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- PDB-3l9v: Crystal Structure of Salmonella enterica serovar Typhimurium SrgA -

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Basic information

Entry
Database: PDB / ID: 3l9v
TitleCrystal Structure of Salmonella enterica serovar Typhimurium SrgA
ComponentsPutative thiol-disulfide isomerase or thioredoxin
KeywordsOXIDOREDUCTASE / thioredoxin-fold / SrgA / thiol-disulfide oxidoreductase / Isomerase
Function / homology
Function and homology information


periplasmic space / oxidoreductase activity
Similarity search - Function
Thiol:disulphide interchange protein DsbA/DsbL / : / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Glutaredoxin / Glutaredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Thioredoxin-like superfamily ...Thiol:disulphide interchange protein DsbA/DsbL / : / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Glutaredoxin / Glutaredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Thiol:disulfide interchange protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.151 Å
AuthorsHeras, B. / Jarrott, R. / Shouldice, S.R. / Guncar, G.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural and functional characterization of three DsbA paralogues from Salmonella enterica serovar typhimurium
Authors: Heras, B. / Totsika, M. / Jarrott, R. / Shouldice, S.R. / Guncar, G. / Achard, M.E.S. / Wells, T.J. / Argente, M.P. / McEwan, A.G. / Schembri, M.A.
History
DepositionJan 5, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 16, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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: Putative thiol-disulfide isomerase or thioredoxin
B: Putative thiol-disulfide isomerase or thioredoxin
C: Putative thiol-disulfide isomerase or thioredoxin
D: Putative thiol-disulfide isomerase or thioredoxin
E: Putative thiol-disulfide isomerase or thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,7049
Polymers107,4025
Non-polymers1,3024
Water11,259625
1
A: Putative thiol-disulfide isomerase or thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8512
Polymers21,4801
Non-polymers3701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative thiol-disulfide isomerase or thioredoxin


Theoretical massNumber of molelcules
Total (without water)21,4801
Polymers21,4801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative thiol-disulfide isomerase or thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1293
Polymers21,4801
Non-polymers6492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative thiol-disulfide isomerase or thioredoxin


Theoretical massNumber of molelcules
Total (without water)21,4801
Polymers21,4801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Putative thiol-disulfide isomerase or thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7632
Polymers21,4801
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.445, 80.441, 104.953
Angle α, β, γ (deg.)90.00, 124.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Putative thiol-disulfide isomerase or thioredoxin / Thiol:disulfide interchange protein dsbA-like / ORF1 / pefB / pefA / pefC / pefD / ORF5 / ORF6 / ...Thiol:disulfide interchange protein dsbA-like / ORF1 / pefB / pefA / pefC / pefD / ORF5 / ORF6 / pefI / ORF7 / ORF8 / ORF9 / rck / ORF11 / 's / 13900 base-pairs / SdiA-regulated gene / putative thiol-disulfide isomerase or thioredoxin


Mass: 21480.438 Da / Num. of mol.: 5 / Fragment: UNP residues 32-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: SL1344 / Gene: PSLT011, srgA / Plasmid: pETLIC / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)/plyss
References: UniProt: Q04815*PLUS, protein disulfide-isomerase
#2: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#3: Chemical ChemComp-P4C / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / POLYETHYLENE 400


Mass: 324.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O8
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE OF THE ENTITY 100% MATCHES WITH DATABASE UNIPROTKB/SWISS-PROT Q04612 (ORF3_HEVMY), UNP ...THE SEQUENCE OF THE ENTITY 100% MATCHES WITH DATABASE UNIPROTKB/SWISS-PROT Q04612 (ORF3_HEVMY), UNP RESIDUES 32-217, BUT HAS THE DIFFERENT STRAIN OF SOURCE. THE N-TERMINAL RESIDUES SER-ASN-ALA BELONG TO EXPRESSION TAG.

