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- PDB-5hm4: Crystal structure of oligopeptide ABC transporter, periplasmic ol... -

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Basic information

Entry
Database: PDB / ID: 5hm4
TitleCrystal structure of oligopeptide ABC transporter, periplasmic oligopeptide-binding protein (TM1226) from THERMOTOGA MARITIMA at 2.0 A resolution
ComponentsMannoside ABC transport system, sugar-binding protein
KeywordsTRANSPORT PROTEIN / ABC transporter
Function / homology
Function and homology information


microcin transport / peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space / periplasmic space / metal ion binding
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Mannoside ABC transport system, sugar-binding protein / Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLu, X. / Ghimire-Rijal, S. / Myles, D.A.A. / Cuneo, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Biochemistry / Year: 2017
Title: Periplasmic Binding Protein Dimer Has a Second Allosteric Event Tied to Ligand Binding.
Authors: Li, L. / Ghimire-Rijal, S. / Lucas, S.L. / Stanley, C.B. / Wright, E. / Agarwal, P.K. / Myles, D.A. / Cuneo, M.J.
History
DepositionJan 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Mannoside ABC transport system, sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8752
Polymers63,8351
Non-polymers401
Water7,296405
1
B: Mannoside ABC transport system, sugar-binding protein
hetero molecules

B: Mannoside ABC transport system, sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,7504
Polymers127,6702
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1380 Å2
ΔGint-10 kcal/mol
Surface area40950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.256, 65.795, 185.658
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Mannoside ABC transport system, sugar-binding protein


Mass: 63835.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: Tmari_1233 / Production host: Escherichia coli (E. coli) / References: UniProt: G4FEC0, UniProt: Q9X0V3*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 293 K / Method: microbatch / Details: 0.2-0.3M Mg or Ca Acetate, 20-30% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 42275 / % possible obs: 97.1 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 3.4 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VR5

1vr5


Resolution: 2→40.435 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 2131 5.05 %Random selection
Rwork0.1734 ---
obs0.1752 42163 97.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→40.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4404 0 1 405 4810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034652
X-RAY DIFFRACTIONf_angle_d0.6546380
X-RAY DIFFRACTIONf_dihedral_angle_d13.0572688
X-RAY DIFFRACTIONf_chiral_restr0.048653
X-RAY DIFFRACTIONf_plane_restr0.005820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04650.27341340.2252618X-RAY DIFFRACTION96
2.0465-2.09770.2521340.21322590X-RAY DIFFRACTION96
2.0977-2.15440.23161450.2072602X-RAY DIFFRACTION97
2.1544-2.21780.25971360.20442626X-RAY DIFFRACTION97
2.2178-2.28940.24111650.18912619X-RAY DIFFRACTION97
2.2894-2.37120.24531290.18272640X-RAY DIFFRACTION98
2.3712-2.46610.24061430.1852671X-RAY DIFFRACTION98
2.4661-2.57840.23951390.18112677X-RAY DIFFRACTION98
2.5784-2.71430.24251500.18772696X-RAY DIFFRACTION98
2.7143-2.88430.23721390.18962686X-RAY DIFFRACTION98
2.8843-3.10690.24821410.19032682X-RAY DIFFRACTION98
3.1069-3.41940.24031520.18632724X-RAY DIFFRACTION98
3.4194-3.91390.19671310.16122740X-RAY DIFFRACTION98
3.9139-4.92970.13821360.13062728X-RAY DIFFRACTION97
4.9297-40.44280.15981570.15912733X-RAY DIFFRACTION92
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)
10.33950.1569-0.32650.58910.04091.59120.0030.0143-0.02920.0338-0.0135-0.0180.1819-0.0107-00.1461-0.0036-0.0040.17410.00480.1846-17.587-28.850226.0522
20.61590.64950.47911.35860.66620.7827-0.01660.0831-0.01050.00440.0847-0.0829-0.17620.03820.00210.22410.00250.00680.20710.00120.2119-6.3157-2.639225.734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 21 through 252 )
2X-RAY DIFFRACTION2chain 'B' and (resid 253 through 560 )

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