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- PDB-6r1b: Crystal structure of UgpB from Mycobacterium tuberculosis in comp... -

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Basic information

Entry
Database: PDB / ID: 6r1b
TitleCrystal structure of UgpB from Mycobacterium tuberculosis in complex with glycerophosphocholine
Components(Putative Sn-glycerol-3-phosphate-binding lipoprotein ...) x 4
KeywordsTRANSPORT PROTEIN / Mycobacterium tuberculosis UgpB substrate-binding protein glycerophosphocholine
Function / homology
Function and homology information


Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CH5 / Sn-glycerol-3-phosphate-binding lipoprotein UgpB / Probable Sn-glycerol-3-phosphate-binding lipoprotein UgpB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27000203237 Å
AuthorsFenn, J. / Nepravishta, R. / Guy, C.S. / Harrison, J. / Angulo, J. / Cameron, A.D. / Fullam, E.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome Trust104193/ Z / 14/ Z United Kingdom
Royal SocietyR G 1 2 0 4 0 5 United Kingdom
Medical Research Council (United Kingdom)MR / J 0 0 3 9 6 4 / 1 United Kingdom
Engineering and Physical Sciences Research CouncilE P /M 0 2 7 5 0 3 /1 United Kingdom
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Structural Basis of Glycerophosphodiester Recognition by theMycobacterium tuberculosisSubstrate-Binding Protein UgpB.
Authors: Fenn, J.S. / Nepravishta, R. / Guy, C.S. / Harrison, J. / Angulo, J. / Cameron, A.D. / Fullam, E.
History
DepositionMar 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB
B: Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB
C: Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB
D: Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,23117
Polymers168,7084
Non-polymers1,52313
Water4,666259
1
A: Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1884
Polymers42,8141
Non-polymers3753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3626
Polymers42,8711
Non-polymers4915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0314
Polymers41,6561
Non-polymers3753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6513
Polymers41,3681
Non-polymers2832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.110, 169.860, 213.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Putative Sn-glycerol-3-phosphate-binding lipoprotein ... , 4 types, 4 molecules ABCD

#1: Protein Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB


Mass: 42813.523 Da / Num. of mol.: 1 / Mutation: K161(MLZ)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ugpB, ERS007679_03701 / Plasmid: pYUB1062 / Production host: Mycobacterium smegmatis (bacteria) / References: UniProt: A0A0U0RXC0, UniProt: P71619*PLUS
#2: Protein Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB


Mass: 42870.574 Da / Num. of mol.: 1 / Mutation: K161(MLZ)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ugpB, ERS007679_03701 / Plasmid: pYUB1062 / Production host: Mycobacterium smegmatis (bacteria) / References: UniProt: A0A0U0RXC0, UniProt: P71619*PLUS
#3: Protein Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB


Mass: 41656.363 Da / Num. of mol.: 1 / Mutation: K161(MLZ)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ugpB, ERS007679_03701 / Plasmid: pYUB1062 / Production host: Mycobacterium smegmatis (bacteria) / References: UniProt: A0A0U0RXC0, UniProt: P71619*PLUS
#4: Protein Putative Sn-glycerol-3-phosphate-binding lipoprotein UgpB


Mass: 41367.969 Da / Num. of mol.: 1 / Mutation: K161(MLZ)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ugpB, ERS007679_03701 / Plasmid: pYUB1062 / Production host: Mycobacterium smegmatis (bacteria) / References: UniProt: A0A0U0RXC0, UniProt: P71619*PLUS

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Non-polymers , 4 types, 272 molecules

#5: Chemical
ChemComp-CH5 / 2-(((R)-2,3-DIHYDROXYPROPYL)PHOSPHORYLOXY)-N,N,N-TRIMETHYLETHANAMINIUM / GLYCERO-3-PHOSPHOCHOLINE / Alpha-GPC


Mass: 258.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H21NO6P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M MgCl2, 0.1 M Tris pH 8.5, 20% PEG 8,000, 10 mM Glycerol-3-phosphocholine

