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- PDB-8eqq: Crystal structure of E.coli DsbA mutant E37A -

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Basic information

Entry
Database: PDB / ID: 8eqq
TitleCrystal structure of E.coli DsbA mutant E37A
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / DsbA mutant / thioredoxin-family protein
Function / homology
Function and homology information


cellular response to antibiotic / protein disulfide isomerase activity / protein-disulfide reductase activity / outer membrane-bounded periplasmic space
Similarity search - Function
Thiol:disulphide interchange protein DsbA/DsbL / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
CITRATE ANION / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsWang, G. / Heras, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1144046 Australia
CitationJournal: Antioxidants / Year: 2023
Title: A Buried Water Network Modulates the Activity of the Escherichia coli Disulphide Catalyst DsbA.
Authors: Wang, G. / Qin, J. / Verderosa, A.D. / Hor, L. / Santos-Martin, C. / Paxman, J.J. / Martin, J.L. / Totsika, M. / Heras, B.
History
DepositionOct 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 25, 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

Downloads & links

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein DsbA
B: Thiol:disulfide interchange protein DsbA
C: Thiol:disulfide interchange protein DsbA
D: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7666
Polymers84,3884
Non-polymers3782
Water8,449469
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2862
Polymers21,0971
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2862
Polymers21,0971
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)21,0971
Polymers21,0971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Thiol:disulfide interchange protein DsbA


Theoretical massNumber of molelcules
Total (without water)21,0971
Polymers21,0971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.840, 81.067, 105.247
Angle α, β, γ (deg.)90.000, 93.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thiol:disulfide interchange protein DsbA


Mass: 21096.988 Da / Num. of mol.: 4 / Mutation: E37A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEG4
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.12 Å3/Da / Density % sol: 60.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 15-20% PEG8000, 0.1M phosphate-citrate, pH 3.8-4.4, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.01→49.1 Å / Num. obs: 68997 / % possible obs: 99.4 % / Redundancy: 3.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.056 / Rrim(I) all: 0.112 / Net I/σ(I): 8.5 / Num. measured all: 266008 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.01-2.053.81.4331568541570.3870.8371.6650.993.1
9.63-49.13.70.02924556620.9980.0170.03431.398.4

