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- PDB-4zec: PBP AccA from A. tumefaciens C58 in complex with agrocin 84 -

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Basic information

Entry
Database: PDB / ID: 4zec
TitlePBP AccA from A. tumefaciens C58 in complex with agrocin 84
ComponentsABC transporter, substrate binding protein (Agrocinopines A and B)
KeywordsTRANSPORT PROTEIN / PBP / CLASS C
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / 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
Chem-C84 / DI(HYDROXYETHYL)ETHER / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsEl Sahili, A. / 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: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.pdbx_Rsym_value
Revision 2.0Feb 10, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_PDB_caveat / diffrn / diffrn_radiation_wavelength / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_torsion / refine / refine_analyze / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct / struct_asym / struct_conf / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._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_label_seq_id / _diffrn.pdbx_serial_crystal_experiment / _entity.formula_weight / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_database_status.deposit_site / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_R_Cruickshank_DPI / _refine.pdbx_overall_SU_R_Blow_DPI / _refine.pdbx_overall_SU_R_free_Blow_DPI / _refine.pdbx_overall_SU_R_free_Cruickshank_DPI / _refine_analyze.Luzzati_coordinate_error_obs / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.pdbx_restraint_function / _refine_ls_restr.weight / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.R_factor_all / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _refine_ls_shell.percent_reflns_R_free / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_high / _reflns.pdbx_Rsym_value / _reflns_shell.d_res_high / _reflns_shell.number_unique_obs / _software.classification / _software.name / _software.version / _struct.pdbx_CASP_flag / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Description: Ligand geometry
Details: I have corrected the glucose geometry within the agrocin 84.
Provider: author / Type: Coordinate replacement
Revision 2.1Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_validate_chiral
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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 (Agrocinopines A and B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0347
Polymers55,9611
Non-polymers1,0736
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint14 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.180, 114.170, 111.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-875-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ABC transporter, substrate binding protein (Agrocinopines A and B) / AccA


Mass: 55960.781 Da / Num. of mol.: 1 / Fragment: UNP residues 30-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Strain: C58 / ATCC 33970 / Gene: accA, Atu6139 / Production host: Escherichia coli (E. coli) / References: UniProt: Q52012

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Non-polymers , 5 types, 231 molecules

#2: Chemical ChemComp-C84 / [(2R,3R,4S,5S,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]oxy-N-[9-[(2R,3S,5R)-5-[[[(2R,3S)-4-methyl-2,3-bis(oxidanyl)pentanoyl]amino]-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]purin-6-yl]phosphonamidic acid / Agrocin 84 (beta-D-glucopyranose form)


Mass: 688.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34N6O16P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.82 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2013
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.147→45 Å / Num. obs: 26755 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 36.95 Å2 / Rsym value: 0.2 / Net I/σ(I): 8.24
Reflection shellResolution: 2.147→2.28 Å / Num. unique obs: 4191 / Rsym value: 1.04 / % possible all: 96.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OUP

4oup
PDB Unreleased entry


Resolution: 2.15→42.06 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 0.273 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.285 / SU Rfree Blow DPI: 0.206 / SU Rfree Cruickshank DPI: 0.205
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 1337 5 %RANDOM
Rwork0.1918 ---
obs0.1941 26728 97.9 %-
Displacement parametersBiso mean: 35.1 Å2
Baniso -1Baniso -2Baniso -3
1-10.4262 Å20 Å20 Å2
2---6.5188 Å20 Å2
3----3.9074 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.15→42.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3945 0 70 225 4240
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084122HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.055595HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1405SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes683HARMONIC5
X-RAY DIFFRACTIONt_it4122HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.82
X-RAY DIFFRACTIONt_other_torsion12.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion522SEMIHARMONIC5
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_contact3592SEMIHARMONIC4
LS refinement shellResolution: 2.15→2.17 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2508 -5.05 %
Rwork0.3202 508 -
all0.3168 535 -
obs--83.26 %
Refinement TLS params.Method: refined / Origin x: -16.7464 Å / Origin y: -26.2935 Å / Origin z: 14.3506 Å
111213212223313233
T-0.2085 Å20.0187 Å2-0.0133 Å2--0.1238 Å2-0.0275 Å2---0.1433 Å2
L1.1889 °20.2414 °2-0.3112 °2-0.9385 °2-0.18 °2--0.5864 °2
S0.0336 Å °0.0346 Å °0.0232 Å °0.065 Å °0.0239 Å °-0.0089 Å °-0.0351 Å °0.0657 Å °-0.0575 Å °
Refinement TLS groupSelection details: { A|* }

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