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- PDB-5hr1: Crystal structure of thioredoxin L107A mutant -

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Basic information

Entry
Database: PDB / ID: 5hr1
TitleCrystal structure of thioredoxin L107A mutant
ComponentsThioredoxin-1
KeywordsOXIDOREDUCTASE / E. coli thioredoxin / thiol-redox reactions
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 / Thioredoxin 1
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.144 Å
AuthorsNoguera, M.E. / Vazquez, D.S. / Howard, E.I. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Santos, J.
CitationJournal: Sci Rep / Year: 2017
Title: Structural variability of E. coli thioredoxin captured in the crystal structures of single-point mutants.
Authors: Noguera, M.E. / Vazquez, D.S. / Ferrer-Sueta, G. / Agudelo, W.A. / Howard, E. / Rasia, R.M. / Manta, B. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Santos, J.
History
DepositionJan 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin-1
B: Thioredoxin-1
C: Thioredoxin-1
D: Thioredoxin-1
E: Thioredoxin-1
F: Thioredoxin-1
G: Thioredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5639
Polymers82,4367
Non-polymers1272
Water1,802100
1
A: Thioredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8402
Polymers11,7771
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8402
Polymers11,7771
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thioredoxin-1


Theoretical massNumber of molelcules
Total (without water)11,7771
Polymers11,7771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Thioredoxin-1


Theoretical massNumber of molelcules
Total (without water)11,7771
Polymers11,7771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Thioredoxin-1


Theoretical massNumber of molelcules
Total (without water)11,7771
Polymers11,7771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Thioredoxin-1


Theoretical massNumber of molelcules
Total (without water)11,7771
Polymers11,7771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Thioredoxin-1


Theoretical massNumber of molelcules
Total (without water)11,7771
Polymers11,7771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.412, 88.693, 115.459
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))
21(chain B and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))
31(chain C and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))
41(chain D and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))
51(chain E and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))
61(chain F and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPILEILE(chain A and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))AA2 - 53 - 6
12LEULEUILEILE(chain A and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))AA7 - 728 - 73
13GLYGLYGLYGLY(chain A and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))AA74 - 8475 - 85
14VALVALALAALA(chain A and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))AA86 - 10787 - 108
21ASPASPILEILE(chain B and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))BB2 - 53 - 6
22LEULEUILEILE(chain B and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))BB7 - 728 - 73
23GLYGLYGLYGLY(chain B and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))BB74 - 8475 - 85
24VALVALALAALA(chain B and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))BB86 - 10787 - 108
31ASPASPILEILE(chain C and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))CC2 - 53 - 6
32LEULEUILEILE(chain C and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))CC7 - 728 - 73
33GLYGLYGLYGLY(chain C and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))CC74 - 8475 - 85
34VALVALALAALA(chain C and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))CC86 - 10787 - 108
41ASPASPILEILE(chain D and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))DD2 - 53 - 6
42LEULEUILEILE(chain D and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))DD7 - 728 - 73
43GLYGLYGLYGLY(chain D and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))DD74 - 8475 - 85
44VALVALALAALA(chain D and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))DD86 - 10787 - 108
51ASPASPILEILE(chain E and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))EE2 - 53 - 6
52LEULEUILEILE(chain E and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))EE7 - 728 - 73
53GLYGLYGLYGLY(chain E and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))EE74 - 8475 - 85
54VALVALALAALA(chain E and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))EE86 - 10787 - 108
61ASPASPILEILE(chain F and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))FF2 - 53 - 6
62LEULEUILEILE(chain F and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))FF7 - 728 - 73
63GLYGLYGLYGLY(chain F and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))FF74 - 8475 - 85
64VALVALALAALA(chain F and (resseq 2:5 or resseq 7:72 or resseq 74:84 or resseq 86:107))FF86 - 10787 - 108

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Components

#1: Protein
Thioredoxin-1 / / Trx-1


Mass: 11776.502 Da / Num. of mol.: 7 / Mutation: L107A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: trxA, Z5291, ECs4714 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA27, UniProt: P0AA25*PLUS
#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.: 100 / 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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: The drop was a 2:1 mix of protein (10 mg/ml in water) and reservoir solution (100 mM sodium acetate, 4 mM CuSO4, 18 % ethanol, pH 4.25), respectively.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9202 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 2.15→38.478 Å / Num. obs: 48356 / % possible obs: 99.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 37.74 Å2 / Rmerge(I) obs: 0.065 / Χ2: 1.068 / Net I/σ(I): 14.7 / Num. measured all: 315275
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.15-2.236.70.51547670.99599.3
2.23-2.326.70.3947861.13399.5
2.32-2.426.70.27447741.07799.6
2.42-2.556.70.21347961.09499.7
2.55-2.716.70.15148231.12599.7
2.71-2.926.70.11648291.0999.7
2.92-3.216.50.08848511.05399.7
3.21-3.686.40.06348741.05699.8
3.68-4.636.30.0449181.03699.8
4.63-505.80.03249381.01495.7

