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- PDB-4gl0: Putative spermidine/putrescine ABC transporter from Listeria mono... -

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Basic information

Entry
Database: PDB / ID: 4gl0
TitlePutative spermidine/putrescine ABC transporter from Listeria monocytogenes
ComponentsLmo0810 protein
KeywordsTRANSPORT PROTEIN / structural genomics / IDP05673 / spermidine / putrescine / ABC transporter / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


polyamine binding / polyamine transport / periplasmic space / membrane
Similarity search - Function
Spermidine/putrescine-binding periplasmic protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Lmo0810 protein
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å
AuthorsOsipiuk, J. / Zhou, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Putative spermidine/putrescine ABC transporter from Listeria monocytogenes
Authors: Osipiuk, J. / Zhou, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A.
History
DepositionAug 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Lmo0810 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,60711
Polymers38,5901
Non-polymers1,01710
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.330, 56.330, 182.493
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lmo0810 protein


Mass: 38590.035 Da / Num. of mol.: 1 / Fragment: UNP Residues 28-357
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: ATCC BAA-679 / EGD-e / Gene: lmo0810 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Y8T4

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Non-polymers , 5 types, 178 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2 M sodium chloride, 0.2 M phosphate buffer, 50% PEG-200, chymotrypsin, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 19, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.92→47.1 Å / Num. all: 26657 / Num. obs: 26657 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.099 / Χ2: 3.373 / Net I/σ(I): 13.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.92-1.956.40.862.0913330.905100
1.95-1.9970.67412800.968100
1.99-2.037.20.58913090.981100
2.03-2.077.70.50813121.014100
2.07-2.118.10.43612811.109100
2.11-2.168.90.38213451.136100
2.16-2.2290.30112821.171100
2.22-2.289.10.27313071.262100
2.28-2.349.10.23913201.329100
2.34-2.429.10.213101.437100
2.42-2.519.10.18613331.629100
2.51-2.619.10.16213101.764100
2.61-2.7290.13713262.06799.9
2.72-2.8790.11613252.44299.8
2.87-3.058.90.09713443.066100
3.05-3.288.90.08613443.937100
3.28-3.618.80.07413455.093100
3.61-4.148.60.06413776.818100
4.14-5.218.40.06213809.701100
5.21-507.50.082149418.29998.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.92→47.1 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.26 / SU B: 5.751 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.141 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 1343 5 %RANDOM
Rwork0.1545 ---
all0.1564 26602 --
obs0.1564 26602 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.09 Å2 / Biso mean: 34.6928 Å2 / Biso min: 16.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20.44 Å20 Å2
2--0.89 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 1.92→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2585 0 67 168 2820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022832
X-RAY DIFFRACTIONr_bond_other_d0.0010.021948
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.9873834
X-RAY DIFFRACTIONr_angle_other_deg0.98934809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52526.241141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17315509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.691156
X-RAY DIFFRACTIONr_chiral_restr0.1060.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213122
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02532
LS refinement shellResolution: 1.92→1.969 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 100 -
Rwork0.24 1608 -
all-1708 -
obs-1708 98.39 %
Refinement TLS params.Method: refined / Origin x: 34.2155 Å / Origin y: 2.0659 Å / Origin z: 14.313 Å
111213212223313233
T0.0114 Å2-0.0166 Å20.0122 Å2-0.0436 Å2-0.024 Å2--0.0179 Å2
L1.3117 °2-0.2422 °2-0.6426 °2-0.3296 °20.3248 °2--1.8091 °2
S0.0136 Å °-0.0107 Å °0.0222 Å °-0.0522 Å °0.051 Å °-0.051 Å °-0.0874 Å °0.1132 Å °-0.0646 Å °

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