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.27→38.69 Å / Num. obs: 78213 / % possible obs: 99.2 % / Redundancy: 7.8 % / Biso Wilson estimate: 41.826250244 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.3
Reflection shellResolution: 2.27→2.33 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
XDS0.0.5data reduction
XDS0.0.5data scaling
PHASER1.12_2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MFI

4mfi


Resolution: 2.27000203237→38.6872573778 Å / SU ML: 0.313926047969 / Cross valid method: FREE R-VALUE / σ(F): 1.34246804547 / Phase error: 27.197890168
RfactorNum. reflection% reflection
Rfree0.255984598665 4039 5.17005235334 %
Rwork0.20604613029 --
obs0.208701378794 78123 99.0993619423 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 54.1944402787 Å2
Refinement stepCycle: LAST / Resolution: 2.27000203237→38.6872573778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11953 0 93 259 12305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061188191585912369
X-RAY DIFFRACTIONf_angle_d0.66307830429916851
X-RAY DIFFRACTIONf_chiral_restr0.04206940657621810
X-RAY DIFFRACTIONf_plane_restr0.004796231152872210
X-RAY DIFFRACTIONf_dihedral_angle_d11.62725026617145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.29670.397642929651220.3091319311832494X-RAY DIFFRACTION96.2826647037
2.2967-2.32470.3715698686611420.2930902639242470X-RAY DIFFRACTION98.1954887218
2.3247-2.35410.2990021808541340.2822819174412504X-RAY DIFFRACTION100
2.3541-2.38510.3450203557571450.2694093746412529X-RAY DIFFRACTION100
2.3851-2.41780.3124229709291300.2692060834092506X-RAY DIFFRACTION97.1260132646
2.4178-2.45230.3291703724371270.251779292490X-RAY DIFFRACTION98.3834586466
2.4523-2.48890.3050339221381240.2501570403632518X-RAY DIFFRACTION99.9621642073
2.4889-2.52780.3219928273411350.2469405545892565X-RAY DIFFRACTION100
2.5278-2.56920.3207162317831320.2358709009422515X-RAY DIFFRACTION96.5001822822
2.5692-2.61350.2928072195171300.2246310274162504X-RAY DIFFRACTION99.9620493359
2.6135-2.6610.2655625558991390.2205706185142550X-RAY DIFFRACTION100
2.661-2.71220.294659489921260.2174713241112534X-RAY DIFFRACTION97.2933430871
2.7122-2.76750.268671429021240.2191388911382527X-RAY DIFFRACTION100
2.7675-2.82770.311564500471310.2059889539642549X-RAY DIFFRACTION100
2.8277-2.89350.2414225695681300.2150483093432543X-RAY DIFFRACTION97.7688368691
2.8935-2.96580.2756762807941620.2097162671752502X-RAY DIFFRACTION100
2.9658-3.0460.2815191577661280.2091558698932591X-RAY DIFFRACTION99.8164464023
3.046-3.13550.2690067459111450.2159357212422517X-RAY DIFFRACTION98.3739837398
3.1355-3.23670.2581415779151370.2031709437652557X-RAY DIFFRACTION99.8887652948
3.2367-3.35230.2258017069111580.1993961497132510X-RAY DIFFRACTION98.6321626617
3.3523-3.48650.2637452345721500.19727383022572X-RAY DIFFRACTION99.9632757988
3.4865-3.6450.2281716970021550.1961936964632558X-RAY DIFFRACTION99.1231275119
3.645-3.8370.2615845533711370.1822769501612616X-RAY DIFFRACTION99.6380745566
3.837-4.07720.2449484865351500.1808625136012540X-RAY DIFFRACTION99.55588453
4.0772-4.39160.2270363514961620.1792345487032580X-RAY DIFFRACTION99.347826087
4.3916-4.83280.2082834455731490.1702181565442599X-RAY DIFFRACTION99.6735582155
4.8328-5.53040.2362077053051350.1892867937552656X-RAY DIFFRACTION99.6785714286
5.5304-6.96110.2698106575121490.2162431094992659X-RAY DIFFRACTION99.5038979447
6.9611-38.69290.2161291690771510.2124246751432829X-RAY DIFFRACTION99.4659546061
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)
