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- PDB-4hwm: Crystal structure of a lipoprotein YedD (KPN_02420) from Klebsiel... -

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Basic information

Entry
Database: PDB / ID: 4hwm
TitleCrystal structure of a lipoprotein YedD (KPN_02420) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.38 A resolution
ComponentsUncharacterized protein yedD
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / YedD-like protein / PF13987 family / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyYedD-like protein / YedD-like protein / YedD-like superfamily / YedD-like protein / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta / Lipoprotein
Function and homology information
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.38 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a lipoprotein YedD (KPN_02420) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.38 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 9, 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: Uncharacterized protein yedD


Theoretical massNumber of molelcules
Total (without water)14,4541
Polymers14,4541
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.810, 51.067, 52.436
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein yedD


Mass: 14453.691 Da / Num. of mol.: 1 / Fragment: UNP residues 16-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: yedD, KPN78578_23820, KPN_02420 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6TB72
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (16-144) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (16-144) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 1.84 Å3/Da / Density % sol: 33.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 30.00% polyethylene glycol 3000, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979133
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 19, 2012 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979133 Å / Relative weight: 1
ReflectionResolution: 1.38→39.81 Å / Num. obs: 22613 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 16.745 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 15.44
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.38-1.430.8411.5154724254199.6
1.43-1.490.5742.31648944251100
1.49-1.550.3713.51402437611100
1.55-1.640.2495.4175564681199.9
1.64-1.740.1638.11558341311100
1.74-1.870.09412.81551541081100
1.87-2.060.05620.1162124288199.9
2.06-2.360.04226.6161124282199.8
2.36-2.970.03333.2155734230199.9
2.97-39.810.02740.7158224258199.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
REFMAC5.5.0110refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.38→39.81 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 2.145 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.059
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. 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 FOR THE REDUCED ...Details: 1. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1795 1152 5.1 %RANDOM
Rwork0.1494 ---
obs0.1509 22564 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.57 Å2 / Biso mean: 21.1093 Å2 / Biso min: 9.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.38→39.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 0 154 1064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221037
X-RAY DIFFRACTIONr_bond_other_d0.0020.02741
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9711431
X-RAY DIFFRACTIONr_angle_other_deg1.0253.0021820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0415145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.57324.08249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04515192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2731510
X-RAY DIFFRACTIONr_chiral_restr0.1030.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211192
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02207
X-RAY DIFFRACTIONr_mcbond_it2.6013639
X-RAY DIFFRACTIONr_mcbond_other1.8513250
X-RAY DIFFRACTIONr_mcangle_it4.0351052
X-RAY DIFFRACTIONr_scbond_it4.6948398
X-RAY DIFFRACTIONr_scangle_it6.59211363
X-RAY DIFFRACTIONr_rigid_bond_restr1.91231778
X-RAY DIFFRACTIONr_sphericity_free7.6083156
X-RAY DIFFRACTIONr_sphericity_bonded4.46831741
LS refinement shellResolution: 1.38→1.416 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 66 -
Rwork0.253 1556 -
all-1622 -
obs--99.88 %

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