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- PDB-4jr6: Crystal structure of DsbA from Mycobacterium tuberculosis (reduced) -

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Basic information

Entry
Database: PDB / ID: 4jr6
TitleCrystal structure of DsbA from Mycobacterium tuberculosis (reduced)
ComponentsPossible conserved membrane or secreted protein
KeywordsOXIDOREDUCTASE / Thiol:disulfide oxidoreductase / Thioredoxin Fold / Disulfide bond formation / Membrane-anchored
Function / homology
Function and homology information


peptidoglycan-based cell wall / cell surface / plasma membrane
Similarity search - Function
Thioredoxin / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Possible conserved membrane or secreted protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.902 Å
AuthorsWang, L.
CitationJournal: Protein Cell / Year: 2013
Title: Structure analysis of the extracellular domain reveals disulfide bond forming-protein properties of Mycobacterium tuberculosis Rv2969c.
Authors: Wang, L. / Li, J. / Wang, X. / Liu, W. / Zhang, X.C. / Li, X. / Rao, Z.
History
DepositionMar 21, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Other
Revision 1.2Jun 11, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Possible conserved membrane or secreted protein
B: Possible conserved membrane or secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5543
Polymers47,4582
Non-polymers961
Water8,143452
1
A: Possible conserved membrane or secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8252
Polymers23,7291
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Possible conserved membrane or secreted protein


Theoretical massNumber of molelcules
Total (without water)23,7291
Polymers23,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.875, 74.935, 119.893
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 Possible conserved membrane or secreted protein


Mass: 23728.912 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 53-255 / Mutation: L156M, L232M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv2969c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: O33272
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 2.23 Å3/Da / Density % sol: 44.77 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Mosaicity: 0.728 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 28% PEG 2000, 0.2M Ammonium Sulfate, 0.1M Sodium Acetate trihydrate, pH 4.3, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97989 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 12, 2011
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97989 Å / Relative weight: 1
ReflectionRedundancy: 6.9 % / Av σ(I) over netI: 13.51 / Number: 233030 / Rmerge(I) obs: 0.128 / Χ2: 1.04 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 33899 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.095099.310.0980.9975.9
3.254.0999.910.0921.0246.6
2.843.2510010.1111.0116.8
2.582.8410010.1441.0096.9
2.392.5899.910.1761.0437
2.252.3910010.211.077
2.142.2510010.2361.0917.1
2.052.1410010.2861.0647.1
1.972.0510010.3571.0687.2
1.91.9710010.4391.047.2
ReflectionResolution: 1.9→50 Å / Num. obs: 63755 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.128 / Χ2: 1.042 / Net I/σ(I): 13.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.977.20.43933291.041100
1.97-2.057.20.35733351.0681100
2.05-2.147.10.28633581.0641100
2.14-2.257.10.23633351.0911100
2.25-2.3970.2133491.071100
2.39-2.5870.17633651.043199.9
2.58-2.846.90.14433741.0091100
2.84-3.256.80.11134041.0111100
3.25-4.096.60.09234361.024199.9
4.09-505.90.09836140.997199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.902→33.123 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.8787 / SU ML: 0.19 / σ(F): 0 / Phase error: 19.3 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2063 3603 5.86 %
Rwork0.1658 --
obs0.1682 61490 96 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.053 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso max: 97.19 Å2 / Biso mean: 25.716 Å2 / Biso min: 12.15 Å2
Baniso -1Baniso -2Baniso -3
1--2.965 Å2-0 Å20 Å2
2---3.1454 Å20 Å2
3---6.1104 Å2
Refinement stepCycle: LAST / Resolution: 1.902→33.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2914 0 5 452 3371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193205
X-RAY DIFFRACTIONf_angle_d1.3524219
X-RAY DIFFRACTIONf_chiral_restr0.111487
X-RAY DIFFRACTIONf_plane_restr0.008561
X-RAY DIFFRACTIONf_dihedral_angle_d11.621115
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9024-1.92740.25811340.22492031216588
1.9274-1.95380.2491340.19832079221388
1.9538-1.98170.25861290.19332058218791
1.9817-2.01130.2681370.19222186232393
2.0113-2.04270.20811280.18082194232294
2.0427-2.07620.24111360.17762187232394
2.0762-2.1120.20321340.17632199233396
2.112-2.15040.22861340.172249238396
2.1504-2.19170.21181330.16062169230295
2.1917-2.23650.21211340.16072232236695
2.2365-2.28510.20041420.16572210235297
2.2851-2.33820.19711440.16122247239195
2.3382-2.39670.20821350.17192216235196
2.3967-2.46140.20621410.16712262240396
2.4614-2.53390.21891350.16562213234896
2.5339-2.61560.23091400.17742246238697
2.6156-2.70910.21951410.17862242238397
2.7091-2.81750.25881410.18282264240598
2.8175-2.94560.20961470.17832306245398
2.9456-3.10080.19381410.17662254239598
3.1008-3.29490.21531460.166623182464100
3.2949-3.54910.21591470.156123322479100
3.5491-3.90570.18141440.142923092453100
3.9057-4.46970.18421380.13852288242699
4.4697-5.62690.14661470.141123092456100
5.6269-33.12790.21021410.1812287242898
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)
10.27580.0416-0.02330.0905-0.1210.3162-0.16720.00890.23380.14480.0277-0.054-0.1490.0846-0.00390.1508-0.009-0.02020.1311-0.00420.1603-4.6663-13.487316.2322
20.2144-0.246-0.1812-0.0563-0.1747-0.10890.0153-0.06730.0165-0.04540.0371-0.01750.0351-0.026200.1552-0.0063-0.00840.1464-0.01460.1619-16.7977-10.890412.3866
30.25120.0478-0.22060.088-0.00450.14150.0032-0.2207-0.1016-0.03670.0740.14680.0674-0.04520.00120.16020.00510.00970.18030.0040.1793-24.4738-12.493512.3767
41.0768-0.52660.35430.2438-0.19130.23420.0036-0.5921-0.23170.26540.10570.1805-0.1823-0.21720.07570.210.01320.03630.30350.01940.1631-25.8132-8.175224.4916
50.028-0.02410.02370.0174-0.01940.01780.038-0.04590.4130.1177-0.05190.1-0.32030.1484-0.00010.2009-0.0262-0.01570.1985-0.00660.2647-14.16292.464814.4697
60.4643-0.21860.01340.16050.00690.08890.17390.17460.4508-0.2073-0.1566-0.477-0.05530.09220.00180.1715-0.02180.00140.20730.06620.1808-6.0734-9.46223.4528
70.04130.0923-0.00560.0560.04660.07660.11780.2984-0.0808-0.1791-0.14050.17470.1499-0.0581-00.18210.018-0.00070.168-0.03390.1533-2.1616-26.03537.3355
80.52430.0094-0.23240.15110.2350.38630.03430.03790.02030.0294-0.01160.0076-0.1029-0.009400.17670.00550.00170.15180.02640.1528-30.698211.9195-9.3061
90.84560.1157-0.38280.5773-0.18520.6303-0.00160.09990.0044-0.0364-0.0270.02280.0504-0.0328-00.14940.012-0.02420.15660.00560.1586-30.698610.9695-9.7693
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 58:89)A58 - 89
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 90:144)A90 - 144
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 145:172)A145 - 172
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 173:198)A173 - 198
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 199:209)A199 - 209
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 210:228)A210 - 228
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 229:255)A229 - 255
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 58:166)B58 - 166
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 167:254)B167 - 254

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