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- PDB-5jj5: Crystal structure of iron uptake ABC transporter substrate-bindin... -

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Basic information

Entry
Database: PDB / ID: 5jj5
TitleCrystal structure of iron uptake ABC transporter substrate-binding protein PiaA from Streptococcus pneumoniae Canada MDR_19A bound to hydroxymate siderophore ferrioxamine E and iron(III)
ComponentsABC transporter substrate-binding protein-iron transport
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 / HYDROXYMATE SIDEROPHORE / FERRIOXAMINE E / PUTATIVE MEMBRANE-ANCHORED LIPOPROTEIN
Function / homology
Function and homology information


ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6L0 / : / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsStogios, P.J. / Wawrzak, Z. / Kurdritska, M. / 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 hydroxymate siderophore ferrioxamine E and iron(III)
Authors: Stogios, P.J.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Source and taxonomy
Revision 1.2Sep 27, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter substrate-binding protein-iron transport
B: ABC transporter substrate-binding protein-iron transport
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,36611
Polymers67,6532
Non-polymers1,7139
Water9,782543
1
A: ABC transporter substrate-binding protein-iron transport
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7016
Polymers33,8261
Non-polymers8745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC transporter substrate-binding protein-iron transport
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6655
Polymers33,8261
Non-polymers8394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.809, 73.844, 87.161
Angle α, β, γ (deg.)90.00, 115.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ABC transporter substrate-binding protein-iron transport / Iron ABC transporter substrate-binding protein / Iron compound ABC uptake transporter substrate- ...Iron ABC transporter substrate-binding protein / Iron compound ABC uptake transporter substrate-binding protein PiaA


Mass: 33826.449 Da / Num. of mol.: 2 / Fragment: residues 35-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: yhfQ, yhfQ_1, yhfQ_2, yhfQ_3 / Plasmid: p15Tv lic 298255319 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A062WLD9

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Non-polymers , 5 types, 552 molecules

#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-6L0 / (8E)-6,17,28-trihydroxy-1,6,12,17,23,28-hexaazacyclotritriacont-8-ene-2,5,13,16,24,27-hexone


Mass: 598.689 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46N6O9
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 543 / 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: 3.33 Å3/Da / Density % sol: 63.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Jeffamine ED-2001 pH 7.0 30%, HEPES 0.1M pH 7.0

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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: Dec 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 39761 / % possible obs: 100 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 17.17
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H59

4h59


Resolution: 2.3→29.24 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.01
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 2468 4.98 %RANDOM
Rwork0.1455 ---
obs0.148 36164 63.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4738 0 111 543 5392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054983
X-RAY DIFFRACTIONf_angle_d0.6166625
X-RAY DIFFRACTIONf_dihedral_angle_d11.3571841
X-RAY DIFFRACTIONf_chiral_restr0.025753
X-RAY DIFFRACTIONf_plane_restr0.003849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2967-2.34090.2549440.1861890X-RAY DIFFRACTION22
2.3409-2.38860.2164680.17761283X-RAY DIFFRACTION31
2.3886-2.44060.2398810.20241531X-RAY DIFFRACTION37
2.4406-2.49730.274870.19711704X-RAY DIFFRACTION41
2.4973-2.55970.2161960.20671778X-RAY DIFFRACTION44
2.5597-2.62890.24191000.21081900X-RAY DIFFRACTION46
2.6289-2.70620.25821070.20852035X-RAY DIFFRACTION50
2.7062-2.79350.25161100.20922091X-RAY DIFFRACTION51
2.7935-2.89320.22961180.19472154X-RAY DIFFRACTION52
2.8932-3.0090.24081220.18712361X-RAY DIFFRACTION57
3.009-3.14580.26651300.17242748X-RAY DIFFRACTION67
3.1458-3.31140.20211720.15363238X-RAY DIFFRACTION79
3.3114-3.51850.17651920.1433591X-RAY DIFFRACTION87
3.5185-3.78970.18922090.12613746X-RAY DIFFRACTION92
3.7897-4.17010.17722010.10583910X-RAY DIFFRACTION95
4.1701-4.77120.15142070.10093967X-RAY DIFFRACTION96
4.7712-6.00270.15662180.12924056X-RAY DIFFRACTION99
6.0027-29.24190.20462060.14964088X-RAY DIFFRACTION99
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)
17.01876.27147.29137.93775.75519.3327-0.1044-0.5970.68450.5269-0.30080.1343-0.6492-0.41290.33350.57750.0824-0.04550.3049-0.01270.2087-5.96853.7793.269
22.6265-0.55530.39761.51230.00224.2108-0.0613-0.1943-0.04410.41310.0896-0.17170.15870.2304-0.01860.3307-0.0062-0.06690.1359-0.01590.1273-0.0436-7.3175-10.208
31.8520.3781-0.34113.0462-0.16317.08170.0828-0.02330.24990.45630.044-0.1258-0.70530.1684-0.10590.23970.01050.00880.0867-0.01750.2513-3.288910.9078-19.8526
43.4853-0.30021.29393.40450.62573.45820.19480.2207-0.16-0.1161-0.22590.25880.1012-0.27370.00950.13030.0197-0.00150.18210.01540.1507-12.4652-2.3228-33.9792
57.18131.06062.8846.8982-0.38867.8619-0.0407-0.25-0.5760.0897-0.04130.44850.5983-0.4109-0.02480.1899-0.01210.06830.0878-0.01630.2222-2.8187-49.0339-22.9601
62.1671-0.07480.17682.857-0.54442.65460.0767-0.18780.03010.3565-0.07050.0822-0.0738-0.05130.00680.1392-0.03570.02580.1214-0.03260.092-3.0796-31.9331-23.822
74.29372.906-3.2755.6938-3.42897.9868-0.24210.5103-0.2205-0.51870.0588-0.09330.1663-0.11910.0850.16180.0717-0.01010.1934-0.07930.16373.7086-36.3925-43.3122
85.19021.3524-0.48362.81770.16382.24990.1601-0.13770.0379-0.0718-0.1328-0.3725-0.13020.2531-0.00930.1459-0.00790.03710.18030.01780.150618.549-22.5513-37.0078
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 34:56
2X-RAY DIFFRACTION2chain A and resi 57:159
3X-RAY DIFFRACTION3chain A and resi 160:205
4X-RAY DIFFRACTION4chain A and resi 206:341
5X-RAY DIFFRACTION5chain B and resi 38:56
6X-RAY DIFFRACTION6chain B and resi 57:159
7X-RAY DIFFRACTION7chain B and resi 160:205
8X-RAY DIFFRACTION8chain B and resi 206:341

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