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- PDB-6ddn: The sulfate-binding protein SubI from Mycobacterium tuberculosis H37Rv -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6ddn
TitleThe sulfate-binding protein SubI from Mycobacterium tuberculosis H37Rv
ComponentsProbable sulfate-binding lipoprotein SubI
KeywordsTRANSPORT PROTEIN / sulfate-binding protein
Function / homology
Function and homology information


ABC-type sulfate transporter activity / Sulfate assimilation / sulfate assimilation / plasma membrane
Similarity search - Function
Thiosulphate/Sulfate-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Probable sulfate-binding lipoprotein SubI
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.295 Å
AuthorsMeza, A.N. / Balan, A. / Nascimento, A.F.Z.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/209216 Brazil
CitationJournal: To Be Published
Title: Structural characterization of SubI, a new target for Mycobacterium tuberculosis
Authors: Meza, A.N. / Nascimento, A.F.Z. / Balan, A.
History
DepositionMay 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable sulfate-binding lipoprotein SubI
B: Probable sulfate-binding lipoprotein SubI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,60824
Polymers74,5552
Non-polymers2,05322
Water2,018112
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A: Probable sulfate-binding lipoprotein SubI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,34913
Polymers37,2781
Non-polymers1,07212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable sulfate-binding lipoprotein SubI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,25811
Polymers37,2781
Non-polymers98110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)243.732, 243.732, 243.732
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
Components on special symmetry positions
IDModelComponents
11A-402-

