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- PDB-4ze8: PBP AccA from A. tumefaciens C58 -

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Basic information

Entry
Database: PDB / ID: 4ze8
TitlePBP AccA from A. tumefaciens C58
ComponentsABC transporter, substrate binding protein (Agrocinopines A and B)ATP-binding cassette transporter
KeywordsTRANSPORT PROTEIN / PBP FROM C CLUSTER
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
DI(HYDROXYETHYL)ETHER / ABC transporter substrate-binding protein / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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: RCSB / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter, substrate binding protein (Agrocinopines A and B)
B: ABC transporter, substrate binding protein (Agrocinopines A and B)
C: ABC transporter, substrate binding protein (Agrocinopines A and B)
D: ABC transporter, substrate binding protein (Agrocinopines A and B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,07621
Polymers228,7124
Non-polymers1,36317
Water34,0841892
1
A: ABC transporter, substrate binding protein (Agrocinopines A and B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7898
Polymers57,1781
Non-polymers6117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter, substrate binding protein (Agrocinopines A and B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4605
Polymers57,1781
Non-polymers2824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ABC transporter, substrate binding protein (Agrocinopines A and B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3984
Polymers57,1781
Non-polymers2203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ABC transporter, substrate binding protein (Agrocinopines A and B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4284
Polymers57,1781
Non-polymers2503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.950, 179.350, 81.600
Angle α, β, γ (deg.)90.00, 93.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 57178.102 Da / Num. of mol.: 4 / Fragment: residues 30-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (strain C58 / ATCC 33970) (bacteria)
Gene: accA, Atu6139 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7D2F4, UniProt: Q52012*PLUS

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Non-polymers , 5 types, 1909 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1892 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25% PEG 8K, 5% GLYCEROL, 0.1M ACETATE NA PH 4.5, 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: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.71→45 Å / Num. obs: 215029 / % possible obs: 96.7 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 18.19 Å2 / Rsym value: 0.094 / Net I/σ(I): 8.9
Reflection shellResolution: 1.71→1.82 Å / Rsym value: 0.543 / % possible all: 82.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTER2.10.0refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OUP

4oup
PDB Unreleased entry


Resolution: 1.72→40.88 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.197 10752 5 %RANDOM
Rwork0.166 ---
obs0.168 215029 97.3 %-
Displacement parametersBiso mean: 24.77 Å2
Baniso -1Baniso -2Baniso -3
1--2.4517 Å20 Å20.5215 Å2
2--1.4029 Å20 Å2
3---1.0488 Å2
Refine analyzeLuzzati coordinate error obs: 0.207 Å
Refinement stepCycle: LAST / Resolution: 1.72→40.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15816 0 81 1892 17789
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0116433HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0322321HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5625SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes408HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2358HARMONIC5
X-RAY DIFFRACTIONt_it16433HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4
X-RAY DIFFRACTIONt_other_torsion16.41
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2070SEMIHARMONIC5
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_contact20539SEMIHARMONIC4
LS refinement shellResolution: 1.72→1.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2653 636 5 %
Rwork0.2303 12086 -
all0.2321 12722 -
obs--97.34 %
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)
10.19990.0189-0.01760.8202-0.26160.81350.00280.00990.01840.0507-0.0615-0.0361-0.04620.08120.0587-0.0025-0.0161-0.0561-0.09850.0081-0.06833.3803-27.252610.1297
20.1387-0.05770.20641.1433-0.22491.32060.01330.021-0.01330.0958-0.0033-0.0480.18720.1089-0.01010.07860.0337-0.0778-0.1296-0.0022-0.1025-2.067312.88919.6465
30.14370.1235-0.23110.8575-0.21010.6747-0.04450.05510.0061-0.15090.04220.09490.0719-0.10340.00230.0712-0.0218-0.0945-0.1036-0.0004-0.070734.660413.248251.3957
40.2453-0.04330.02940.73760.23921.34360.0621-0.0121-0.00960.0844-0.0224-0.02360.0293-0.0426-0.03970.0544-0.0203-0.0721-0.11230.0243-0.1012-3.9259-36.197330.6141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1A 31 A 521
2X-RAY DIFFRACTION2B 31 B 521
3X-RAY DIFFRACTION3C 31 C 521
4X-RAY DIFFRACTION4D 31 D 521

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