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- PDB-8h5s: Crystal structure of Rv3400 from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 8h5s
TitleCrystal structure of Rv3400 from Mycobacterium tuberculosis
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / Beta-phosphoglucomutase / Haloacid dehalogenase family protein / crystal / G1P
Function / homologyBeta-phosphoglucomutase hydrolase / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily / HAD-like superfamily / Uncharacterized protein Rv3400
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsSingh, L. / Karthikeyan, S. / Thakur, K.G.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)MLP0018 India
CitationJournal: To Be Published
Title: Crystal structure of Rv3400 from Mycobacterium tuberculosis
Authors: Singh, L. / Karthikeyan, S. / Thakur, K.G.
History
DepositionOct 13, 2022Deposition site: PDBJ / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3425
Polymers28,1171
Non-polymers2254
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-16 kcal/mol
Surface area10740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.903, 106.389, 81.204
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-304-

CL

21A-508-

HOH

31A-707-

HOH

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Components

#1: Protein Beta-phosphoglucomutase /


Mass: 28116.562 Da / Num. of mol.: 1 / Mutation: L126M, L197M, L202M, H123L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv3400, MTCY78.28c / Plasmid: pET DuetN-Rv3400 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P9WKZ7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 3.82 Å3/Da / Density % sol: 67.8 % / Description: Rectangular
Crystal growTemperature: 293 K / Method: microbatch / pH: 4.5
Details: 0.2 M Ammonium Sulphate 0.05 M sodium acetate pH 4.5 30% PEG 8000
PH range: 4-5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2020
RadiationCollimation: Mirrors were cylindrical collimating and Toroidal focussing mirror
Monochromator: Double crystal monochromator / Analyzer: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.7→41.92 Å / Num. obs: 85784 / % possible obs: 95.4 % / Observed criterion σ(I): 1.6 / Redundancy: 11.1 % / Biso Wilson estimate: 22.87 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.057 / Net I/σ(I): 30.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1601 / CC1/2: 0.65 / % possible all: 66.2

