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- PDB-4eqb: 1.5 Angstrom Crystal Structure of Spermidine/Putrescine ABC Trans... -

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Basic information

Entry
Database: PDB / ID: 4eqb
Title1.5 Angstrom Crystal Structure of Spermidine/Putrescine ABC Transporter Substrate-Binding Protein PotD from Streptococcus pneumoniae strain Canada MDR_19A in Complex with Calcium and HEPES
ComponentsSpermidine/putrescine ABC superfamily ATP binding cassette transporter, binding protein
KeywordsTRANSPORT PROTEIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / spermidine/putrescine ABC transporter / periplasmic protein
Function / homology
Function and homology information


polyamine binding / polyamine transport / periplasmic space / metal ion binding
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 / ABC transporter, solute-binding protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae TCH8431 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMinasov, G. / Wawrzak, Z. / Stogios, P.J. / Kudritska, M. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.5 Angstrom Crystal Structure of Spermidine/Putrescine ABC Transporter Substrate-Binding Protein from Streptococcus pneumoniae strain Canada MDR_19A in Complex with Calcium and HEPES.
Authors: Minasov, G. / Wawrzak, Z. / Stogios, P.J. / Kudritska, M. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Other
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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: Spermidine/putrescine ABC superfamily ATP binding cassette transporter, binding protein
B: Spermidine/putrescine ABC superfamily ATP binding cassette transporter, binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,27215
Polymers76,2982
Non-polymers97413
Water17,457969
1
A: Spermidine/putrescine ABC superfamily ATP binding cassette transporter, binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6898
Polymers38,1491
Non-polymers5407
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Spermidine/putrescine ABC superfamily ATP binding cassette transporter, binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5837
Polymers38,1491
Non-polymers4346
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.635, 54.347, 76.704
Angle α, β, γ (deg.)75.83, 80.87, 77.56
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Spermidine/putrescine ABC superfamily ATP binding cassette transporter, binding protein


Mass: 38148.777 Da / Num. of mol.: 2
Fragment: spermidine/putrescine ABC transporter (unp residues 30-356)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae TCH8431 (bacteria)
Strain: Canada MDR_19A / Gene: HMPREF0837_11161 / Plasmid: pMSCG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: D6ZS00

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Non-polymers , 5 types, 982 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 969 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein: 0.3M Sodium chloride, 0.01M HEPES; Screen: 0.2M Lithium citrate, 2% Tascimate, 20% (w/v) PEG 3350; Cryo: paratone, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 12, 2012 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 107591 / Num. obs: 107591 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 33.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5284 / % possible all: 95.6

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
BALBESphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1POT

1pot


Resolution: 1.5→29.1 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.397 / SU ML: 0.043
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18554 5324 5 %RANDOM
Rwork0.15498 ---
all0.15651 102120 --
obs0.15651 102120 96.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.102 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0.37 Å20.19 Å2
2--0.23 Å20.43 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5272 0 47 969 6288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225899
X-RAY DIFFRACTIONr_bond_other_d0.0010.023935
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9728058
X-RAY DIFFRACTIONr_angle_other_deg0.91539726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9165733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04326.382293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.585151044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.416156
X-RAY DIFFRACTIONr_chiral_restr0.0960.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216711
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021127
X-RAY DIFFRACTIONr_mcbond_it1.1521.53517
X-RAY DIFFRACTIONr_mcbond_other0.3891.51392
X-RAY DIFFRACTIONr_mcangle_it1.925765
X-RAY DIFFRACTIONr_scbond_it3.05232382
X-RAY DIFFRACTIONr_scangle_it4.6564.52293
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 387 -
Rwork0.211 7367 -
obs-7367 94.58 %
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)
11.70450.1718-0.54940.8506-0.03711.2113-0.0566-0.1172-0.21980.0077-0.0272-0.05420.07090.06140.08370.01030.00240.00090.01050.01840.0385.50351.21286.7606
20.98720.4172-0.36840.9386-0.12631.0644-0.06060.1036-0.207-0.11310.0138-0.07260.2095-0.04750.04690.0833-0.020.01910.0216-0.03580.0781-0.2538-2.4495-7.4714
31.15120.1465-0.20321.3289-0.19651.669-0.01250.1210.1338-0.0008-0.0385-0.0951-0.03690.08510.0510.0212-0.0083-0.00320.02760.01010.05497.762822.9866-17.0289
41.197-0.2972-0.31930.5966-0.11050.99050.0030.0431-0.0174-0.01910.0001-0.02910.0009-0.0975-0.00310.023-0.01340.00350.0208-0.00930.0305-5.87987.7802-0.3938
52.47291.0265-0.92931.5121-0.97591.5358-0.23340.2018-0.3843-0.2486-0.0252-0.25670.30240.1120.25860.07830.01550.05580.0522-0.01530.074911.87111.3692-24.2463
62.03050.03390.02251.1291-0.15371.1384-0.0215-0.14820.13080.00670.0309-0.0506-0.10720.018-0.00930.02510.00660.00650.0314-0.0150.016828.143314.669711.051
71.93550.15740.06541.3224-0.14031.38580.0194-0.42940.10760.22210.0224-0.0347-0.273-0.0749-0.04170.1070.03130.00410.1365-0.03970.020122.712317.893425.343
81.6937-0.23130.76462.0447-0.42652.19240.06360.0562-0.1785-0.15350.1022-0.06080.1581-0.042-0.16570.0232-0.0238-0.01220.06540.01370.036131.0338-8.410234.4613
91.40070.46570.16940.9744-0.16741.04810.0423-0.2499-0.09570.06430.0179-0.0363-0.0593-0.1188-0.06030.01610.01550.0030.08230.02190.017917.08527.64918.2499
104.8283-2.18821.71092.0196-1.49421.996-0.21-0.25210.56210.19170.0109-0.4363-0.2967-0.09120.19910.06970.0054-0.03010.08570.01610.123535.1763.146241.5033
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 75
2X-RAY DIFFRACTION2A76 - 138
3X-RAY DIFFRACTION3A139 - 261
4X-RAY DIFFRACTION4A262 - 325
5X-RAY DIFFRACTION5A326 - 356
6X-RAY DIFFRACTION6B34 - 75
7X-RAY DIFFRACTION7B76 - 138
8X-RAY DIFFRACTION8B139 - 261
9X-RAY DIFFRACTION9B262 - 325
10X-RAY DIFFRACTION10B326 - 356

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