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- PDB-5c7r: Revealing surface waters on an antifreeze protein by fusion prote... -

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Basic information

Entry
Database: PDB / ID: 5c7r
TitleRevealing surface waters on an antifreeze protein by fusion protein crystallography
ComponentsFusion protein of Maltose-binding periplasmic protein and Type-3 ice-structuring protein HPLC 12
KeywordsANTIFREEZE PROTEIN / fusion protein
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / extracellular region / membrane
Similarity search - Function
Antifreeze, type III / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II ...Antifreeze, type III / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / 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
alpha-maltotriose / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein / Type-3 ice-structuring protein HPLC 12
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Zoarces americanus (ocean pout)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsSun, T. / Gauthier, S. / Campbell, R.L. / Davies, P.L.
Citation
Journal: J.Phys.Chem.B / Year: 2015
Title: Revealing Surface Waters on an Antifreeze Protein by Fusion Protein Crystallography Combined with Molecular Dynamic Simulations.
Authors: Sun, T. / Gauthier, S.Y. / Campbell, R.L. / Davies, P.L.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: Understanding the mechanism of ice binding by type III antifreeze proteins.
Authors: Antson, A.A. / Smith, D.J. / Roper, D.I. / Lewis, S. / Caves, L.S. / Verma, C.S. / Buckley, S.L. / Lillford, P.J. / Hubbard, R.E.
History
DepositionJun 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.journal_id_CSD / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Fusion protein of Maltose-binding periplasmic protein and Type-3 ice-structuring protein HPLC 12
B: Fusion protein of Maltose-binding periplasmic protein and Type-3 ice-structuring protein HPLC 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2256
Polymers97,0242
Non-polymers1,2014
Water9,728540
1
A: Fusion protein of Maltose-binding periplasmic protein and Type-3 ice-structuring protein HPLC 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1133
Polymers48,5121
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fusion protein of Maltose-binding periplasmic protein and Type-3 ice-structuring protein HPLC 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1133
Polymers48,5121
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.050, 110.800, 96.570
Angle α, β, γ (deg.)90.00, 94.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fusion protein of Maltose-binding periplasmic protein and Type-3 ice-structuring protein HPLC 12 / MBP / MMBP / Maltodextrin-binding protein / Antifreeze protein QAE(HPLC 12) / ISP type III HPLC 12


Mass: 48512.152 Da / Num. of mol.: 2
Fragment: UNP P0AEY0 residues 27-384, UNP P19614 residues 1-63
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Zoarces americanus (ocean pout)
Gene: malE, Z5632, ECs5017 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEY0, UniProt: P19614, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4 / Details: 1.75 M (NH4)2SO4, 100 mM NaOAC (pH 4.4)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.987 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.94→48.2 Å / Num. obs: 72126 / % possible obs: 96.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 9.36
Reflection shellResolution: 1.94→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.362 / Mean I/σ(I) obs: 1.1 / % possible all: 86.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HG7,3G7W

1hg7

3g7w


Resolution: 1.94→48.158 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 2000 2.77 %
Rwork0.1764 --
obs0.178 72081 96.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→48.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6668 0 78 540 7286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127077
X-RAY DIFFRACTIONf_angle_d1.329662
X-RAY DIFFRACTIONf_dihedral_angle_d13.2142594
X-RAY DIFFRACTIONf_chiral_restr0.0541092
X-RAY DIFFRACTIONf_plane_restr0.0061251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9397-1.98820.3641260.3174462X-RAY DIFFRACTION86
1.9882-2.0420.29341390.25794979X-RAY DIFFRACTION97
2.042-2.10210.25211290.24074954X-RAY DIFFRACTION96
2.1021-2.16990.27211570.2214986X-RAY DIFFRACTION97
2.1699-2.24750.28091290.20475016X-RAY DIFFRACTION97
2.2475-2.33750.24571490.19764985X-RAY DIFFRACTION97
2.3375-2.44390.26871470.18694991X-RAY DIFFRACTION97
2.4439-2.57270.21041510.17825070X-RAY DIFFRACTION97
2.5727-2.73390.24521410.17985022X-RAY DIFFRACTION98
2.7339-2.94490.25911470.1835101X-RAY DIFFRACTION98
2.9449-3.24120.24441460.1865077X-RAY DIFFRACTION98
3.2412-3.71010.2221430.15395113X-RAY DIFFRACTION98
3.7101-4.67370.18231450.12965124X-RAY DIFFRACTION99
4.6737-48.17240.20951510.15095201X-RAY DIFFRACTION99

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