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- PDB-4hu7: E. coli thioredoxin variant with Pro76 as single proline residue -

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Basic information

Entry
Database: PDB / ID: 4hu7
TitleE. coli thioredoxin variant with Pro76 as single proline residue
ComponentsThioredoxin-1
KeywordsOXIDOREDUCTASE / 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 / molecular replacement / Resolution: 1.4 Å
AuthorsGlockshuber, R. / Scharer, M.A. / Capitani, G. / Rubini, M.
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 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _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_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_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_ref_seq_dif.details / _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: Thioredoxin-1
B: Thioredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3175
Polymers23,1662
Non-polymers1503
Water3,405189
1
A: Thioredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6703
Polymers11,5831
Non-polymers872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6472
Polymers11,5831
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Thioredoxin-1
hetero molecules

B: Thioredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3175
Polymers23,1662
Non-polymers1503
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area1420 Å2
ΔGint-33 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.850, 60.880, 45.330
Angle α, β, γ (deg.)90.000, 100.380, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thioredoxin-1 /


Mass: 11583.238 Da / Num. of mol.: 2 / 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 / Plasmid: pTrx1P / Production host: Escherichia coli (E. coli) / 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / 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 Å3/Da / Density % sol: 38.36 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 20 mM acetic acid-NaOH, 2 mM CuCl2, 35 % (v/v) MPD , pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99986 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2012 / Details: Dynamically bendable mirror
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986 Å / Relative weight: 1
ReflectionNumber: 294078 / Rmerge(I) obs: 0.089 / D res high: 1.3 Å / Num. obs: 44121 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
1.31.485579711.021
1.41.5655998.810.78
1.51.6507799.510.54
1.61.7394599.610.382
1.71.8310799.810.289
1.82455699.810.163
22.5596210010.091
2.53265499.810.06
34211899.610.042
46110110010.049
61037510010.042
10209410010.038
20301210010.04
ReflectionResolution: 1.3→99.108 Å / Num. obs: 44121 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.55 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 10.52

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.59 Å
Translation2.5 Å44.59 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
RemDAqdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TRX

2trx


Resolution: 1.4→44.589 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8779 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 19.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1976 890 2.5 %random
Rwork0.1623 ---
obs0.1631 35542 99.64 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.25 Å2 / Biso mean: 18.7289 Å2 / Biso min: 6.97 Å2
Refinement stepCycle: LAST / Resolution: 1.4→44.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1593 0 3 189 1785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071698
X-RAY DIFFRACTIONf_angle_d1.0582309
X-RAY DIFFRACTIONf_chiral_restr0.074271
X-RAY DIFFRACTIONf_plane_restr0.004295
X-RAY DIFFRACTIONf_dihedral_angle_d12.86608
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.48770.26651470.26095713586099
1.4877-1.60260.23791470.203957435890100
1.6026-1.76390.21051480.178757545902100
1.7639-2.01910.20591480.153757665914100
2.0191-2.54390.16871490.148958125961100
2.5439-44.61150.19081510.148458646015100
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)
10.18750.11890.12550.1490.13540.50060.127-0.0259-0.16630.19620.0674-0.0118-0.1038-0.10950.10020.1518-0.00520.00570.08430.0080.13553.5855-8.627723.8661
20.11310.08880.00070.1597-0.12780.16850.008-0.0591-0.08020.0184-0.0625-0.1291-0.05120.0605-0.12440.0895-0.0052-0.00990.07740.02080.136316.571-1.572621.4816
30.1070.0981-0.06390.0994-0.08360.0628-0.02880.0278-0.04570.04980.0096-0.02770.0992-0.065-0.0210.0968-0.01080.00110.08370.00860.09748.8105-4.542617.9421
40.150.0519-0.01250.127-0.04180.22370.02660.04340.00190.03950.01870.0215-0.0406-0.04020.08380.09350.0016-0.00550.08190.00970.09897.17976.514619.0532
50.1128-0.00430.00360.25320.01710.0151-0.02050.06-0.0383-0.11030.0132-0.0066-0.1170.3366-0.0360.0943-0.0465-0.00490.26970.0220.1044-6.22115.7518-2.1405
60.0333-0.0379-0.00970.1137-0.03250.04090.01790.07750.0608-0.0716-0.0774-0.0405-0.1641-0.0418-0.03280.1988-0.0025-0.0070.09770.03180.1068-12.755416.54355.7149
70.2415-0.1539-0.03640.2584-0.03330.03150.03670.1167-0.0538-0.1015-0.07920.010.05620.1394-0.04530.1382-0.05710.00590.19650.04410.1015-7.43617.70030.2648
80.132-0.0934-0.02020.24550.04650.0031-0.1193-0.0082-0.01280.00670.09480.01620.04890.2074-0.01870.0825-0.00350.00230.1569-0.00110.0954-4.67243.9948.2543
90.01670.00930.0050.00880.00960.0169-0.0085-0.02030.1439-0.03170.0232-0.093-0.09090.076200.1504-0.0040.02110.10280.00460.1531-2.696516.412213.2792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 21 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 48 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 76 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 107 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 32 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 33 through 48 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 49 through 69 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 70 through 95 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 96 through 107 )B0

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