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- PDB-1j1n: Structure Analysis of AlgQ2, A Macromolecule(Alginate)-Binding Pe... -

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Basic information

Entry
Database: PDB / ID: 1j1n
TitleStructure Analysis of AlgQ2, A Macromolecule(Alginate)-Binding Periplasmic Protein Of Sphingomonas Sp. A1., Complexed with an Alginate Tetrasaccharide
ComponentsAlgQ2
KeywordsSUGAR BINDING PROTEIN / ALGINATE
Function / homology
Function and homology information


periplasmic space / metal ion binding
Similarity search - Function
: / Bacterial extracellular solute-binding protein / 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
Biological speciesSphingomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMomma, K. / Mikami, B. / Mishima, Y. / Hashimoto, W. / Murata, K.
Citation
Journal: J.BIOL.CHEM. / Year: 2003
Title: Crystal structure of AlgQ2, a macromolecule (alginate)-binding protein of Sphingomonas sp. A1, complexed with an alginate tetrasaccharide at 1.6-A resolution
Authors: Mishima, Y. / Momma, K. / Hashimoto, W. / Mikami, B. / Murata, K.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of AlgQ2, a macromolecule (alginate)-binding protein of Sphingomonas sp. A1 at 2.0A resolution
Authors: Momma, K. / Mikami, B. / Mishima, Y. / Hashimoto, W. / Murata, K.
History
DepositionDec 11, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / 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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 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: AlgQ2
B: AlgQ2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,0296
Polymers114,5032
Non-polymers1,5254
Water15,421856
1
A: AlgQ2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0143
Polymers57,2521
Non-polymers7632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AlgQ2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0143
Polymers57,2521
Non-polymers7632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.630, 53.881, 114.924
Angle α, β, γ (deg.)90.00, 107.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AlgQ2 / alginate-binding protein


Mass: 57251.715 Da / Num. of mol.: 2 / Fragment: residues 1-492
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. (bacteria) / Strain: A1 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: GenBank: 9501762, UniProt: Q9KWT5*PLUS
#2: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid- ...beta-D-mannopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 722.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAa1-4LGulpAa1-4DManpAa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a1122A-1a_1-5][a1121A-1a_1-5][a1122A-1b_1-5]/1-2-1-3/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-ManpA]{[(4+1)][a-L-GulpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-4-deoxy-ManpA]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 856 / 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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, ammmonium acetate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Momma, K., (2002) J. Mol. Biol., 316, 1061.

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: OXFORD / Detector: CCD / Date: Mar 29, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→61.57 Å / Num. all: 512032 / Num. obs: 159065 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15.7 Å2
Reflection shellResolution: 1.6→1.66 Å / % possible all: 98.7
Reflection
*PLUS
Lowest resolution: 61.6 Å / Num. obs: 175841 / % possible obs: 98.3 % / Redundancy: 7.4 % / Num. measured all: 559708 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 94.6 % / Num. unique obs: 16776 / Num. measured obs: 47676 / Rmerge(I) obs: 0.242

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Processing

Software
NameVersionClassification
CNS1refinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo AlgQ2 (1KWH)

1kwh


Resolution: 1.6→28.73 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1784538.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 14534 10 %RANDOM
Rwork0.19 ---
obs0.19 145984 98.9 %-
all-147621 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.5841 Å2 / ksol: 0.377847 e/Å3
Displacement parametersBiso mean: 13.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å2-0.76 Å2
2--1.64 Å20 Å2
3----1.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.6→28.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8092 0 98 856 9046
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_mcbond_it1.891.5
X-RAY DIFFRACTIONc_mcangle_it2.322
X-RAY DIFFRACTIONc_scbond_it3.192
X-RAY DIFFRACTIONc_scangle_it4.122.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.254 2361 9.9 %
Rwork0.22 21512 -
obs--97.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3PARAM3.CHO
X-RAY DIFFRACTION4ION.PARAM
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 61.6 Å / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0053
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03
LS refinement shell
*PLUS
Lowest resolution: 1.65 Å / Rfactor Rwork: 0.22 / Num. reflection Rwork: 12879

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