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- PDB-4kv3: Ubiquitin-like domain of the Mycobacterium tuberculosis type VII ... -

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Basic information

Entry
Database: PDB / ID: 4kv3
TitleUbiquitin-like domain of the Mycobacterium tuberculosis type VII secretion system protein EccD1 as maltose-binding protein fusion
ComponentsChimera fusion protein of ESX-1 secretion system protein eccD1 and Maltose-binding periplasmic protein
KeywordsPROTEIN TRANSPORT / ESX-1 / ESX / snm4 / ubiquitin / YukD / PF08817 / membrane protein / protein secretion / mbp fusion
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / : / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsKorotkov, K.V. / Evans, T.J.
CitationJournal: Bmc Struct.Biol. / Year: 2016
Title: Structures of EccB1 and EccD1 from the core complex of the mycobacterial ESX-1 type VII secretion system.
Authors: Wagner, J.M. / Chan, S. / Evans, T.J. / Kahng, S. / Kim, J. / Arbing, M.A. / Eisenberg, D. / Korotkov, K.V.
History
DepositionMay 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Chimera fusion protein of ESX-1 secretion system protein eccD1 and Maltose-binding periplasmic protein
B: Chimera fusion protein of ESX-1 secretion system protein eccD1 and Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7464
Polymers100,0612
Non-polymers6852
Water7,530418
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-20 kcal/mol
Surface area35710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.680, 125.680, 124.490
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Chimera fusion protein of ESX-1 secretion system protein eccD1 and Maltose-binding periplasmic protein / MBP / MMBP / Maltodextrin-binding protein


Mass: 50030.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Mycobacterium tuberculosis (bacteria)
Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P0AEX9, UniProt: I6X8K0
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.84 Å3/Da / Density % sol: 56.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES PH 7.5, 1.4M SODIUM CITRATE, vapor diffusion, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. obs: 56556 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.5 % / Biso Wilson estimate: 44.57 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 17.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.2-2.2611.51.0972.88478564161100
2.26-2.323.59469904084100
2.32-2.394.44455543953100
2.39-2.465.03444703853100
2.46-2.546.03427553703100
2.54-2.637.59417043608100
2.63-2.739402693484100
2.73-2.8411.3385943329100
2.84-2.9713.89369303191100
2.97-3.1117.23357143085100
3.11-3.2822338832927100
3.28-3.4826.48319962775100
3.48-3.7231.4298292588100
3.72-4.0235.46278192420100
4.02-4.440255302232100
4.4-4.9243.13231912027100
4.92-5.6842.82203771790100
5.68-6.9644.02171901517100
6.96-9.8451.94131561175100
9.8454.41688565499.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å49.85 Å
Translation2.5 Å49.85 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ANF

1anf


Resolution: 2.2→49.91 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.1982 / WRfactor Rwork: 0.1581 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8806 / SU B: 9.507 / SU ML: 0.127 / SU R Cruickshank DPI: 0.2028 / SU Rfree: 0.1704 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2047 2862 5.1 %RANDOM
Rwork0.1628 ---
obs0.1649 53741 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.49 Å2 / Biso mean: 42.0955 Å2 / Biso min: 21.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.22 Å20 Å2
2---0.22 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6970 0 46 418 7434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.027180
X-RAY DIFFRACTIONr_bond_other_d0.0010.026832
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.9759784
X-RAY DIFFRACTIONr_angle_other_deg0.762315796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7625910
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46225.676296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.818151156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8031518
X-RAY DIFFRACTIONr_chiral_restr0.0720.21110
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218122
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021500
X-RAY DIFFRACTIONr_mcbond_it1.4192.4173646
X-RAY DIFFRACTIONr_mcbond_other1.4192.4163645
X-RAY DIFFRACTIONr_mcangle_it2.3473.624554
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 199 -
Rwork0.229 3960 -
all-4159 -
obs--100 %
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)
12.5751-0.1330.92540.4001-0.21571.16730.03310.134-0.1496-0.0754-0.01840.07330.13330.0713-0.01460.10790.0350.00360.08240.01840.061517.24440.98-39.535
23.9010.02642.25590.6682-0.20651.4387-0.1087-0.43820.3607-0.0414-0.0610.05270.0264-0.17610.16970.13810.0863-0.00590.1555-0.00740.131217.43244.83-30.4
33.13470.7054-0.251.8135-0.93111.5302-0.0093-0.12040.23080.28390.05050.2188-0.1559-0.0539-0.04120.1212-0.04750.02740.0812-0.03140.081-14.25158.972-12.374
42.91891.63741.03141.3880.63280.89060.0302-0.075-0.05580.0862-0.04040.00170.162-0.00610.01020.1353-0.0641-0.00980.0839-0.02620.0946-30.40431.886-5.665
52.97771.4771.14782.16580.45890.5114-0.26360.41110.2888-0.19680.20420.162-0.00380.12360.05950.1974-0.1429-0.05030.1758-0.00610.1416-32.36237.099-15.17
63.2038-0.3945-0.23923.2772-0.55830.8410.10650.22810.3697-0.2931-0.2414-0.1037-0.0218-0.0320.13490.12090.0058-0.02920.1470.07220.1065-7.85359.882-33.094
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 308
2X-RAY DIFFRACTION2A309 - 369
3X-RAY DIFFRACTION3A373 - 461
4X-RAY DIFFRACTION4B6 - 310
5X-RAY DIFFRACTION5B311 - 371
6X-RAY DIFFRACTION6B372 - 461

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