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- PDB-4pob: Crystal structure of a thioredoxin Rv1471 ortholog from Mycobacte... -

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Basic information

Entry
Database: PDB / ID: 4pob
TitleCrystal structure of a thioredoxin Rv1471 ortholog from Mycobacterium abscessus
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / National Institute for Allergy and Infectious Diseases / tuberculosis / ortholog / redox homeostasis
Function / homology
Function and homology information


glycerol ether metabolic process / protein-disulfide reductase activity / cell redox homeostasis
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
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a thioredoxin Rv1471 ortholog from Mycobacterium abscessus
Authors: Edwards, T.E. / Abendroth, J. / Sacchettini, J.C. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionFeb 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / pdbx_struct_conn_angle / 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_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
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7124
Polymers25,6272
Non-polymers852
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-18 kcal/mol
Surface area10060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.500, 47.490, 108.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thioredoxin


Mass: 12813.530 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / DSM 44196 / Gene: MAB_4941 / Production host: Escherichia coli (E. coli) / References: UniProt: B1MMM4
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#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


Mass: 18.015 Da / Num. of mol.: 181 / 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: 1.89 Å3/Da / Density % sol: 34.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: SSGCID-MyabA.01255.a at 15.42 mg/mL against MCSG screen condition B4, 0.2 M sodium thiocyanate pH 6.9, 25% PEG 3350 supplemented with 20% ethylene glycol as cryo-protectant, crystal tracking ...Details: SSGCID-MyabA.01255.a at 15.42 mg/mL against MCSG screen condition B4, 0.2 M sodium thiocyanate pH 6.9, 25% PEG 3350 supplemented with 20% ethylene glycol as cryo-protectant, crystal tracking ID 252343d4, unique puck ID ekd3-10, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 21770 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 25.696 Å2 / Rmerge(I) obs: 0.051 / Χ2: 0.988 / Net I/σ(I): 20.22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.740.5233.037739159099.9
1.74-1.790.3883.957588156599.6
1.79-1.840.3234.697283149999.6
1.84-1.90.246.427180147899.3
1.9-1.960.1888.217048144699.8
1.96-2.030.15110.266689136299.1
2.03-2.110.12612.016533134099.2
2.11-2.190.114.876315128898.9
2.19-2.290.0818.296008122798.6
2.29-2.40.06620.955775118798.6
2.4-2.530.05823.985485112698.7
2.53-2.690.04927.965185106798.5
2.69-2.870.04429.664864100097.9
2.87-3.10.03636.54455093098
3.1-3.40.02842.95419786796.2
3.4-3.80.02448.58373577797.7
3.8-4.390.0253.71330768895.8
4.39-5.380.0256.12283259695.7
5.38-7.60.02250.24211346995.5
7.60.01955.42108926889.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2L4Q

2l4q


Resolution: 1.7→30.87 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.1931 / WRfactor Rwork: 0.1575 / FOM work R set: 0.8739 / SU B: 4.1 / SU ML: 0.069 / SU R Cruickshank DPI: 0.1093 / SU Rfree: 0.1044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1977 999 4.8 %RANDOM
Rwork0.1654 ---
obs0.1669 20893 94.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.09 Å2 / Biso mean: 21.873 Å2 / Biso min: 9.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1574 0 5 181 1760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021640
X-RAY DIFFRACTIONr_bond_other_d0.0010.021591
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9632250
X-RAY DIFFRACTIONr_angle_other_deg0.83533665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7065222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28225.48462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97415265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.98157
X-RAY DIFFRACTIONr_chiral_restr0.0930.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02332
X-RAY DIFFRACTIONr_mcbond_it0.9811.475858
X-RAY DIFFRACTIONr_mcbond_other0.9811.472857
X-RAY DIFFRACTIONr_mcangle_it1.5482.2041072
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 66 -
Rwork0.212 1325 -
all-1391 -
obs--87.7 %
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)
10.8173-0.45970.11131.1407-0.24410.7371-0.0161-0.02970.02520.00660.0385-0.0393-0.0205-0.0289-0.02240.00830.0011-0.00430.0095-0.0030.02775.9152-8.4865-24.4219
21.6079-0.32370.29671.5007-0.16342.255-0.0757-0.2203-0.02790.19660.049-0.05470.01070.07490.02660.03820.0262-0.00730.05240.00310.005224.1732-21.2007-5.4773
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 109
2X-RAY DIFFRACTION2B5 - 109

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