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- PDB-4kyd: Partial Structure of the C-terminal domain of the HPIV4B phosphop... -

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Basic information

Entry
Database: PDB / ID: 4kyd
TitlePartial Structure of the C-terminal domain of the HPIV4B phosphoprotein, fused to MBP.
ComponentsMaltose-binding periplasmic protein, Phosphoprotein, chimeric construct
Keywordsbinding protein / viral protein / 3 helix bundle / viral nucleocapsid
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
P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / 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 / Phosphoprotein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Human parainfluenza virus 4b
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsYegambaram, K. / Bulloch, E.M.M. / Kingston, R.L.
CitationJournal: Protein Sci. / Year: 2013
Title: Protein domain definition should allow for conditional disorder.
Authors: Yegambaram, K. / Bulloch, E.M. / Kingston, R.L.
History
DepositionMay 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
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 / pdbx_struct_assembly_gen / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id / _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: Maltose-binding periplasmic protein, Phosphoprotein, chimeric construct
B: Maltose-binding periplasmic protein, Phosphoprotein, chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,84810
Polymers91,9082
Non-polymers1,9408
Water3,513195
1
A: Maltose-binding periplasmic protein, Phosphoprotein, chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1336
Polymers45,9541
Non-polymers1,1795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maltose-binding periplasmic protein, Phosphoprotein, chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7154
Polymers45,9541
Non-polymers7613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-0 kcal/mol
Surface area33500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.830, 142.830, 114.312
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1613-

HOH

21A-1675-

HOH

31A-1745-

HOH

DetailsAUTHOR REMARK. IN SOLUTION THE C-TERMINAL DOMAIN OF THE HPIV4B PHOSPHOPROTEIN FORMS A MONOMERIC 3-HELIX BUNDLE. IN THE CRYSTAL, DISPLACEMENT OF THE FINAL HELIX AND PARTIAL REPACKING OF THE HYDROPHOBIC CORE LEAD TO FORMATION OF A HOMO-DIMERIC 4-HELIX BUNDLE. WE HAVE FOUND NO EVIDENCE THAT THIS HOMO-DIMER PERSISTS IN SOLUTION. SEE PRIMARY CITATION

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Components

#1: Protein Maltose-binding periplasmic protein, Phosphoprotein, chimeric construct / MBP / MMBP / Maltodextrin-binding protein / Protein P


Mass: 45953.973 Da / Num. of mol.: 2
Fragment: unp P0AEX9 residues 27-392, unp P21738 residues 351-399
Mutation: D82A,K83A, E359A, K362A, D363A, C368S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Human parainfluenza virus 4b
Strain: K12, 68-333 Strain / Gene: b4034, JW3994, malE, P, P/V / Plasmid: pMAL(A) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AEX9, UniProt: P21738
#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: Chemical
ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 24 %(w/v) PEG 2000 0.2 M MOPS/KOH, pH 7.30, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 23, 2001 / Details: Osmic mirror optics
RadiationMonochromator: Rigaku Varimax HF confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.21→38.1 Å / Num. all: 43158 / Num. obs: 43158 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Net I/σ(I): 4.3
Reflection shellResolution: 2.21→2.25 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.7 / % possible all: 82.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB accession code 1HSJ

1hsj


Resolution: 2.21→38.1 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.274 / SU ML: 0.137
Isotropic thermal model: 1 TLS group per protein molecule + Residual Isotropic B-Factors
Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22167 2138 5 %RANDOM
Rwork0.17398 ---
obs0.17631 41013 99.41 %-
all-43158 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.365 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.28 Å20 Å2
2---0.28 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 2.21→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6173 0 124 195 6492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.026465
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9848783
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3635809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24225.897273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.324151071
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.421514
X-RAY DIFFRACTIONr_chiral_restr0.0910.2978
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214814
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.222.3843212
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8873.5694014
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2332.7163253
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.213→2.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 168 -
Rwork0.252 2835 -
obs--93.49 %
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)
11.8227-0.6263-0.27361.55660.27791.108-0.0755-0.08910.0460.1450.0513-0.33720.13550.16860.02420.02490.0213-0.02070.0270.00250.208-43.13238.505-17.22
22.45541.30350.44673.89840.71690.9353-0.00610.08830.2485-0.4254-0.11090.6285-0.1783-0.20390.1170.25250.083-0.06270.3819-0.11460.3535-62.5384.868-56.711
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 370
2X-RAY DIFFRACTION1A1351 - 1381
3X-RAY DIFFRACTION2B1 - 370
4X-RAY DIFFRACTION2B1351 - 1380

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