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- PDB-1kwh: Structure Analysis AlgQ2, a Macromolecule(alginate)-Binding Perip... -

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Basic information

Entry
Database: PDB / ID: 1kwh
TitleStructure Analysis AlgQ2, a Macromolecule(alginate)-Binding Periplasmic Protein of Sphingomonas sp. A1.
ComponentsMacromolecule-Binding Periplasmic Protein
KeywordsPROTEIN BINDING / 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 / MIR / Resolution: 2 Å
AuthorsMomma, K. / Mikami, B. / Mishima, Y. / Hashimoto, W. / Murata, K.
CitationJournal: 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
DepositionJan 29, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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 / _struct_conn.pdbx_dist_value / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Macromolecule-Binding Periplasmic Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2922
Polymers57,2521
Non-polymers401
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.703, 96.369, 139.863
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Macromolecule-Binding Periplasmic Protein / AlgQ2


Mass: 57251.715 Da / Num. of mol.: 1 / Fragment: residues 1-492
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. (bacteria) / Strain: A1 / Gene: algQ2 / Plasmid: pAQ2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9KWT5
#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.: 151 / 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: 49.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, ammonium acetate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19 mg/mlprotein1drop
230 %(w/v)PEG40001reservoir
30.2 Mammonium acetate1reservoir
40.1 Msodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 11, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→42 Å / Num. all: 149287 / Num. obs: 42596 / % possible obs: 93.71 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 15.9 Å2 / Rsym value: 0.077 / Net I/σ(I): 7.63
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 1.63 % / Mean I/σ(I) obs: 5.83 / Num. unique all: 3416 / Rsym value: 0.454 / % possible all: 76.98
Reflection
*PLUS
% possible obs: 93.7 % / Num. measured all: 149287 / Rmerge(I) obs: 0.077

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Processing

Software
NameVersionClassification
PHASESphasing
CNS1refinement
FRAMBOdata collection
SAINTdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2→14.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 763581.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 3151 9.8 %RANDOM
Rwork0.185 ---
all-31853 --
obs-28703 81.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.7433 Å2 / ksol: 0.337425 e/Å3
Displacement parametersBiso mean: 29.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å20 Å20 Å2
2--3.79 Å20 Å2
3----5.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4046 0 1 151 4198
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it3.871.5
X-RAY DIFFRACTIONc_mcangle_it4.722
X-RAY DIFFRACTIONc_scbond_it5.992
X-RAY DIFFRACTIONc_scangle_it7.52.5
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 384 9.9 %
Rwork0.243 4163 -
obs-3481 72.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3CARBOHYDRATE.PARAM
X-RAY DIFFRACTION4ION.PARAM
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 15 Å / Num. reflection obs: 31854 / Rfactor obs: 0.183 / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0061
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
X-RAY DIFFRACTIONc_mcbond_it3.871.5
X-RAY DIFFRACTIONc_scbond_it5.992
X-RAY DIFFRACTIONc_mcangle_it4.722
X-RAY DIFFRACTIONc_scangle_it7.52.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.288 / Rfactor Rwork: 0.243

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