SO4

21A-402-

SO4

31B-404-

SO4

41B-404-

SO4

51A-511-

HOH

61B-518-

HOH

71B-553-

HOH

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Components

#1: Protein Probable sulfate-binding lipoprotein SubI


Mass: 37277.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: subI, Rv2400c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P71744
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Tris 100 mM pH 8.5, Sodium acetate 200 mM e PEG 4000 16% (w/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.295→46.91 Å / Num. obs: 27656 / % possible obs: 97.6 % / Redundancy: 65.6 % / Biso Wilson estimate: 61.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.379 / Rrim(I) all: 0.382 / Net I/σ(I): 15.65
Reflection shellResolution: 2.295→2.43 Å / Redundancy: 30.8 % / Rmerge(I) obs: 11.3 / Mean I/σ(I) obs: 0.32 / Num. unique obs: 4395 / CC1/2: 0.604 / Rrim(I) all: 11.5 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSNov 11, 2017 BUILT=20180124data reduction
XDSNov 11, 2017 BUILT=20180124data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SBP
Resolution: 2.295→46.906 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 45.84
RfactorNum. reflection% reflection
Rfree0.313 1338 4.99 %
Rwork0.2698 --
obs0.272 26803 94.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 61.09 Å2
Refinement stepCycle: LAST / Resolution: 2.295→46.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4324 0 117 112 4553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054541
X-RAY DIFFRACTIONf_angle_d0.7016203
X-RAY DIFFRACTIONf_dihedral_angle_d18.472638
X-RAY DIFFRACTIONf_chiral_restr0.047681
X-RAY DIFFRACTIONf_plane_restr0.004811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2954-2.37740.7731830.73251662X-RAY DIFFRACTION64
2.3774-2.47260.42191360.45032534X-RAY DIFFRACTION97
2.4726-2.58510.43071390.39722619X-RAY DIFFRACTION99
2.5851-2.72140.45011370.37142605X-RAY DIFFRACTION99
2.7214-2.89190.33491390.30122652X-RAY DIFFRACTION100
2.8919-3.11510.39911300.36192473X-RAY DIFFRACTION93
3.1151-3.42850.34331400.25932664X-RAY DIFFRACTION100
3.4285-3.92440.28381410.21732691X-RAY DIFFRACTION99
3.9244-4.94350.23891400.19382672X-RAY DIFFRACTION98
4.9435-46.9160.23411530.20222893X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.5650.84684.25642.63620.46467.24111.63962.39041.5217-1.0729-0.7635-0.911-0.97950.1388-0.23880.76260.24010.28751.08210.46250.599349.860315.7442.3374
20.858-1.31660.3987.7454-3.85123.32120.0394-0.55190.0009-0.5149-0.4349-0.15880.54420.30340.26620.3817-0.0424-0.04940.67140.05550.58438.534812.70698.0483
32.01256.2926-7.48593.8626-4.60115.46910.39931.09951.54530.21020.3211-1.3242-1.18390.96850.17780.8983-0.22290.12050.84020.09080.720445.1627.28564.8791
41.97150.94662.05747.9707-0.65862.2659-0.01870.5415-0.4206-0.1903-0.1654-0.39350.0611.16680.03970.65730.040.15450.6122-0.09720.637845.84014.8937.3305
57.5491-0.0446-1.99147.4509-0.6616.1786-0.5467-0.3630.26250.24170.0552-0.59160.52280.65260.30790.54580.04330.02910.61260.01750.600748.91324.409513.6664
66.8993-0.0714-4.36622.70674.04869.79620.21811.04680.72541.1660.4948-1.98760.42871.1252-0.65030.50720.0318-0.11270.73180.09830.538956.05394.609218.6312
74.0627-4.7273-4.59575.63665.385.1718-0.66971.10310.998-0.4661-0.1647-0.5295-2.8771-1.18090.31420.98280.0624-0.15070.82290.05790.758849.141114.028624.6183
80.5365-0.2848-1.24790.95821.59412.64290.4003-0.1715-0.34870.1515-0.3074-0.15930.2504-0.6702-0.03430.4572-0.0081-0.19840.48610.19270.350724.08390.871119.3193
