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- PDB-3w9w: Crystal structure of DING protein -

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Basic information

Entry
Database: PDB / ID: 3w9w
TitleCrystal structure of DING protein
ComponentsDING protein
KeywordsTRANSPORT PROTEIN / phosphate binding protein / phosphate
Function / homology
Function and homology information


phosphate ion transport / extracellular region
Similarity search - Function
PBP superfamily domain / PBP 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: 1.35 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 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DING protein
B: DING protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,08912
Polymers77,1622
Non-polymers92710
Water21,6181200
1
A: DING protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0446
Polymers38,5811
Non-polymers4635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DING protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0446
Polymers38,5811
Non-polymers4635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.270, 87.140, 88.600
Angle α, β, γ (deg.)90.000, 90.820, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1051-

HOH

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Components

#1: Protein DING 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)
Production host: Escherichia coli (E. coli) / 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.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1200 / 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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 298 K / Method: sitting drop / pH: 8
Details: Tris, PEG 8000, NaCl, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→43.57 Å / Num. obs: 150208 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.593 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.15
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
1.35-1.430.8550.3853.217439525283216220.45685.5
1.43-1.530.9330.2715.028710023721228810.31596.5
1.53-1.650.970.1757.668177122093214560.20497.1
1.65-1.810.9860.11511.277553020290198110.13497.6
1.81-2.020.9950.0717.56900718422181020.08198.3
2.02-2.340.9970.04625.386117016271160660.05498.7
2.34-2.860.9980.03731.425197213784136690.04399.2
2.86-4.040.9980.02840.734026110713106540.03399.4
4.040.9990.02644.8622013599259470.03199.2

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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: 2V3Q

2v3q


Resolution: 1.35→43.57 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9146 / SU ML: 0.11 / σ(F): 1.99 / Phase error: 15.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1696 7462 4.97 %RANDOM
Rwork0.1484 ---
obs0.1495 150204 95.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.32 Å2 / Biso mean: 11.7315 Å2 / Biso min: 0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.35→43.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5442 0 58 1200 6700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065737
X-RAY DIFFRACTIONf_angle_d1.0597842
X-RAY DIFFRACTIONf_chiral_restr0.071899
X-RAY DIFFRACTIONf_plane_restr0.0061028
X-RAY DIFFRACTIONf_dihedral_angle_d10.871988
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 (%)
1.3504-1.36580.25621900.22673481367170
1.3658-1.38180.25841700.21593942411280
1.3818-1.39870.24372240.2144371459588
1.3987-1.41640.23052580.19374683494196
1.4164-1.4350.21042540.18384754500896
1.435-1.45470.19512400.17754779501996
1.4547-1.47550.19132590.17514734499396
1.4755-1.49750.21782480.16784800504897
1.4975-1.52090.19532300.16554766499697
1.5209-1.54590.19932560.1574771502797
1.5459-1.57250.16182550.1594826508197
1.5725-1.60110.17132670.1574801506897
1.6011-1.63190.1822460.15194780502697
1.6319-1.66520.16812410.14864829507097
1.6652-1.70140.18642640.14964842510698
1.7014-1.7410.16542470.14694827507498
1.741-1.78450.16522510.14754879513098
1.7845-1.83280.17642680.1464822509098
1.8328-1.88670.17842720.14414854512698
1.8867-1.94760.16492890.14344820510998
1.9476-2.01720.16932570.14094853511098
2.0172-2.0980.15562670.14414865513299
2.098-2.19350.16862470.13974914516199
2.1935-2.30910.14542430.1364938518199
2.3091-2.45380.16082560.14044903515999
2.4538-2.64320.16972690.14864933520299
2.6432-2.90920.17282400.14634971521199
2.9092-3.330.15642380.1424960519899
3.33-4.19490.14652640.128549825246100
4.1949-43.59270.1412520.13645062531499

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