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- PDB-4ony: Crystal structure of a ABC transporter, periplasmic substrate-bin... -

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Basic information

Entry
Database: PDB / ID: 4ony
TitleCrystal structure of a ABC transporter, periplasmic substrate-binding protein from Brucella melitensis
ComponentsExtracellular solute-binding protein family 5
KeywordsTRANSPORT PROTEIN / SSGCID / ABC transporter / periplasmic substrate-binding protein / extracellular solute-binding protein family 5 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space
Similarity search - Function
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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Extracellular solute-binding protein family 5
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a ABC transporter, periplasmic substrate-binding protein from Brucella melitensis
Authors: Abendroth, J. / Clifton, M.C. / Lorimer, D. / Edwards, T.
History
DepositionJan 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extracellular solute-binding protein family 5
B: Extracellular solute-binding protein family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,5697
Polymers135,0822
Non-polymers4875
Water21,8161211
1
A: Extracellular solute-binding protein family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8314
Polymers67,5411
Non-polymers2903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Extracellular solute-binding protein family 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7393
Polymers67,5411
Non-polymers1982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.560, 124.320, 172.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 12 - 594 / Label seq-ID: 12 - 594

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Extracellular solute-binding protein family 5


Mass: 67540.953 Da / Num. of mol.: 2 / Fragment: UNP residues 29-615
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: ATCC 23457 / Gene: BMEA_B0549 / Plasmid: BrmeB.17356.a.B2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C0RL96
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Diethylene glycol diethyl ether


Mass: 162.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1211 / 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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: RigakuReagents JCSG+ screen, H3: 25% PEG 3350, 100mM BisTris, pH 5.5; cryo 20% EG; BrmeB.17356.a.B2.PS01888 at 17.1mg/ml, tray 248209h3, puck xtp3-5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 17, 2013
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 81772 / Num. obs: 81188 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 15.02
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.150.4343.15199.8
2.15-2.210.3714.01199.7
2.21-2.280.3484.58199.9
2.28-2.350.2965.42199.8
2.35-2.420.2496.37199.7
2.42-2.510.2157.3199.7
2.51-2.60.1948.22199.5
2.6-2.710.1669.46199.6
2.71-2.830.13611.53199.6
2.83-2.970.11213.83199.5
2.97-3.130.09216.6199.4
3.13-3.320.07220.49199.4
3.32-3.550.05725.19199.4
3.55-3.830.04629.96198.8
3.83-4.20.03835.22199.2
4.2-4.70.03636.7198.5
4.7-5.420.03636.33198.4
5.42-6.640.03933.5198
6.64-9.390.03238.15197.1
9.39-500.02346.46191.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.5phasing
REFMAC5.8.0071refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3pam modified with CCP4 program chainsaw

3pam


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.496 / SU ML: 0.107 / SU R Cruickshank DPI: 0.1841 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19603 4054 5 %RANDOM
Rwork0.15509 ---
obs0.15717 77067 99.3 %-
all-81772 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.124 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2---0.67 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9237 0 30 1211 10478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199641
X-RAY DIFFRACTIONr_bond_other_d0.0050.028850
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9513142
X-RAY DIFFRACTIONr_angle_other_deg1.061320329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39651194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94123.214476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.163151470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3791581
X-RAY DIFFRACTIONr_chiral_restr0.0890.21378
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02111118
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022365
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_it0.9781.384707
X-RAY DIFFRACTIONr_mcbond_other0.9741.3794706
X-RAY DIFFRACTIONr_mcangle_it1.532.0645891
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5761.5574934
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 34357 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 292 -
Rwork0.204 5658 -
obs--99.77 %
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)
10.3521-0.053-0.04070.4946-0.03590.5545-0.01490.00210.0045-0.01570.0326-0.0199-0.16310.012-0.01770.1145-0.0054-0.00520.0144-0.01420.018955.945121.76319.795
20.3458-0.01890.10610.67260.28230.56090.00440.00240.0013-0.00760.0038-0.04230.0171-0.0051-0.00820.03770.00920.01130.02310.00520.037640.91791.33316.668
30.755-0.18490.11161.2046-0.1950.5070.0558-0.0056-0.02690.12-0.0147-0.10750.13440.061-0.04110.15760.069-0.0270.0382-0.00480.041457.55195.39255.603
40.1991-0.05660.0020.44180.1350.05360.03590.01830.01130.0098-0.0304-0.02250.0160.0002-0.00550.04190.01670.00680.01140.00420.002547.4946128.44861.3967
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 304
2X-RAY DIFFRACTION1A565 - 594
3X-RAY DIFFRACTION2A305 - 564
4X-RAY DIFFRACTION3B12 - 304
5X-RAY DIFFRACTION3B565 - 594
6X-RAY DIFFRACTION4B305 - 564

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