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- PDB-4h59: Crystal structure of iron uptake ABC transporter substrate-bindin... -

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Basic information

Entry
Database: PDB / ID: 4h59
TitleCrystal structure of iron uptake ABC transporter substrate-binding protein PiaA from Streptococcus pneumoniae Canada MDR_19A bound to Bis-tris propane
ComponentsIron-compound ABC transporter, iron compound-binding protein
KeywordsTRANSPORT PROTEIN / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / NIAID / National Institute of Allergy and Infectious Diseases / ALPHA AND BETA PROTEIN / PERIPLASMIC BINDING PROTEIN TYPE III FOLD / iron transport / iron uptake ABC transport system substrate binding protein / HYDROXYMATE SIDEROPHORE / putative membrane-anchored lipoprotein
Function / homology
Function and homology information


iron coordination entity transport / outer membrane-bounded periplasmic space
Similarity search - Function
: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ABC transporter substrate-binding protein-iron transport / Iron-compound ABC transporter, iron compound-binding protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.658 Å
AuthorsStogios, P.J. / Wawrzak, Z. / Kudritska, M. / Minasov, G. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of iron uptake ABC transporter substrate-binding protein PiaA from Streptococcus pneumoniae Canada MDR_19A bound to Bis-tris propane
Authors: Stogios, P.J. / Wawrzak, Z. / Kudritska, M. / Minasov, G. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Structure summary
Revision 1.2Nov 27, 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

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Assembly

Deposited unit
A: Iron-compound ABC transporter, iron compound-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4125
Polymers33,9671
Non-polymers4454
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.041, 68.045, 99.272
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Iron-compound ABC transporter, iron compound-binding protein / piaA


Mass: 33967.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: Canada MDR_19A / Gene: SpneCM_010100006939 / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97R09, UniProt: Q8DPY6*PLUS
#2: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O
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: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2 M ammonium citrate pH 7.0, 0.1 M Bis-tris propane pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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: Jun 30, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.66→30 Å / Num. obs: 46004 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 4.6 % / Rsym value: 0.075 / Net I/σ(I): 34.24
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.03 / Num. unique all: 2252 / Rsym value: 0.605 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.658→29.22 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1912 1874 4.36 %random
Rwork0.1655 ---
obs0.1666 45955 97.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.658→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 27 405 2800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072540
X-RAY DIFFRACTIONf_angle_d1.0763459
X-RAY DIFFRACTIONf_dihedral_angle_d13.791018
X-RAY DIFFRACTIONf_chiral_restr0.072388
X-RAY DIFFRACTIONf_plane_restr0.005443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6579-1.67880.3049650.27542838X-RAY DIFFRACTION90
1.6788-1.70090.2624700.26493055X-RAY DIFFRACTION98
1.7009-1.72420.2967730.25183112X-RAY DIFFRACTION99
1.7242-1.74890.2073710.22883062X-RAY DIFFRACTION99
1.7489-1.7750.254710.21813117X-RAY DIFFRACTION99
1.775-1.80270.2312700.21633089X-RAY DIFFRACTION99
1.8027-1.83220.2862700.21743085X-RAY DIFFRACTION99
1.8322-1.86380.264700.20673076X-RAY DIFFRACTION99
1.8638-1.89770.2599690.20433151X-RAY DIFFRACTION99
1.8977-1.93420.2388740.19723096X-RAY DIFFRACTION99
1.9342-1.97370.1994720.18873127X-RAY DIFFRACTION99
1.9737-2.01660.2157700.19193099X-RAY DIFFRACTION98
2.0166-2.06350.2232700.17833069X-RAY DIFFRACTION99
2.0635-2.11510.2143720.16913123X-RAY DIFFRACTION98
2.1151-2.17220.2224700.17173031X-RAY DIFFRACTION98
2.1722-2.23610.194700.16823055X-RAY DIFFRACTION98
2.2361-2.30830.2066690.17033100X-RAY DIFFRACTION98
2.3083-2.39080.2093680.17053048X-RAY DIFFRACTION98
2.3908-2.48640.1825700.17393068X-RAY DIFFRACTION98
2.4864-2.59950.2138680.17883055X-RAY DIFFRACTION97
2.5995-2.73650.2036680.17473026X-RAY DIFFRACTION97
2.7365-2.90780.1975690.16753013X-RAY DIFFRACTION96
2.9078-3.13210.1926700.16013009X-RAY DIFFRACTION96
3.1321-3.44680.1546700.14313000X-RAY DIFFRACTION96
3.4468-3.94450.1585670.13452961X-RAY DIFFRACTION95
3.9445-4.96570.1561680.12712935X-RAY DIFFRACTION93
4.9657-29.22420.1712620.16842824X-RAY DIFFRACTION90
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)
14.6803-1.36690.12158.7887-3.92154.6897-0.4960.33910.8979-0.14280.27490.3059-0.7634-0.26550.18910.47140.0162-0.08850.21650.03790.293554.963843.998316.1018
23.15590.7002-0.60233.1393-1.13313.92780.00440.1025-0.127-0.4041-0.0050.20310.2519-0.27360.01340.22730.02-0.06450.12730.01050.19250.749527.767923.055
32.3917-0.6738-1.06672.17740.05087.574-0.1012-0.24710.21690.18010.09810.3041-0.7426-0.456-0.05560.27090.06850.01290.1835-0.03470.29949.111640.486338.9827
43.3672-1.89281.30912.9427-1.50563.1712-0.0779-0.2408-0.0370.160.0681-0.1121-0.07680.15090.00130.135-0.01640.00230.17710.0060.1662.135125.270647.4211
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 36:56
2X-RAY DIFFRACTION2chain A and resi 57:159
3X-RAY DIFFRACTION3chain A and resi 160:205
4X-RAY DIFFRACTION4chain A and resi 206:341

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