5KCN

Crystal Structure of full-length LpoA from Haemophilus influenzae at 1.97 angstrom resolution

> Summary

Summary for 5KCN

Related3CKM 4P29 5VAT 5VBG
DescriptorPenicillin-binding protein activator LpoA, CHLORIDE ION (3 entities in total)
Functional Keywordsouter membrane lipoprotein, pbp1a, transpeptidase. peptidoglycan, biosynthetic protein
Biological sourceHaemophilus influenzae
Cellular locationCell outer membrane ; Lipid- anchor ; Periplasmic side  P45299
Total number of polymer chains1
Total molecular weight60045.53
Authors
Sathiyamoorthy, K.,Saper, M.A. (deposition date: 2016-06-06, release date: 2017-09-13)
Primary citation
Sathiyamoorthy, K.,Vijayalakshmi, J.,Tirupati, B.,Fan, L.,Saper, M.A.
Structural analyses of the Haemophilus influenzae peptidoglycan synthase activator LpoA suggest multiple conformations in solution
J.Biol.Chem., 2017
DOI: 10.1074/jbc.M117.804997
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.965 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.214200.2%11.0%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5kcn
no rotation
Molmil generated image of 5kcn
rotated about x axis by 90°
Molmil generated image of 5kcn
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
APenicillin-binding protein activator LpoApolymer54360010.11
UniProt (P45299)
Pfam (PF04348)
Haemophilus influenzaePBP activator LpoA
CHLORIDE IONnon-polymer35.51
waterwater18.0392

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight60010.1
Non-Polymers*Number of molecules1
Total molecular weight35.5
All*Total molecular weight60045.5
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.965 Å)

Cell axes65.86668.427128.404
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits31.78 - 1.97
the highest resolution shell value2.035 - 1.965
R-factor0.1792
R-work0.17740
the highest resolution shell value0.207
R-free0.21420
the highest resolution shell value0.241
RMSD bond length0.004
RMSD bond angle0.624

Data Collection Statistics

Resolution limits50.00 - 1.97
the highest resolution shell value -
Number of reflections42000
Rmerge_l_obs0.058
the highest resolution shell value0.171
Completeness99.8
Redundancy6.5
the highest resolution shell value5.5

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP4295

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC15binding site for residue CL A 601
ChainResidue
ATHR296
APRO319
ALEU320
ALEU321
AASN324

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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