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- PDB-4ze9: Se-PBP AccA from A. tumefaciens C58 in complex with agrocinopine A -

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Basic information

Entry
Database: PDB / ID: 4ze9
TitleSe-PBP AccA from A. tumefaciens C58 in complex with agrocinopine A
ComponentsABC transporter substrate-binding protein
KeywordsTRANSPORT PROTEIN / PBP FROM CLASS C
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 2-O-phosphono-alpha-L-arabinopyranose / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesAgrobacterium fabrum str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsEl Sahili, A. / Guimaraes, B.G. / Morera, S.
CitationJournal: Plos Pathog. / Year: 2015
Title: A Pyranose-2-Phosphate Motif Is Responsible for Both Antibiotic Import and Quorum-Sensing Regulation in Agrobacterium tumefaciens.
Authors: El Sahili, A. / Li, S.Z. / Lang, J. / Virus, C. / Planamente, S. / Ahmar, M. / Guimaraes, B.G. / Aumont-Nicaise, M. / Vigouroux, A. / Soulere, L. / Reader, J. / Queneau, Y. / Faure, D. / Morera, S.
History
DepositionApr 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_src_gen / 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_nonpoly_scheme / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _entity_src_gen.gene_src_strain
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Apr 20, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / pdbx_branch_scheme / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn
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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_branch_descriptor.descriptor / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id
Revision 4.0Jan 25, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / entity_src_gen / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_validate_chiral / software / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_branch_scheme.mon_id / _pdbx_branch_scheme.pdb_mon_id / _pdbx_chem_comp_identifier.comp_id / _pdbx_chem_comp_identifier.identifier / _pdbx_entity_branch_link.comp_id_1 / _pdbx_entity_branch_link.comp_id_2 / _pdbx_entity_branch_list.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.beg_label_asym_id / _pdbx_refine_tls_group.beg_label_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.end_label_asym_id / _pdbx_refine_tls_group.end_label_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly.details / _pdbx_struct_assembly_prop.value / _software.classification / _software.name / _software.version / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 4.1May 24, 2023Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Refinement description / Structure summary
Category: pdbx_entity_instance_feature / pdbx_entry_details ...pdbx_entity_instance_feature / pdbx_entry_details / pdbx_molecule_features / pdbx_refine_tls_group / struct_conn
Item: _pdbx_refine_tls_group.beg_label_asym_id / _pdbx_refine_tls_group.beg_label_seq_id ..._pdbx_refine_tls_group.beg_label_asym_id / _pdbx_refine_tls_group.beg_label_seq_id / _pdbx_refine_tls_group.end_label_asym_id / _pdbx_refine_tls_group.end_label_seq_id / _pdbx_refine_tls_group.selection_details / _struct_conn.pdbx_value_order
Revision 5.0Jun 14, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_molecule_features / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_validate_chiral / struct_conn
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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _database_PDB_caveat.text / _entity.pdbx_description / _pdbx_branch_scheme.mon_id / _pdbx_branch_scheme.pdb_mon_id / _pdbx_entity_branch_descriptor.descriptor / _pdbx_entity_branch_link.entity_branch_list_num_1 / _pdbx_entity_branch_link.entity_branch_list_num_2 / _pdbx_entity_branch_list.comp_id / _pdbx_molecule_features.class / _pdbx_molecule_features.name / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_validate_chiral.auth_seq_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6423
Polymers58,0691
Non-polymers5722
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.690, 114.720, 109.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ABC transporter substrate-binding protein


Mass: 58069.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum str. C58 (bacteria)
Gene: accA / Production host: Escherichia coli (E. coli) / References: UniProt: Q52012
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: phosphodiester of sucrose and L-arabinose / References: BIRD: PRD_002470
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Gulp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-LAO / 2-O-phosphono-alpha-L-arabinopyranose / 2-O-phosphono-alpha-L-arabinose / 2-O-phosphono-L-arabinose / 2-O-phosphono-arabinose


Type: L-saccharide, alpha linking, Oligosaccharide / Class: Nutrient / Mass: 230.110 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P / Details: phosphodiester of sucrose and L-arabinose / Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002470
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Compound detailsA member of the class of agrocinopines that consists of sucrose and L-arabinose units joined via a ...A member of the class of agrocinopines that consists of sucrose and L-arabinose units joined via a phosphodiester linkage between position 4F of sucrose and position 2 of arabinose.

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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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% PEG 4K, 0.2M ACNH4, 0.1M NA CITRATE PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
PH range: 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97895 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2013
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.65→42 Å / Num. obs: 14551 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 10.6 % / Biso Wilson estimate: 56.73 Å2 / Rsym value: 0.119 / Net I/σ(I): 11.78
Reflection shellResolution: 2.65→2.81 Å / Rsym value: 0.642 / % possible all: 98.9

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.65→41.59 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.894 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 725 5 %RANDOM
Rwork0.168 ---
obs0.171 14498 100 %-
Displacement parametersBiso mean: 43.61 Å2
Baniso -1Baniso -2Baniso -3
1-8.0985 Å20 Å20 Å2
2---5.628 Å20 Å2
3----2.4706 Å2
Refine analyzeLuzzati coordinate error obs: 0.294 Å
Refinement stepCycle: LAST / Resolution: 2.65→41.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3939 0 36 49 4024
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084085HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.055553HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1388SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes101HARMONIC2
X-RAY DIFFRACTIONt_gen_planes578HARMONIC5
X-RAY DIFFRACTIONt_it4085HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion18.48
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion512SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4815SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.86 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2857 147 4.99 %
Rwork0.1835 2796 -
all0.1885 2943 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: 16.8237 Å / Origin y: 26.3395 Å / Origin z: 14.1521 Å
111213212223313233
T-0.0875 Å20.0297 Å20.0239 Å2--0.069 Å20.0098 Å2---0.0754 Å2
L1.0679 °20.3953 °20.3079 °2-1.168 °20.2822 °2--0.5996 °2
S0.0123 Å °0.0049 Å °0.0767 Å °0.1047 Å °0.0099 Å °0.1107 Å °0.0218 Å °-0.0334 Å °-0.0222 Å °
Refinement TLS groupSelection details: { A|32 - A|521 }

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