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- PDB-4hua: E. coli thioredoxin variant with (4R)-FluoroPro76 as single proli... -

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Basic information

Entry
Database: PDB / ID: 4hua
TitleE. coli thioredoxin variant with (4R)-FluoroPro76 as single proline residue
ComponentsThioredoxin-1
KeywordsOXIDOREDUCTASE / 4r-fluoroproline / cisproline / thioredoxin fold / protein disulfide oxidoreductase activity
Function / homology
Function and homology information


DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytosol / cytoplasm
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Thioredoxin 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsScharer, M.A. / Rubini, M. / Capitani, G. / Glockshuber, R.
CitationJournal: Chembiochem / Year: 2013
Title: (4R)- and (4S)-Fluoroproline in the Conserved cis-Prolyl Peptide Bond of the Thioredoxin Fold: Tertiary Structure Context Dictates Ring Puckering.
Authors: Rubini, M. / Scharer, M.A. / Capitani, G. / Glockshuber, R.
History
DepositionNov 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Oct 11, 2017Group: Advisory / Data collection / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / reflns_shell / software
Item: _reflns_shell.percent_possible_all / _software.name
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6652
Polymers11,6011
Non-polymers641
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.360, 48.690, 31.490
Angle α, β, γ (deg.)90.000, 101.980, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thioredoxin-1


Mass: 11601.229 Da / Num. of mol.: 1 / Mutation: P34A, P40A, P64A, P68A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: trxA, fipA, tsnC / Plasmid: pTrx1P / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P0AA25
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 20 mM acetic acid-NaOH pH 4.5, 2 mM CuCl2, 35 % (v/v) MPD, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorDetector: PIXEL / Date: Jun 18, 2012 / Details: mirrors
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 1 Å / Num. obs: 101582 / % possible obs: 73.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.007 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 11.45
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1-1.10.9111.0216063474413.8
1.1-1.20.7011.7785801759773.3
1.2-1.40.513.041754712876596.7
1.4-1.60.2436.831121551663999.8
1.6-20.10814.741098521653699.7
2-40.04236.241029871513299.6
4-60.02562.1811058151999.9
6-80.02558.84283938499.5
8-100.0267.13962129100
10-200.01969.6283811898.3
20-300.02567.098815100
30-400.01860.5641100
400.02858.2113100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
RemDAqdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HU7

4hu7


Resolution: 1.1→43.217 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.905 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1719 2088 2.28 %random
Rwork0.1593 ---
obs0.1596 91593 87.77 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 43.17 Å2 / Biso mean: 12.3843 Å2 / Biso min: 2.85 Å2
Refinement stepCycle: LAST / Resolution: 1.1→43.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms815 0 1 144 960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01944
X-RAY DIFFRACTIONf_angle_d1.0621282
X-RAY DIFFRACTIONf_chiral_restr0.067149
X-RAY DIFFRACTIONf_plane_restr0.003166
X-RAY DIFFRACTIONf_dihedral_angle_d12.593342
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.12560.3233750.30243255333047
1.1256-1.15380.3093990.27654152425162
1.1538-1.1850.26021170.24455167528476
1.185-1.21990.20671370.21285623576083
1.2199-1.25920.21791420.20265927606987
1.2592-1.30420.22761420.18815966610889
1.3042-1.35650.19471410.17896220636192
1.3565-1.41820.19471480.15956357650594
1.4182-1.4930.19121440.14486557670196
1.493-1.58650.14641560.1346622677898
1.5865-1.7090.1811520.13426646679898
1.709-1.8810.13051590.13546733689299
1.881-2.15320.18541580.13946722688099
2.1532-2.71270.16521600.15436760692099
2.7127-43.25050.14061580.152567986956100

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