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- PDB-3d02: Crystal structure of periplasmic sugar-binding protein (YP_001338... -

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Basic information

Entry
Database: PDB / ID: 3d02
TitleCrystal structure of periplasmic sugar-binding protein (YP_001338366.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.30 A resolution
ComponentsPutative LACI-type transcriptional regulator
KeywordsSUGAR BINDING PROTEIN / YP_001338366.1 / periplasmic sugar-binding protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / TRANSCRIPTION
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / carbohydrate binding
Similarity search - Function
: / Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LACI-type transcriptional regulator
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of periplasmic sugar-binding protein (YP_001338366.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative LACI-type transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6595
Polymers33,4611
Non-polymers1984
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.240, 76.960, 113.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-519-

HOH

DetailsAUTHOR STATE THAT THE RESULTS FROM SIZE EXCLUSION CHROMATOGRAPHY SUPPORT THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative LACI-type transcriptional regulator


Mass: 33460.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: strain ATCC 700721 / MGH 78578 / Gene: YP_001338366.1, KPN78578_46750, KPN_04753 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6THR5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 26-327 OF THE FULL LENGTH PROTEIN.

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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: 2.17 Å3/Da / Density % sol: 43.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1.00M LiCl, 30.00% PEG-6000, 0.1M Citrate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97932,0.97918
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 16, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979321
30.979181
ReflectionResolution: 1.3→28.63 Å / Num. obs: 70966 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 10.873 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 11.43
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.3-1.350.40522350912539184.9
1.35-1.40.3292.42396712275195.8
1.4-1.460.2483.22550212822197.8
1.46-1.540.1724.72906114373199
1.54-1.640.1216.62913214174199.1
1.64-1.760.08792700112992198.8
1.76-1.940.05712.92903013911198.4
1.94-2.220.03918.52839713537197.6
2.22-2.80.02923.52887413646197.7
2.8-28.630.02230.12848013372196.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.3→28.63 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.727 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.048
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.CHLORIDE IONS FROM CRYSTALLIZATION AND GLYCEROL MOLECULE FROM CRYO CONDITION ARE MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.172 3596 5.1 %RANDOM
Rwork0.157 ---
obs0.158 70928 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.239 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.3→28.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2263 0 9 313 2585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222680
X-RAY DIFFRACTIONr_bond_other_d0.0010.021778
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.9663684
X-RAY DIFFRACTIONr_angle_other_deg1.00934391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5975373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.32525.273110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25415464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9261513
X-RAY DIFFRACTIONr_chiral_restr0.1030.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213176
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02510
X-RAY DIFFRACTIONr_mcbond_it1.41231730
X-RAY DIFFRACTIONr_mcbond_other0.4113689
X-RAY DIFFRACTIONr_mcangle_it2.32552842
X-RAY DIFFRACTIONr_scbond_it4.0018950
X-RAY DIFFRACTIONr_scangle_it5.92611842
LS refinement shellResolution: 1.3→1.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 245 -
Rwork0.266 4655 -
all-4900 -
obs--93.49 %

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