98.51652.66-1.88992.6656-0.3992.3429-0.5821-0.5354-0.0819-0.3070.3642-0.02320.04040.22320.13340.55630.0144-0.05810.52570.0120.590228.7224-7.568321.7289
104.6459-3.561-4.62319.6193.49964.4744-0.3274-1.0416-0.15421.9119-0.83950.78280.370.05660.85970.682-0.0829-0.08780.5069-0.08110.517132.6082-4.716732.516
117.05164.74411.99413.47631.48737.32460.5071-1.66760.4021-0.0296-0.8676-2.43240.53540.05210.53791.02610.2052-0.20990.91310.07120.749934.7746-9.284837.7993
126.12252.2621-2.27037.69543.58173.6623-0.1744-0.5177-1.49741.4305-0.07731.17870.4944-1.32970.40030.70970.0503-0.03080.65380.06690.700130.682-13.992828.4118
138.82476.544-6.01075.4159-5.08675.1329-1.10460.8788-0.7579-1.23891.21620.27171.0493-1.4549-0.01440.5145-0.0621-0.02470.5792-0.04030.479131.5996-13.855917.5022
145.03634.9419-2.39985.1146-2.8365.98750.11260.4377-1.2973-0.26130.0547-0.65741.13090.2086-0.09230.70260.05950.03660.61290.07240.498726.9072-6.12089.1463
156.8927-0.767-5.65154.6983-2.3956.5025-0.3438-0.0243-0.4791-0.6010.0375-0.18671.41892.355-0.54320.7318-0.242-0.34550.5281-0.02260.545828.54251.27916.6426
164.66365.0883.38966.78491.82616.4695-0.2542-0.86490.8826-0.3975-0.44860.74520.2895-1.29030.63750.63060.08570.12770.55080.14250.747121.56524.484410.8145
173.44642.5447-4.42842.6698-4.14756.1166-0.8907-1.1671-0.3472-0.29230.0833-0.52880.80640.84160.5090.4869-0.03460.00020.4531-0.15160.45739.43266.791120.8382
182.22820.1358-4.54372.0368-0.06483.29180.4995-0.16260.55710.3148-0.04180.1743-0.2560.2987-0.25940.51830.0251-0.15320.5877-0.05570.586235.621517.445618.3501
199.3042.775-7.14375.2422-4.44577.0368-0.7625-1.0376-0.68911.56170.1218-0.8404-0.82822.63350.67020.530.0291-0.12081.2712-0.22910.454640.2861.709832.4844
206.807-3.5257-1.53387.7093.01684.79671.3188-0.81310.47052.6976-2.9343-0.3081-1.97933.26651.00221.6089-0.29930.2121.48590.07590.854443.7017-8.176728.2626
211.9548-4.75220.64446.20943.11865.1782-0.7527-1.1851-4.29110.7431-0.6361.29540.5896-1.57451.43610.4164-0.37160.28970.9386-0.35640.861272.11392.394115.6957
221.065-0.93011.34093.9056-2.66642.32310.2966-0.1112-0.6998-0.06630.03760.23270.0381.0126-0.28240.5072-0.0080.0540.5263-0.04180.613583.6028.404112.1214
238.34311.15280.20074.0328-0.82691.2084-0.3481-1.427-0.52151.26-0.2127-0.26121.7437-0.94350.48990.8517-0.01430.14240.87890.18470.682276.57813.101724.4724
248.9109-1.12341.63575.33540.08265.91280.06390.2579-1.0464-0.28950.20210.6606-0.80890.2322-0.34640.5158-0.0341-0.0940.78680.00020.668475.08578.8571.7947
253.94041.02640.60042.7116-0.6524.07980.6426-0.8447-0.7217-0.3745-0.18020.29590.2328-1.1102-0.09980.35630.0286-0.0940.90870.24260.775572.679214.98514.443
265.4523-4.80014.56875.469-2.70435.38770.9852-1.1541-0.05890.31390.02442.6603-1.00170.1193-0.87560.5892-0.14480.19331.0665-0.03250.599964.668419.48187.4791
272.6804-0.1483-0.59540.5171-1.03142.1299-0.55630.4563-0.02060.080.29720.13980.1141-0.48210.20140.4530.01020.04310.5315-0.13870.545990.515320.99614.7596
282.07391.47620.1376.99120.11953.78420.2395-0.2630.2632-0.3393-0.13170.0007-0.3062-0.136-0.08040.56010.0233-0.02970.5262-0.03340.46792.096124.6776-6.9053
295.23320.8456-0.3717.79648.89161.9932-0.3630.449-0.12810.4413-1.17682.0955-0.164-2.15140.18391.20870.2293-0.00390.79320.12540.329386.99838.1015-9.2099
305.7889-1.556-4.69782.05552.66544.88991.23780.71961.173-3.0699-0.1788-1.0514-1.3079-0.2806-0.88420.6392-0.13940.1160.7488-0.09680.551592.164926.2423-15.1634
