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- PDB-5dvf: Crystal structure of unliganded periplasmic glucose binding prote... -

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Basic information

Entry
Database: PDB / ID: 5dvf
TitleCrystal structure of unliganded periplasmic glucose binding protein (ppGBP) from P. putida CSV86
ComponentsBinding protein component of ABC sugar transporter
KeywordsTRANSPORT PROTEIN / Periplasmic glucose binding protein / ABC transporter / Pseudomonas / crystallization
Function / homology: / cell envelope / 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 / Probable sugar-binding periplasmic protein
Function and homology information
Biological speciesPseudomonas putida CSV86 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPandey, S. / Modak, A. / Phale, P.S. / Bhaumik, P.
Funding support India, 2items
OrganizationGrant numberCountry
Dept. of Biotechnology, Govt. of IndiaBT/PR4954/BRB/10/1063/2012 India
Ramalingaswami Fellowship, Dept. of Biotechnology, Govt. of India India
CitationJournal: J.Biol.Chem. / Year: 2016
Title: High Resolution Structures of Periplasmic Glucose-binding Protein of Pseudomonas putida CSV86 Reveal Structural Basis of Its Substrate Specificity
Authors: Pandey, S. / Modak, A. / Phale, P.S. / Bhaumik, P.
History
DepositionSep 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Apr 27, 2016Group: Database references
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Binding protein component of ABC sugar transporter
B: Binding protein component of ABC sugar transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4344
Polymers90,2422
Non-polymers1922
Water4,270237
1
A: Binding protein component of ABC sugar transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2172
Polymers45,1211
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-14 kcal/mol
Surface area16350 Å2
MethodPISA
2
B: Binding protein component of ABC sugar transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2172
Polymers45,1211
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-10 kcal/mol
Surface area16370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.440, 154.620, 60.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-656-

HOH

21B-712-

HOH

31B-713-

HOH

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Components

#1: Protein Binding protein component of ABC sugar transporter / Periplasmic glucose binding protein / ppGBP


Mass: 45120.875 Da / Num. of mol.: 2 / Fragment: UNP residues 24-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida CSV86 (bacteria) / Strain: CSV86 / Gene: CSV86_10737 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H7BRJ8
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 237 / 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

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.04 % / Description: Rod shaped crystals
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1 M phosphate citrate buffer and 2 M ammonium sulphate
PH range: 4.2 - 4.8 / Temp details: 295

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 28150 / % possible obs: 99.7 % / Redundancy: 7.24 % / Net I/σ(I): 9.27
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 7.24 % / Mean I/σ(I) obs: 2.25 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.68 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.888 / SU B: 20.733 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.811 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25323 1408 5 %RANDOM
Rwork0.18112 ---
obs0.18478 26741 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.309 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å2-0 Å2-0 Å2
2--0.74 Å2-0 Å2
3----1.55 Å2
Refinement stepCycle: 1 / Resolution: 2.5→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5936 0 10 239 6185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196080
X-RAY DIFFRACTIONr_bond_other_d0.0010.025774
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9418264
X-RAY DIFFRACTIONr_angle_other_deg0.8233.00113286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3875774
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56825.896268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.30415988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6781516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2908
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217016
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021352
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7571.4893108
X-RAY DIFFRACTIONr_mcbond_other0.7571.4893107
X-RAY DIFFRACTIONr_mcangle_it1.3052.2293878
X-RAY DIFFRACTIONr_mcangle_other1.3052.233879
X-RAY DIFFRACTIONr_scbond_it0.9441.6042972
X-RAY DIFFRACTIONr_scbond_other0.9251.5972964
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5742.3424374
X-RAY DIFFRACTIONr_long_range_B_refined2.90811.976951
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 102 -
Rwork0.268 1929 -
obs--99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5507-1.48670.04455.3553.05048.0157-0.0270.02040.014-0.0036-0.19260.2107-0.3152-0.33630.21960.0658-0.00540.00150.2336-0.0030.338496.5546169.887942.3471
23.64061.2417-0.82445.4861-0.68693.92160.05110.0485-0.12090.0915-0.00140.33620.067-0.2518-0.04970.0620.01160.00990.0464-0.00210.0344107.3762157.597846.0218
30.4896-0.01140.29920.61740.20030.8834-0.02710.00810.0901-0.0140.00960.0593-0.127-0.05810.01750.0210.00770.00730.01440.0050.0429110.6896167.350767.5038
43.1169-0.2371-0.48460.464-1.65136.7226-0.16010.0717-0.221-0.0963-0.1603-0.1530.50310.4780.32040.27330.0038-0.0260.31210.07870.524985.8867172.390180.793
50.60880.1516-0.03751.0352-0.91292.52450.0028-0.0288-0.0744-0.05-0.0666-0.12360.09030.21950.06380.02870.0054-0.01360.0286-0.01240.084174.751180.7261.555
60.6088-0.04570.26220.9503-0.62772.9924-0.0343-0.01320.07620.0879-0.0956-0.1524-0.19920.18430.12990.0261-0.0026-0.00810.0543-0.00590.084771.258180.90760.181
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 59
2X-RAY DIFFRACTION2A60 - 141
3X-RAY DIFFRACTION3A142 - 421
4X-RAY DIFFRACTION4B26 - 74
5X-RAY DIFFRACTION5B75 - 330
6X-RAY DIFFRACTION6B331 - 421

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