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- PDB-4pz0: The crystal structure of a solute binding protein from Bacillus a... -

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Basic information

Entry
Database: PDB / ID: 4pz0
TitleThe crystal structure of a solute binding protein from Bacillus anthracis str. Ames in complex with quorum-sensing signal autoinducer-2 (AI-2)
Componentssugar ABC transporter, sugar-binding protein
KeywordsSUGAR BINDING PROTEIN / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology
Function and homology information


carbohydrate-importing ABC transporter activity / carbohydrate transport / ATP-binding cassette (ABC) transporter complex
Similarity search - Function
Autoinducer 2 ABC transporter, substrate-binding protein LsrB / Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PAV / Autoinducer 2 ABC transporter substrate-binding protein LsrB / Autoinducer 2-binding protein LsrB
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 Å
AuthorsTan, K. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of a solute binding protein from Bacillus anthracis str. Ames in complex with quorum-sensing signal autoinducer-2 (AI-2).
Authors: Tan, K. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionMar 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: sugar ABC transporter, sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,64110
Polymers36,0211
Non-polymers6209
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.005, 58.067, 63.194
Angle α, β, γ (deg.)90.00, 95.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein sugar ABC transporter, sugar-binding protein / solute binding protein


Mass: 36020.637 Da / Num. of mol.: 1 / Fragment: UNP residues 27-347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BA_2975, BAS2763, GBAA_2975 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q81P43, UniProt: A0A6H3AKG3*PLUS
#2: Sugar ChemComp-PAV / (2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O5
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 1.98 Å3/Da / Density % sol: 37.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris-HCl, 28% w/v PEG2000 MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 10, 2012 / Details: mirror
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.25→23.5 Å / Num. all: 74237 / Num. obs: 74237 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 5 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 33.3
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3477 / % possible all: 90.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.25→23.25 Å / SU ML: 0.09 / σ(F): 1.35 / Phase error: 14.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1488 3732 5.03 %RANDOM
Rwork0.1281 ---
obs0.1291 74180 95.61 %-
all-74180 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→23.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 0 39 318 2816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062617
X-RAY DIFFRACTIONf_angle_d1.1033556
X-RAY DIFFRACTIONf_dihedral_angle_d12.407982
X-RAY DIFFRACTIONf_chiral_restr0.073401
X-RAY DIFFRACTIONf_plane_restr0.005459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.26580.23081000.20522233X-RAY DIFFRACTION82
1.2658-1.28250.2361210.17522481X-RAY DIFFRACTION92
1.2825-1.30.2031380.1692578X-RAY DIFFRACTION93
1.3-1.31860.20061370.15542524X-RAY DIFFRACTION93
1.3186-1.33830.16821400.15312518X-RAY DIFFRACTION94
1.3383-1.35920.16431250.14342569X-RAY DIFFRACTION95
1.3592-1.38150.1691490.13782587X-RAY DIFFRACTION95
1.3815-1.40530.17381200.13032600X-RAY DIFFRACTION95
1.4053-1.43080.15511290.12432596X-RAY DIFFRACTION95
1.4308-1.45840.1921440.12082575X-RAY DIFFRACTION95
1.4584-1.48810.16161320.10922599X-RAY DIFFRACTION96
1.4881-1.52050.14351380.10862597X-RAY DIFFRACTION96
1.5205-1.55580.15451390.10412628X-RAY DIFFRACTION96
1.5558-1.59470.12781430.09952599X-RAY DIFFRACTION96
1.5947-1.63780.12251540.09882601X-RAY DIFFRACTION96
1.6378-1.6860.12751480.09832633X-RAY DIFFRACTION97
1.686-1.74040.14611500.10392612X-RAY DIFFRACTION97
1.7404-1.80260.13831230.10952679X-RAY DIFFRACTION97
1.8026-1.87480.12641300.10852649X-RAY DIFFRACTION97
1.8748-1.960.1461490.11652661X-RAY DIFFRACTION98
1.96-2.06330.15141620.11742647X-RAY DIFFRACTION98
2.0633-2.19250.14961320.12212687X-RAY DIFFRACTION98
2.1925-2.36160.15271490.12342668X-RAY DIFFRACTION98
2.3616-2.5990.14841490.14142707X-RAY DIFFRACTION98
2.599-2.97440.15891440.14132704X-RAY DIFFRACTION99
2.9744-3.74490.14581410.13642734X-RAY DIFFRACTION99
3.7449-23.25430.12891460.13922782X-RAY DIFFRACTION99

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