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_it1.7093.6721723
X-RAY DIFFRACTIONr_mcbond_other1.7093.6711722
X-RAY DIFFRACTIONr_mcangle_it2.6595.4912151
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5773.7891667
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: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 136 -
Rwork0.305 2864 -
obs--73.96 %
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)
10.27360.36980.3030.52620.27951.2122-0.0242-0.06960.0708-0.0388-0.10160.086-0.0745-0.0440.12590.02130.00960.00130.0245-0.02260.101536.194-2.49541.027
20.3575-0.26020.31560.3239-0.29882.50510.05530.0004-0.01220.0125-0.0794-0.0499-0.27590.03710.0240.0721-0.0304-0.02380.04590.03450.028617.68-1.207-10.055
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 223
2X-RAY DIFFRACTION2B3 - 223

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