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- PDB-5joq: Crystal Structure of an ABC Transporter Substrate-Binding Protein... -

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Basic information

Entry
Database: PDB / ID: 5joq
TitleCrystal Structure of an ABC Transporter Substrate-Binding Protein from Listeria monocytogenes EGD-e
ComponentsLmo2184 protein
KeywordsHYDROLASE / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / ferrichrome ABC transporter substrate-binding protein
Function / homology
Function and homology information


heme transport / cellular response to iron ion / heme binding / membrane
Similarity search - Function
ABC transporter, high-affinity heme uptake system protein IsdE / FatB domain / 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
CITRIC ACID / High-affinity heme uptake system protein IsdE
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsBrunzelle, J.S. / Wawrzak, Z. / Kudritska, M. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal Structure of an ABC Transporter Substrate-Binding Protein from Listeria monocytogenes EGD-e
Authors: Brunzelle, J.S. / Wawrzak, Z. / Kudritska, M. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Derived calculations / Category: citation_author / pdbx_struct_oper_list
Item: _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lmo2184 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4573
Polymers32,2291
Non-polymers2282
Water6,179343
1
A: Lmo2184 protein
hetero molecules

A: Lmo2184 protein
hetero molecules

A: Lmo2184 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3719
Polymers96,6883
Non-polymers6836
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6050 Å2
ΔGint-67 kcal/mol
Surface area34750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.380, 118.380, 106.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-474-

HOH

21A-674-

HOH

31A-737-

HOH

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Components

#1: Protein Lmo2184 protein


Mass: 32229.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: lmo2184 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q7AP55
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 343 / 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: 3.74 Å3/Da / Density % sol: 67.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2M NH4 Citrate pH 7, 0.1M Bis-Tris Propane pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 17, 2013 / Details: Beryllium Lens
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.99→33.41 Å / Num. obs: 30557 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 21.7
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 4.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(DEV_2203)refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q8Q

2q8q


Resolution: 1.99→33.41 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.73
RfactorNum. reflection% reflectionSelection details
Rfree0.171 1540 5.05 %0
Rwork0.151 ---
obs0.152 30517 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.99→33.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2008 0 14 343 2365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142125
X-RAY DIFFRACTIONf_angle_d1.0022881
X-RAY DIFFRACTIONf_dihedral_angle_d11.8331331
X-RAY DIFFRACTIONf_chiral_restr0.073331
X-RAY DIFFRACTIONf_plane_restr0.006375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.05430.21461380.17762561X-RAY DIFFRACTION100
2.0543-2.12770.17021560.16652568X-RAY DIFFRACTION100
2.1277-2.21290.20861190.15542605X-RAY DIFFRACTION100
2.2129-2.31350.16141450.14622593X-RAY DIFFRACTION100
2.3135-2.43550.21661220.15362606X-RAY DIFFRACTION100
2.4355-2.5880.18711290.16282642X-RAY DIFFRACTION100
2.588-2.78780.21631390.16542620X-RAY DIFFRACTION100
2.7878-3.06810.17591500.16462611X-RAY DIFFRACTION100
3.0681-3.51170.17321430.15382666X-RAY DIFFRACTION100
3.5117-4.42270.13811630.12152676X-RAY DIFFRACTION100
4.4227-33.40970.15141360.14962829X-RAY DIFFRACTION98
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)
12.2441-0.4733-1.47862.74720.05433.4297-0.15340.59450.1941-0.5679-0.04380.2721-0.31840.19570.09260.246-0.0822-0.09020.24480.04880.1443-22.939461.5549-14.3773
21.54380.75820.5961.1797-0.0652.9155-0.35660.39840.4503-0.48620.2668-0.0286-0.78580.38130.13220.4262-0.1576-0.06820.31470.09150.2252-19.251468.3749-14.6054
30.67171.05870.35982.23470.80371.6448-0.0780.01060.2213-0.1645-0.0330.2836-0.302-0.150.15020.1578-0.0044-0.04010.16080.00780.1659-26.974861.7187-4.5435
47.5685-5.56017.12946.6796-5.05287.86480.26970.5479-0.3801-0.3046-0.1257-0.08320.41490.3684-0.14010.1243-0.03930.00680.1906-0.04380.1686-20.699841.9862-8.0208
51.6752-0.17730.2050.8106-0.21711.29670.0581-0.0651-0.01390.0508-0.0042-0.10720.0820.0081-0.03130.1087-0.0072-0.03490.08190.00060.1337-4.899352.136512.5664
63.07730.55551.30473.6154-0.56156.0544-0.07250.3182-0.0453-0.2288-0.0434-0.54650.24490.34490.07210.0926-0.02680.00830.1698-0.01270.1367-7.522648.4549-1.1345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 33 THROUGH 50 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 51 THROUGH 92 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 93 THROUGH 139 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 140 THROUGH 161 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 162 THROUGH 262 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 263 THROUGH 290 )

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