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- PDB-1keb: Crystal Structure of Double Mutant M37L,P40S E.coli Thioredoxin -

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Basic information

Entry
Database: PDB / ID: 1keb
TitleCrystal Structure of Double Mutant M37L,P40S E.coli Thioredoxin
ComponentsThioredoxin 1
KeywordsELECTRON TRANSPORT / Thioredoxin fold / Proline / alpha-helix
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRudresh / Jain, R. / Dani, V. / Mitra, A. / Srivastava, S. / Sarma, S.P. / Varadarajan, R. / Ramakumar, S.
CitationJournal: PROTEIN ENG. / Year: 2002
Title: Structural Consequences of Replacement of an alpha-helical Pro Residue in E.coli Thioredoxin
Authors: Rudresh / Jain, R. / Dani, V. / Mitra, A. / Srivastava, S. / Sarma, S.P. / Varadarajan, R. / Ramakumar, S.
History
DepositionNov 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / software / 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_asym_id / _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_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_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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin 1
B: Thioredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4464
Polymers23,3192
Non-polymers1272
Water2,396133
1
A: Thioredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7232
Polymers11,6591
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7232
Polymers11,6591
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.320, 37.500, 50.740
Angle α, β, γ (deg.)69.25, 79.71, 85.39
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Thioredoxin 1 / / TRX


Mass: 11659.312 Da / Num. of mol.: 2 / Mutation: M37L,P40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET20bP40S / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AA25
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.03 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 100mM sodium acetate buffer, 10mM cupric acetate, 25% ethanol as precipitant, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Details: Chakrabarti, A., (1999) J. Appl. Crystallogr., 30, 2455.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 29, 1998 / Details: Mirrors
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 16633 / Num. obs: 16633 / % possible obs: 90.11 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 7.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.41
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.73 / Num. unique all: 2355 / Rsym value: 0.364 / % possible all: 84.9
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 15560 / % possible obs: 84.49 % / Redundancy: 2.37 % / Rmerge(I) obs: 0.0621

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Processing

Software
NameVersionClassification
DENZOdata reduction
AUTOMARdata reduction
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TRX

2trx


Resolution: 1.8→20 Å / Isotropic thermal model: Isotropic / Cross valid method: throught / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 1356 7.4 %Random
Rwork0.1825 ---
all-13549 --
obs-13549 73.5 %-
Displacement parametersBiso mean: 18.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.12 Å20.4 Å2
2--2.27 Å21.05 Å2
3----2.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 2 133 1777
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.67
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
1.8-1.940.2452980.2027X-RAY DIFFRACTION893
2.03-2.130.2181380.1784X-RAY DIFFRACTION1129
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.17
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68

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