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- PDB-3w9v: Crystal structure of refolded DING protein -

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Basic information

Entry
Database: PDB / ID: 3w9v
TitleCrystal structure of refolded DING protein
ComponentsPhosphate-binding protein
KeywordsTRANSPORT PROTEIN / DING / refolded / phosphate binding Apolipoprotein / phosphate
Function / homology
Function and homology information


phosphate ion transport / extracellular region
Similarity search - Function
: / PBP domain / PBP superfamily domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Phosphate-binding protein
Similarity search - Component
Biological speciesunidentified prokaryotic organism (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.031 Å
AuthorsGai, Z.Q. / Nakamura, A. / Tanaka, Y. / Hirano, N. / Tanaka, I. / Yao, M.
CitationJournal: J.SYNCHROTRON RADIAT. / Year: 2013
Title: Crystal structure analysis, overexpression and refolding behaviour of a DING protein with single mutation.
Authors: Gai, Z.Q. / Nakamura, A. / Tanaka, Y. / Hirano, N. / Tanaka, I. / Yao, M.
History
DepositionApr 17, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphate-binding protein
B: Phosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8139
Polymers77,1622
Non-polymers6507
Water20,1951121
1
A: Phosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9525
Polymers38,5811
Non-polymers3714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8604
Polymers38,5811
Non-polymers2793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.340, 86.890, 88.640
Angle α, β, γ (deg.)90.000, 90.810, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-549-

HOH

21B-519-

HOH

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Components

#1: Protein Phosphate-binding protein / HPBP


Mass: 38581.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified prokaryotic organism (environmental samples)
Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE) / References: UniProt: P85173
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1121 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 298 K / Method: sitting drop
Details: PEG 8000, NaCl, Tris, pH 7.0-9.0, sitting drop, temperature 298K
PH range: 7.0-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.03→44.32 Å / Num. obs: 346764 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.212 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.03-1.060.8280.5882.087457525919245410.71794.7
1.06-1.090.890.4432.77717425178247150.53898.2
1.09-1.120.9240.343.57661624429241080.41198.7
1.12-1.150.9480.2684.347608223790235730.32299.1
1.15-1.190.9650.2215.227521023072229000.26599.3
1.19-1.230.9710.1995.837433422336222050.23799.4
1.23-1.280.9760.1746.597305921550214300.20799.4
1.28-1.330.9820.1517.417124020691205740.17999.4
1.33-1.390.9870.1258.756919919919198160.14899.5
1.39-1.460.990.09910.686595618984189170.11799.6
1.46-1.540.9940.10513.838148318055180310.11899.9
1.54-1.630.9960.10918.0311250317131171010.11899.8
1.63-1.740.9970.08723.2811935616114160950.09399.9
1.74-1.880.9980.06431.0611085714975149690.069100
1.88-2.060.9980.04327.295737713815138090.05100
2.06-2.310.9990.03233.914693512463124530.03799.9
2.31-2.660.9990.02640.764161511041110240.0399.8
2.66-3.260.9990.02248.3834954932692970.02699.7
3.26-4.610.9990.0256.4126623727472490.02399.7
4.610.9990.01758.2214528402539570.0298.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V3Q

2v3q


Resolution: 1.031→29.544 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.868 / SU ML: 0.09 / σ(F): 1.99 / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.184 17185 4.96 %RANDOM
Rwork0.1735 ---
obs0.174 346693 99.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.04 Å2 / Biso mean: 12.5911 Å2 / Biso min: 2.9 Å2
Refinement stepCycle: LAST / Resolution: 1.031→29.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5442 0 40 1121 6603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045724
X-RAY DIFFRACTIONf_angle_d1.0417831
X-RAY DIFFRACTIONf_chiral_restr0.071901
X-RAY DIFFRACTIONf_plane_restr0.0061028
X-RAY DIFFRACTIONf_dihedral_angle_d10.2311980
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0312-1.04290.28285150.279101191063491
1.0429-1.05520.29055360.2704108471138398
1.0552-1.0680.26565820.26108291141198
1.068-1.08160.27165730.2512107851135898
1.0816-1.09580.25165460.2452109081145498
1.0958-1.11080.24435580.2339109561151499
1.1108-1.12670.24746000.2271109151151599
1.1267-1.14350.23075970.2265109281152599
1.1435-1.16140.2255800.2213109681154899
1.1614-1.18040.23025580.217109831154199
1.1804-1.20080.23125680.2123109631153199
1.2008-1.22260.2265570.2098110461160399
1.2226-1.24610.22245770.2074109841156199
1.2461-1.27150.21215660.2042110281159499
1.2715-1.29920.20135870.2028109601154799
1.2992-1.32940.22365790.2031110381161799
1.3294-1.36270.21955620.1956110831164599
1.3627-1.39950.22245880.19331098611574100
1.3995-1.44070.18885670.18681100011567100
1.4407-1.48720.19435830.18441108611669100
1.4872-1.54030.17965860.17631105511641100
1.5403-1.6020.18395900.17411109911689100
1.602-1.67490.16825380.16431110711645100
1.6749-1.76320.18416090.16281101611625100
1.7632-1.87370.16725900.15841111511705100
1.8737-2.01830.17076300.15651106911699100
2.0183-2.22130.15855640.15531113711701100
2.2213-2.54260.15435670.15481112711694100
2.5426-3.20280.18385610.16071116911730100
3.2028-29.55580.14835710.142112021177399

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