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- PDB-5fny: Low solvent content crystal form of Zn containing Iron sulfur clu... -

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Basic information

Entry
Database: PDB / ID: 5fny
TitleLow solvent content crystal form of 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
Iron-sulfur cluster repair protein YftE / Repair of iron centres family / 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: 2.01 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 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Derived calculations
Revision 1.2Jun 15, 2016Group: Database references
Revision 1.3Jul 13, 2016Group: Atomic model / Database references
Revision 1.4Jan 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.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

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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)50,4029
Polymers49,7032
Non-polymers6997
Water2,486138
1
A: IRON-SULFUR CLUSTER REPAIR PROTEIN YTFE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9984
Polymers24,8521
Non-polymers1473
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)25,4035
Polymers24,8521
Non-polymers5524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.024, 86.495, 51.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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


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)

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Non-polymers , 5 types, 145 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsOXO GROUP (OXO): U-OXO BRIDGE IN THE DIMETALIC CENTER
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: 2.06 Å3/Da / Density % sol: 40.33 % / Description: NONE
Crystal growpH: 9
Details: 0.1M BICINE PH9.0, 2.4M AMMONIUM REMARK 280 SULFATE, 2% PEG400

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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: Jun 28, 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: 2.01→25.2 Å / Num. obs: 26225 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.11
Reflection shellResolution: 2.01→2.06 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.42 / % possible all: 75.2

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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: 2.01→25.17 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.831 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23476 1274 4.9 %RANDOM
Rwork0.18874 ---
obs0.19094 24951 93.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.124 Å2
Baniso -1Baniso -2Baniso -3
1--2.52 Å20 Å20 Å2
2--1.13 Å20 Å2
3---1.39 Å2
Refinement stepCycle: LAST / Resolution: 2.01→25.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3289 0 34 138 3461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193407
X-RAY DIFFRACTIONr_bond_other_d0.0040.023213
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9824624
X-RAY DIFFRACTIONr_angle_other_deg1.15537398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6755439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.28924.586133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52915556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.5241516
X-RAY DIFFRACTIONr_chiral_restr0.0780.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213819
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02695
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_it1.313.1011750
X-RAY DIFFRACTIONr_mcbond_other1.3093.11749
X-RAY DIFFRACTIONr_mcangle_it2.0924.6452185
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9233.291657
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: 2.006→2.058 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 87 -
Rwork0.28 1445 -
obs--75.25 %
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)
10.6447-0.1886-0.08090.72910.29850.1330.0162-0.0234-0.0593-0.07680.0129-0.0058-0.05220.0288-0.02920.1304-0.01090.01250.052-0.03590.038918.6642.53724.538
20.9988-0.1455-0.29480.28860.30580.3939-0.0114-0.03720.0110.01620.02030.03910.00840.0519-0.00890.14970.02070.03140.04430.00720.03992.21418.57649.78
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 302
2X-RAY DIFFRACTION2B3 - 302

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