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- PDB-1lax: CRYSTAL STRUCTURE OF MALE31, A DEFECTIVE FOLDING MUTANT OF MALTOS... -

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Entry
Database: PDB / ID: 1lax
TitleCRYSTAL STRUCTURE OF MALE31, A DEFECTIVE FOLDING MUTANT OF MALTOSE-BINDING PROTEIN
ComponentsMALTOSE-BINDING PROTEIN MUTANT MALE31
KeywordsSUGAR BINDING PROTEIN / misfolding mutant / sugar transport
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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSaul, F.A. / Mourez, M. / Vulliez-le Normand, B. / Sassoon, N. / Bentley, G.A. / Betton, J.M.
Citation
Journal: PROTEIN SCI. / Year: 2003
Title: Crystal structure of a defective folding protein
Authors: Saul, F.A. / Mourez, M. / Vulliez-le Normand, B. / Sassoon, N. / Bentley, G.A. / Betton, J.M.
#1: Journal: J.Biol.Chem. / Year: 1998
Title: Degradation versus aggregation of misfolded maltose-binding protein in the periplasm of Escherichia coli
Authors: Betton, J.M. / Sassoon, N. / Hofnung, M. / Laurent, M.
#2: Journal: J.Biol.Chem. / Year: 1996
Title: Folding of a mutant maltose-binding protein of Escherichia coli which forms inclusion bodies
Authors: Betton, J.M. / Hofnung, M.
History
DepositionMar 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / 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 / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / 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_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600 Heterogen Atoms O1 of GLC B 401 and GLC D 401 are missing

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MALTOSE-BINDING PROTEIN MUTANT MALE31
C: MALTOSE-BINDING PROTEIN MUTANT MALE31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2754
Polymers81,5902
Non-polymers6852
Water14,646813
1
A: MALTOSE-BINDING PROTEIN MUTANT MALE31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1372
Polymers40,7951
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: MALTOSE-BINDING PROTEIN MUTANT MALE31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1372
Polymers40,7951
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.043, 89.115, 95.975
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MALTOSE-BINDING PROTEIN MUTANT MALE31 / Maltodextrin-binding protein mutant


Mass: 40795.145 Da / Num. of mol.: 2 / Fragment: MALE31 / Mutation: G32D I33P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MALE / Production host: Escherichia coli (E. coli) / Strain (production host): MC4100 Derivative / References: UniProt: P02928, UniProt: P0AEX9*PLUS
#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
[][D-1-deoxy-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 813 / 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: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, TRIS/HCl, ISOPROPANOL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMTris-HCl1reservoirpH8.5
210 %isopropanol1reservoir
320 %(w/v)PEG40001reservoir
43.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 19, 2000
RadiationMonochromator: Diamond(111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.85→26 Å / Num. all: 60245 / Num. obs: 60245 / % possible obs: 99.8 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 9.2
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 3.4 / Num. unique all: 8705 / % possible all: 99.2
Reflection
*PLUS
Lowest resolution: 26 Å
Reflection shell
*PLUS
% possible obs: 99.2 % / Num. unique obs: 8670

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ANF

1anf


Resolution: 1.85→26 Å / SU B: 3.703 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.129 / Stereochemistry target values: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.20227 3049 5.1 %RANDOM
Rwork0.15719 ---
all0.1594 60237 --
obs0.15947 57188 99.78 %-
Displacement parametersBiso mean: 13.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20.1 Å2
2--0.53 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.85→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5722 0 44 813 6579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225909
X-RAY DIFFRACTIONr_bond_other_d0.0010.025250
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9688028
X-RAY DIFFRACTIONr_angle_other_deg0.763312319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1263734
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.134151045
X-RAY DIFFRACTIONr_chiral_restr0.0880.2883
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026538
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021092
X-RAY DIFFRACTIONr_nbd_refined0.2260.31395
X-RAY DIFFRACTIONr_nbd_other0.1980.35166
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.5700
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0320.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.315
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1990.347
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.533
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.10723672
X-RAY DIFFRACTIONr_mcangle_it1.90835887
X-RAY DIFFRACTIONr_scbond_it2.10232237
X-RAY DIFFRACTIONr_scangle_it3.36242141
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.873 Å / Total num. of bins used: 40
RfactorNum. reflection
Rfree0.251 121
Rwork0.167 -
obs-2069
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.202 / Rfactor Rwork: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS

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