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PHENIX1.20_4459refinement
XDSJan 10, 2022data reduction
XDSJan 10, 2022data scaling
PHENIX1.20-4459phasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→33.34 Å / SU ML: 0.1645 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.5171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1728 4163 4.85 %
Rwork0.154 81612 -
obs0.1549 85775 94.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.9 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 12 310 2174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061969
X-RAY DIFFRACTIONf_angle_d0.75772680
X-RAY DIFFRACTIONf_chiral_restr0.0528303
X-RAY DIFFRACTIONf_plane_restr0.0069363
X-RAY DIFFRACTIONf_dihedral_angle_d11.7814725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.3043980.28691673X-RAY DIFFRACTION58.51
1.72-1.740.26691080.26271970X-RAY DIFFRACTION69.38
1.74-1.760.30491260.24642121X-RAY DIFFRACTION74.16
1.76-1.780.20541240.22932359X-RAY DIFFRACTION82.03
1.78-1.810.25391310.25222441X-RAY DIFFRACTION85.73
1.81-1.830.22761260.21942550X-RAY DIFFRACTION90.47
1.83-1.860.23671240.2222746X-RAY DIFFRACTION94.38
1.86-1.880.1731300.20112785X-RAY DIFFRACTION97.59
1.88-1.910.22541320.19212902X-RAY DIFFRACTION99.35
1.91-1.950.22271360.17732832X-RAY DIFFRACTION99.7
1.95-1.980.1841850.16462859X-RAY DIFFRACTION100
1.98-2.010.19021270.1562875X-RAY DIFFRACTION100
2.01-2.050.20131480.15562847X-RAY DIFFRACTION100
2.05-2.10.13971470.15152841X-RAY DIFFRACTION100
2.1-2.140.19251530.16182887X-RAY DIFFRACTION100
2.14-2.190.18381220.1462877X-RAY DIFFRACTION100
2.19-2.250.15111180.14472856X-RAY DIFFRACTION100
2.25-2.310.16351650.13992858X-RAY DIFFRACTION99.93
2.31-2.370.15661760.1532846X-RAY DIFFRACTION100
2.37-2.450.18131640.15182828X-RAY DIFFRACTION99.97
2.45-2.540.19281780.17042827X-RAY DIFFRACTION100
2.54-2.640.18831530.16012852X-RAY DIFFRACTION99.93
2.64-2.760.17551360.17442886X-RAY DIFFRACTION100
2.76-2.910.20921170.16372895X-RAY DIFFRACTION100
2.91-3.090.19111380.16142873X-RAY DIFFRACTION99.97
3.09-3.320.1561280.15082872X-RAY DIFFRACTION99.87
3.33-3.660.17571660.13532844X-RAY DIFFRACTION100
3.66-4.190.12671300.1222888X-RAY DIFFRACTION99.97
4.19-5.270.13641420.12112854X-RAY DIFFRACTION99.93
5.27-33.340.14031350.14512868X-RAY DIFFRACTION99.17
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)
12.71145703798-2.57959975175-1.154805126345.520406738030.7996956636734.06094251282-0.00938125324089-0.03917005780150.2614767327680.1176191586010.03992931757970.175240455901-0.129134964735-0.266869589508-0.01808110512180.1555270564840.000258315584964-0.0009228823998530.167043927715-0.007108172814060.1476994863722.236240113439.649478811945.778097114
23.1583198644-1.08389529055-2.722644852720.7596991015651.054616486535.517863370560.0188029373315-0.01117026822660.0575142427412-0.01479353627610.029848618697-0.0334162683627-0.0572020271630.221475040317-0.05871523695050.156334211373-0.02322367261520.002687523909390.1427836989490.007700170489670.19448309222539.9812285233.605710976223.7802408902
32.123227513261.05432865949-0.3242063889693.51537906268-1.868714487823.088797749160.07679232684490.0658522827069-0.0416013089244-0.211618228843-0.008921363676130.1677260220060.261243753469-0.00572879711999-0.07558734135240.1898224411810.00660838637456-0.01899013554530.179303313415-0.008920952301260.16468564890633.328576500725.430718097520.5928142786
48.269036904930.5775004590521.893088199076.167948839740.2520179100694.476595544020.00786579743356-0.4989792686740.2215213839950.7076843852380.0866427315655-0.5906621063340.2478403382740.270480101837-0.08847601164730.2518513315930.0510502366403-0.03158533629940.175153103474-0.01865986403650.23008619343640.320159915924.261593063432.397699975
53.73831332963-1.0494481844-5.310724744294.517763299892.444752205598.60004503962-0.230306660093-0.555594377268-0.1338392983520.3521161339410.306320094058-0.4053391544270.3072449989170.690889259214-0.02251618533750.2118865389860.0356506193561-0.05412084113810.1978723585350.003551946199240.19083684574330.9646835338.684189224351.8778488066
62.73858646125-0.701228661748-2.729344922811.217428424821.716378235017.09956082868-0.09458309576490.080633311411-0.2574362463480.159218076642-0.0170213119091-0.05899613008510.5059119873190.1842403419190.08954190950550.213390182717-0.002930487922140.002391863700150.1460420314270.02725571739050.21827636339227.275285153929.131198364145.3965701453
72.336642517090.1533105168941.523026457123.18813822097-0.3715752613416.52291081930.0573109282566-0.0945489093598-0.2513840876880.0360659717756-0.0212724622562-0.03140302596850.8409636271880.0197701664295-0.05149341970530.211303815656-0.01247641170320.02305756929210.1638361220660.02048799572560.20665900236422.635193294326.703706565540.5010333044
87.42806303907-0.106741936877-6.496359522332.88425371634-0.8617112036429.4074989211-0.09598649829250.310034327354-0.207755797768-0.13164347110.1262968651840.3108342173640.525391793406-0.948665840067-0.02717371700590.177809317703-0.0720628552351-0.01319906713910.2905762779560.01243648433590.26669601402313.659208657830.737806314339.9027350268
93.05988410921.335917046240.5083665547744.009193573270.03859623377553.23910242629-0.02243300368670.07239865284720.0200536746756-0.1472245957120.05865901953-0.0305985790257-0.184448680769-0.123436072903-0.04049245979270.1343947322310.02630208038110.007468875811610.108025066519-0.002444830735310.14339908338823.997086229945.130382774737.7267635605
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 16 through 37 )16 - 371 - 22
22chain 'A' and (resid 38 through 81 )38 - 8123 - 66
33chain 'A' and (resid 82 through 110 )82 - 11067 - 95
44chain 'A' and (resid 111 through 128 )111 - 12896 - 113
55chain 'A' and (resid 129 through 146 )129 - 146114 - 131
66chain 'A' and (resid 147 through 167 )147 - 167132 - 152
77chain 'A' and (resid 168 through 193 )168 - 193153 - 178
88chain 'A' and (resid 194 through 206 )194 - 206179 - 191
99chain 'A' and (resid 207 through 262 )207 - 262192 - 247

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