12.4041118123-0.2707239393940.6809281051492.51005039276-0.2456908575822.885741422820.0805207091595-0.325207461394-0.2712289817090.2894858127420.08882006695570.353819791270.0833678430402-0.35350813774-0.1627881419370.296606226766-0.0302901243844-0.009556761983670.3760366530670.1133721124120.517767058247-19.659388998932.4074900877-16.6461720772
22.20904845426-1.263724792080.7030741230434.41125402033-1.279439089611.668546409260.05100632085450.146544893113-0.0313218263443-0.299728289059-0.0733822385366-0.2455263543410.2384658098140.06048905011340.0324223468970.257575170396-0.0132608210024-0.00924610046240.278566657117-0.002324364146510.414843344839-5.0359384690534.791218141-38.9418753813
31.563103297790.1494498935380.01167326644012.89965767348-0.3504912091181.96054695186-0.0719007018614-0.1461605014860.2006494044670.3959809352150.0253166135189-0.134565486614-0.1231565612270.0478162811510.03921419728370.354761809851-0.03341605233920.112649249540.307708042626-0.08847608051850.473505821439-24.5115330619-9.56747143163-15.0313363028
41.55489764258-1.15580460088-0.4666671456833.25183714350.3859954761031.3164756707-0.02014192731670.197545772744-0.0467583929841-0.150748650209-0.05534931216210.231241579355-0.0214026577496-0.008079845500730.07940569599050.330241523357-0.05402383478110.09874313119720.32472012833-0.03456237999150.460267072656-38.9926367858-11.8328874356-37.6566866187
51.54574030834-0.294695806284-0.36667692312.2423770294-0.1457873486142.644220484350.4330795920680.1859692590260.0287872606753-0.497195357796-0.154802620692-0.4682324245511.033861075391.08961056979-0.2558195489450.7736028273380.4134153450830.06000083127440.748145213333-0.1306048819540.585138833623-15.1895388794-46.6229851085-35.0298907711
62.213445996390.0137645123372-0.2980083257835.009792535760.4514488801613.284916303180.0848659554277-0.0397958325094-0.2932423086510.2928506177530.0675495430210.2866925285931.070425861180.121399113345-0.1239578717020.5849534777550.0571546584719-0.04344224748040.3053709083360.00945575761240.353680796177-31.059974675-51.1454800405-13.237682622
72.130752416290.3702800612550.0850921794362.78238360950.09120515496463.42769006734-0.111030286360.2553954527-0.0780115352381-0.1348213869120.187324588786-0.266667523734-0.4523054524070.916550328724-0.04633844654670.277774941651-0.1669606979530.02225576973310.544641186384-0.03207509847540.430414751999-15.0039692141-16.3572855401-70.4803590645
81.58569326830.7442526483420.736088498735.441127163760.5571563307752.51842091952-0.2609265255440.2875090942680.406385681236-0.8558198595680.08044234371550.785898291343-0.8922085337320.1161051101350.1560575832860.730539619848-0.0875862019134-0.1854708197280.4566066060410.06748909401080.601787662317-29.8665829015-11.1460844659-92.9533115435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and ((resid 36 through 153 ) or ( resid 305:377))
2X-RAY DIFFRACTION2chain A and not ((resid 36 through 153) or (resid 305:377))
3X-RAY DIFFRACTION3chain B and ((resid 35 through 153) or (resid 305:377))
4X-RAY DIFFRACTION4chain B and not ((resid 35 through 153) or (resid 305:377))
5X-RAY DIFFRACTION5chain C and ((resid 35 through 153) or (resid 305:377))
6X-RAY DIFFRACTION6chain C and not ((resid 35 through 153) or (resid 305:377))
7X-RAY DIFFRACTION7chain D and ((resid 35 through 153) or (resid 305:377))
8X-RAY DIFFRACTION8chain D and not ((resid 35 through 153) or (resid 305:377))

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