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 2.13→49.1 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2308 2799 4.82 %
Rwork0.1843 55235 -
obs0.1865 58034 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.11 Å2 / Biso mean: 44.509 Å2 / Biso min: 20.84 Å2
Refinement stepCycle: final / Resolution: 2.13→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5896 0 36 469 6401
Biso mean--57.77 45.48 -
Num. residues----750
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.13-2.170.31941490.286826952844100
2.17-2.210.29751410.270427712912100
2.21-2.250.28521360.239427552891100
2.25-2.290.28161600.241627242884100
2.29-2.340.28041320.228927332865100
2.34-2.40.30241440.222827622906100
2.4-2.460.26531640.213827552919100
2.46-2.530.25731390.199927242863100
2.53-2.60.24241530.19627602913100
2.6-2.680.22711150.190228102925100
2.68-2.780.2361060.198127632869100
2.78-2.890.24381350.195827762911100
2.89-3.020.2811340.202327542888100
3.02-3.180.24971530.204227532906100
3.18-3.380.27091470.191127742921100
3.38-3.640.21981450.176327682913100
3.64-4.010.21761330.15832735286899
4.01-4.590.20221320.14232778291099
4.59-5.780.17291380.154928152953100
5.78-49.10.17811430.16752830297399
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)
15.3874-1.25330.4689.54242.3688.52990.159-0.6527-0.37321.2093-0.79550.05730.9534-0.40930.71080.4505-0.14570.14020.5335-0.02110.4059-19.2206-26.58417.263
20.57-0.0394-1.09873.71480.76462.44040.0340.0396-0.0216-0.1402-0.15470.1141-0.2341-0.22050.11020.29550.023-0.04290.309-0.03630.2883-10.7798-15.2076-8.5433
31.0039-0.53690.05563.54261.38792.08220.05850.0253-0.0235-0.1498-0.17130.1008-0.1506-0.22230.09380.21760.0355-0.01220.304-0.04390.2627-11.4428-15.3374-5.3582
44.8639-1.4640.95843.1671-0.85593.33820.19190.01010.0267-0.1514-0.2041-0.24590.30360.28470.02160.44950.0087-0.02060.30520.06850.3056-28.2363-11.41938.7052
54.703-2.9040.80325.40950.78421.62180.31090.2162-0.5629-0.1333-0.21470.50840.3796-0.038-0.07460.5124-0.0569-0.10920.29460.04370.3571-42.3611-24.309941.1712
61.7475-1.04810.91684.0887-0.72332.43130.18660.18950.0455-0.1873-0.2692-0.31760.35340.22490.11180.30550.0204-0.00320.33020.04820.2553-28.4327-15.572939.4369
74.33380.45520.22378.22280.77966.3186-0.17670.36520.464-0.2634-0.140.5757-0.6301-0.76320.37510.25650.0813-0.04390.43380.05210.4731-23.874814.871611.4561
84.25261.21651.05882.87940.23930.75420.0478-0.06870.00750.21190.04170.0059-0.05610.0388-0.0810.28750.0128-0.00130.27290.02860.2612-9.667710.180620.5443
93.15641.3871.27712.61450.90942.67390.0576-0.0069-0.08270.1096-0.1258-0.0098-0.05750.11230.0210.26830.0086-0.02690.24010.01690.27392.44482.172121.646
103.43060.92751.10262.57781.37542.79160.1590.0424-0.31420.3232-0.0941-0.12950.4375-0.0438-0.06740.31290.0130.00990.2635-0.01830.2931-4.4951-6.357315.7268
113.6746-0.8382-0.32835.31820.48615.5615-0.0065-0.14640.36050.07820.0970.4216-0.3692-0.319-0.06260.26290.04880.03460.30720.01550.3755-18.00217.16617.5084
121.5927-1.1691-0.26092.771-1.38971.44620.2048-1.222-0.70981.6243-0.19490.77270.7665-0.8851-0.01931.3477-0.22240.18920.85310.24880.71121.54-13.682365.4678
131.80180.6677-0.78193.72690.9933.10160.033-0.11960.21490.5977-0.09210.39490.0756-0.25790.02880.4864-0.0472-0.00230.36460.03850.3675.4896-1.748951.6801
142.0593-0.6135-0.00673.72771.17023.03920.03680.05420.06540.1389-0.08970.0738-0.09380.0150.02570.3315-0.0443-0.06090.27050.03130.294911.03665.538738.3011
152.38693.24331.25485.40053.78726.9392-0.56550.35571.1706-0.4142-0.1250.7738-1.5925-0.30750.63220.54850.0008-0.14010.32580.04060.47239.634517.961538.2228
162.9806-1.52441.37846.6898-1.13054.76870.0695-0.38830.07940.5633-0.30790.0295-0.27620.09450.10110.4429-0.1057-0.03350.3247-0.0430.284113.840411.607954.2979
173.4008-0.55341.25324.58220.87373.33010.0692-0.6141-0.34720.9899-0.17850.7830.503-0.77050.13480.6773-0.19470.16840.54550.06620.45772.9403-9.227957.6663
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 21 )A1 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 97 )A22 - 97
3X-RAY DIFFRACTION3chain 'A' and (resid 98 through 188 )A98 - 188
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 65 )B1 - 65
5X-RAY DIFFRACTION5chain 'B' and (resid 66 through 114 )B66 - 114
6X-RAY DIFFRACTION6chain 'B' and (resid 115 through 188 )B115 - 188
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 21 )C1 - 21
8X-RAY DIFFRACTION8chain 'C' and (resid 22 through 65 )C22 - 65
9X-RAY DIFFRACTION9chain 'C' and (resid 66 through 115 )C66 - 115
10X-RAY DIFFRACTION10chain 'C' and (resid 116 through 145 )C116 - 145
11X-RAY DIFFRACTION11chain 'C' and (resid 146 through 188 )C146 - 188
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 11 )D1 - 11
13X-RAY DIFFRACTION13chain 'D' and (resid 12 through 65 )D12 - 65
14X-RAY DIFFRACTION14chain 'D' and (resid 66 through 115 )D66 - 115
15X-RAY DIFFRACTION15chain 'D' and (resid 116 through 128 )D116 - 128
16X-RAY DIFFRACTION16chain 'D' and (resid 129 through 144 )D129 - 144
17X-RAY DIFFRACTION17chain 'D' and (resid 145 through 188 )D145 - 188

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