315.5083-1.6018-1.91065.1616-1.25752.44310.7535-0.46740.6063-1.35850.20360.23060.16020.475-1.02070.5941-0.11930.10910.7623-0.12350.697288.132112.373-8.9174
328.1884-2.86993.54274.7962-5.21325.80330.80430.3356-1.9101-3.2278-0.34850.2886-0.67090.0308-0.43970.9564-0.02750.14640.5219-0.25610.732394.21818.1458-5.6863
335.3945-0.5689-5.46772.39960.02486.2217-0.65130.24540.55910.3176-0.0991-0.4070.97020.36060.68240.4955-0.1997-0.11970.6407-0.04510.545394.966515.537-1.7607
342.3727-1.3728-3.93813.22962.17927.034-0.0358-1.6294-0.5123-0.45920.20820.96951.12030.13640.21910.72090.0351-0.09440.5458-0.06180.5472100.296810.81454.4963
352.88634.0703-1.06465.2529-1.9084.13281.6897-0.56650.25341.3453-0.55630.4936-0.6205-0.1969-0.82120.40310.08210.09290.6176-0.00770.564885.486322.95015.9512
369.66372.04447.60874.28323.66696.9918-0.9443-0.02390.5715-0.77951.13341.2999-0.0216-0.5106-0.21020.5312-0.2361-0.1080.92930.25340.691269.16339.619116.7807
374.9247-0.57321.87295.47350.87213.8376-0.6745-0.1441-0.103-0.0220.87590.04210.1636-0.2043-0.04350.5936-0.04990.0160.4603-0.06640.419386.060316.016918.5397
382.0049-1.92022.62763.0256-3.22953.654-0.65550.2450.21150.4860.4706-0.2409-0.02721.10980.37830.4406-0.0012-0.01450.57070.0370.602194.435923.796717.5749
391.96598.86492.52748.48471.69735.11871.3537-1.76623.5757-0.6439-1.42191.208-0.2079-1.26320.37520.73280.1829-0.14890.65660.13780.611984.024132.58652.4523
406.85574.2596-3.82062.6725-2.93957.79920.88090.31410.6123-0.15842.25722.54550.366-2.4387-1.09681.0936-0.0128-0.52261.16480.52411.575977.952828.1661-7.9168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 55:60)
2X-RAY DIFFRACTION2(chain A and resid 61:78)
3X-RAY DIFFRACTION3(chain A and resid 79:84)
4X-RAY DIFFRACTION4(chain A and resid 85:102)
5X-RAY DIFFRACTION5(chain A and resid 103:119)
6X-RAY DIFFRACTION6(chain A and resid 120:130)
7X-RAY DIFFRACTION7(chain A and resid 131:139)
8X-RAY DIFFRACTION8(chain A and resid 140:158)
9X-RAY DIFFRACTION9(chain A and resid 159:185)
10X-RAY DIFFRACTION10(chain A and resid 186:196)
11X-RAY DIFFRACTION11(chain A and resid 197:204)
12X-RAY DIFFRACTION12(chain A and resid 205:211)
13X-RAY DIFFRACTION13(chain A and resid 212:222)
14X-RAY DIFFRACTION14(chain A and resid 223:235)
15X-RAY DIFFRACTION15(chain A and resid 236:244)
16X-RAY DIFFRACTION16(chain A and resid 245:256)
17X-RAY DIFFRACTION17(chain A and resid 257:276)
18X-RAY DIFFRACTION18(chain A and resid 277:323)
19X-RAY DIFFRACTION19(chain A and resid 324:334)
20X-RAY DIFFRACTION20(chain A and resid 335:341)
21X-RAY DIFFRACTION21(chain B and resid 55:60)
22X-RAY DIFFRACTION22(chain B and resid 61:77)
23X-RAY DIFFRACTION23(chain B and resid 78:87)
24X-RAY DIFFRACTION24(chain B and resid 88:104)
25X-RAY DIFFRACTION25(chain B and resid 105:123)
26X-RAY DIFFRACTION26(chain B and resid 124:131)
27X-RAY DIFFRACTION27(chain B and resid 132:158)
28X-RAY DIFFRACTION28(chain B and resid 159:196)
29X-RAY DIFFRACTION29(chain B and resid 197:204)
30X-RAY DIFFRACTION30(chain B and resid 205:215)
31X-RAY DIFFRACTION31(chain B and resid 216:223)
32X-RAY DIFFRACTION32(chain B and resid 224:231)
33X-RAY DIFFRACTION33(chain B and resid 232:244)
34X-RAY DIFFRACTION34(chain B and resid 245:256)
35X-RAY DIFFRACTION35(chain B and resid 257:273)
36X-RAY DIFFRACTION36(chain B and resid 274:285)
37X-RAY DIFFRACTION37(chain B and resid 286:305)
38X-RAY DIFFRACTION38(chain B and resid 306:320)
39X-RAY DIFFRACTION39(chain B and resid 321:334)
40X-RAY DIFFRACTION40(chain B and resid 335:341)

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