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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: 3.01 Å3/Da / Density % sol: 59.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.45M sodium malonate, 0.5% (w/v) Jeffamine ED-2001, 100mM HEPES pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.956661 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 28, 2008 / Details: Mirrors
RadiationMonochromator: Double Si with sagittaly bent second crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956661 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 67898 / Num. obs: 67898 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.5 % / Biso Wilson estimate: 38.11 Å2 / Rmerge(I) obs: 0.08 / Χ2: 1.065 / Net I/σ(I): 15.3
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 15.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.63 / Num. unique all: 3314 / Χ2: 1.1 / % possible all: 97.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
Blu-IceGUI interface to EPICS controldata collection
PHENIXAutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.151→36.477 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.799 / SU ML: 0.34 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3433 5.06 %RANDOM
Rwork0.213 ---
all0.2153 67898 --
obs0.215 67882 98.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.446 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso max: 183.54 Å2 / Biso mean: 48.594 Å2 / Biso min: 12.73 Å2
Baniso -1Baniso -2Baniso -3
1-2.232 Å20 Å21.424 Å2
2--1.99 Å2-0 Å2
3----4.222 Å2
Refinement stepCycle: LAST / Resolution: 2.151→36.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7170 0 88 625 7883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097563
X-RAY DIFFRACTIONf_angle_d1.06910233
X-RAY DIFFRACTIONf_chiral_restr0.071092
X-RAY DIFFRACTIONf_plane_restr0.0051324
X-RAY DIFFRACTIONf_dihedral_angle_d15.3772781
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.151-2.2280.3443260.2556262658896
2.228-2.3170.2923310.2386414674597
2.317-2.4230.2993300.2386377670798
2.423-2.550.3093340.2326398673298
2.55-2.710.2983840.2266400678498
2.71-2.9190.2753200.2256484680498
2.919-3.2130.2693770.2216456683399
3.213-3.6770.2513430.1916492683599
3.677-4.6320.2143220.1716586690899
4.632-36.4820.2513660.2186580694698
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)
10.2791-0.2470.54310.1671-0.38430.79180.38650.2413-0.3934-0.7253-0.0693-0.26481.3497-0.2719-0.00020.89190.16480.05540.59150.17940.54610.1665.7471-4.5108
20.95680.3220.56180.282-0.41861.8730.36691.15840.3525-0.0703-0.2309-0.30380.06380.38650.00830.76620.18530.07190.86810.13330.487213.145573.0693-9.3377
31.86-2.33821.44153.4704-2.50452.03290.98281.01681.1454-1.0712-0.1847-0.63210.72190.52060.36540.55730.13460.14531.36640.01990.978520.511277.1625-16.5566
4-0.00210.00510.00340.02620.0049-0.0025-0.75750.89380.13390.51660.36460.7372-0.9373-0.36520.00221.49380.3346-0.03340.62750.07370.283312.673581.1419-14.4283
54.70213.61892.13783.34092.71753.56990.2672-0.0775-0.418-0.9401-1.2384-0.0570.1818-0.0106-0.74070.86350.29240.06830.5350.16590.41334.216182.6916-19.8984
62.3003-4.3246-1.01318.45711.83820.4585-0.08720.3471-0.1531-1.5647-0.4030.3541-0.18590.817-0.1790.51570.1120.08090.7890.32530.17415.81882.7466-24.3635
70.1137-0.1179-0.00660.11030.0012-0.007-0.97950.39220.368-0.87760.1118-0.35891.16981.2327-0.00141.6490.6284-0.09611.3850.16550.465916.289875.1101-30.5547
80.99370.04311.53030.72290.76322.84180.13470.70170.122-0.5254-0.27590.29050.27740.83870.03280.69410.29930.00730.83550.08870.552911.64662.6011-8.8392
90.0132-0.03940.00750.12450.0230.0291-0.82610.63090.62740.2236-0.21861.21960.35080.6422-0.00011.3327-0.4816-0.14171.03740.25380.69283.331874.323510.1403
100.1999-0.31750.01530.3057-0.045-0.00450.19231.03340.24390.3007-1.06090.0302-0.48450.51830.00030.6642-0.0166-0.04130.48590.04610.56613.631773.03948.2789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain E and resid 5:30)E5 - 30
2X-RAY DIFFRACTION2(chain E and resid 31:77)E31 - 77
3X-RAY DIFFRACTION3(chain E and resid 78:82)E78 - 82
4X-RAY DIFFRACTION4(chain E and resid 83:88)E83 - 88
5X-RAY DIFFRACTION5(chain E and resid 89:106)E89 - 106
6X-RAY DIFFRACTION6(chain E and resid 107:114)E107 - 114
7X-RAY DIFFRACTION7(chain E and resid 115:125)E115 - 125
8X-RAY DIFFRACTION8(chain E and resid 126:160)E126 - 160
9X-RAY DIFFRACTION9(chain E and resid 161:166)E161 - 166
10X-RAY DIFFRACTION10(chain E and resid 167:185)E167 - 185

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