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Processing

Software
NameVersionClassification
PHENIXdev_2247refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TRX
Resolution: 2.144→38.478 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 2451 5.07 %random
Rwork0.2064 45846 --
obs0.2078 48297 99.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 212.03 Å2 / Biso mean: 68.4285 Å2 / Biso min: 19.86 Å2
Refinement stepCycle: final / Resolution: 2.144→38.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5439 0 2 100 5541
Biso mean--75.89 41.91 -
Num. residues----715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075554
X-RAY DIFFRACTIONf_angle_d0.5747528
X-RAY DIFFRACTIONf_chiral_restr0.043867
X-RAY DIFFRACTIONf_plane_restr0.003962
X-RAY DIFFRACTIONf_dihedral_angle_d17.9672041
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3568X-RAY DIFFRACTION6.073TORSIONAL
12B3568X-RAY DIFFRACTION6.073TORSIONAL
13C3568X-RAY DIFFRACTION6.073TORSIONAL
14D3568X-RAY DIFFRACTION6.073TORSIONAL
15E3568X-RAY DIFFRACTION6.073TORSIONAL
16F3568X-RAY DIFFRACTION6.073TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1442-2.18540.29191380.26372404254295
2.1854-2.230.28741310.24762518264999
2.23-2.27850.28131370.241925412678100
2.2785-2.33150.29341400.233224942634100
2.3315-2.38980.2511250.226925432668100
2.3898-2.45440.25521310.23052549268099
2.4544-2.52660.25121390.227625322671100
2.5266-2.60820.26891250.221825622687100
2.6082-2.70140.2681560.234925092665100
2.7014-2.80950.29611320.236825732705100
2.8095-2.93730.26381400.244925242664100
2.9373-3.09210.28031410.233425612702100
3.0921-3.28570.21961310.211925772708100
3.2857-3.53930.26111390.21525702709100
3.5393-3.89510.21381270.187525922719100
3.8951-4.45810.2051320.173826162748100
4.4581-5.61390.17821460.16626242770100
5.6139-38.4840.21721410.20662557269893
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.28111.53781.12693.58520.49963.6896-0.05220.36030.1444-0.20510.23310.4169-0.2162-0.1626-0.11470.17890.0329-0.01930.37410.02330.2861-24.8131-11.31556.927
24.5988-1.111-1.08345.0416-0.02334.403-0.1345-0.09250.03970.03710.0883-0.3321-0.19640.38420.11560.1897-0.06860.00140.3434-0.05330.2324-1.3705-10.42766.5582
33.5001-1.80120.94084.2022-0.67112.97630.55890.1103-0.765-0.3909-0.07770.49350.79260.8954-0.330.44490.2243-0.1510.6277-0.00350.4914-11.7626-5.2168-22.9301
46.3238-0.00261.3513.17770.11574.6957-0.29610.49920.2068-0.05550.0359-0.20440.21530.41520.2170.62-0.0033-0.10470.31860.09070.3089-4.8953-29.731731.3585
51.99920.0204-0.46533.02161.75161.20790.0917-0.0843-0.1311.2351-0.35550.08371.5583-1.36810.16670.7122-0.35550.05580.77550.01130.3426-34.0817-17.937236.428
63.47831.0605-0.09363.6044-0.0651.8916-0.64810.50160.4579-0.64640.3038-0.0452-0.2664-0.05460.29441.0761-0.2212-0.26480.39080.03140.47935.834220.50013.6314
78.8377-7.16581.90925.8173-1.37795.81060.41210.5581-0.78240.13521.0328-1.34951.66521.5354-1.20360.6230.2435-0.27120.9417-0.28911.1196-25.239-32.9263-1.5473
85.212-4.6246-0.13365.248-0.71660.60991.09711.5957-0.5234-0.26850.1653-0.9410.50881.0214-0.22620.54830.3378-0.29691.1238-0.53131.2023-13.0699-30.25852.9384
90.4039-0.86140.22771.8779-0.67550.87260.25360.5294-0.172-0.3304-0.3347-0.32120.38890.3414-0.17441.00020.5661-0.61691.2011-0.76141.9177-13.8912-39.83-0.1517
100.68430.42231.62713.04982.11234.55-0.17970.237-1.67440.2668-0.0447-0.44241.04260.10620.17861.0836-0.0647-0.60940.52270.0392.4651-25.9918-44.27894.7788
110.4325-1.44180.38525.1873-1.12454.3344-0.14720.1846-0.1752-0.0013-0.12870.49370.82750.32150.3071.00870.2409-0.62280.4826-0.11862.6826-14.1193-45.7438.0797
120.28510.141-0.65360.0793-0.28241.5465-0.07010.1832-2.26240.46870.59131.19911.1760.303-0.35910.72330.0836-0.29410.52170.13771.8379-17.3144-39.642711.8619
132.6149-3.8528-1.75387.8307-0.8426.62230.3054-0.9061-1.92970.94060.9248-0.64920.99830.7938-0.85620.98450.1315-0.67620.910.10521.4585-10.2043-33.106713.3152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 107 )A1 - 107
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 107 )B1 - 107
3X-RAY DIFFRACTION3chain 'C' and (resid 2 through 107 )C2 - 107
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 107 )D1 - 107
5X-RAY DIFFRACTION5chain 'E' and (resid 2 through 107 )E2 - 107
6X-RAY DIFFRACTION6chain 'F' and (resid 2 through 107 )F2 - 107
7X-RAY DIFFRACTION7chain 'G' and (resid 28 through 32 )G28 - 32
8X-RAY DIFFRACTION8chain 'G' and (resid 33 through 48 )G33 - 48
9X-RAY DIFFRACTION9chain 'G' and (resid 49 through 63 )G49 - 63
10X-RAY DIFFRACTION10chain 'G' and (resid 64 through 76 )G64 - 76
11X-RAY DIFFRACTION11chain 'G' and (resid 77 through 84 )G77 - 84
12X-RAY DIFFRACTION12chain 'G' and (resid 85 through 95 )G85 - 95
13X-RAY DIFFRACTION13chain 'G' and (resid 96 through 103 )G96 - 103

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