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- PDB-3nrk: The crystal structure of the leptospiral hypothetical protein LIC12922 -

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Basic information

Entry
Database: PDB / ID: 3nrk
TitleThe crystal structure of the leptospiral hypothetical protein LIC12922
ComponentsLIC12922
KeywordsUNKNOWN FUNCTION / NC domain / parvulin domain / SurA homology / probable CHAPERONE
Function / homology
Function and homology information


peptidyl-prolyl cis-trans isomerase activity
Similarity search - Function
Putative peptidyl-prolyl cis-trans isomerase, LIC12922 family / SurA-like N-terminal domain / Triger factor/SurA peptide-binding fold / Porin chaperone SurA, peptide-binding domain / PPIC-type PPIASE domain / : / Trigger factor/SurA domain superfamily / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 ...Putative peptidyl-prolyl cis-trans isomerase, LIC12922 family / SurA-like N-terminal domain / Triger factor/SurA peptide-binding fold / Porin chaperone SurA, peptide-binding domain / PPIC-type PPIASE domain / : / Trigger factor/SurA domain superfamily / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PpiC domain-containing protein
Similarity search - Component
Biological speciesLeptospira interrogans serovar Copenhageni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.1 Å
AuthorsGiuseppe, P.O. / Atzingen, M.V. / Nascimento, A.L.T.O. / Zanchin, N.I.T. / Guimaraes, B.G.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: The crystal structure of the leptospiral hypothetical protein LIC12922 reveals homology with the periplasmic chaperone SurA.
Authors: Giuseppe, P.O. / Von Atzingen, M. / Nascimento, A.L. / Zanchin, N.I. / Guimaraes, B.G.
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIC12922


Theoretical massNumber of molelcules
Total (without water)37,8401
Polymers37,8401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: LIC12922

A: LIC12922

A: LIC12922


Theoretical massNumber of molelcules
Total (without water)113,5203
Polymers113,5203
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
Buried area6950 Å2
ΔGint-45 kcal/mol
Surface area46750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.110, 137.110, 137.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23

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Components

#1: Protein LIC12922


Mass: 37840.008 Da / Num. of mol.: 1 / Fragment: residues 48-362
Source method: isolated from a genetically manipulated source
Details: Predicted signal peptide not included in the recombinant protein. N-terminal Histag added. The first 10 residues of the sequence correspond to part of the his-tag.
Source: (gene. exp.) Leptospira interrogans serovar Copenhageni (bacteria)
Strain: Copenhageni, Fiocruz L1-130 isolate / Gene: LIC12922, LIC_12922 / Plasmid: pDEST / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q72NB3

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
15.6878.33
2
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium citrate pH 5.5, 1 M ammonium phosphate, 0.2 M sodium chloride, 0.2 % low melting point agarose, Microseeding, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2009
RadiationMonochromator: Si 111 CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→35 Å / Num. all: 15918 / Num. obs: 15880 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 10.3 % / Biso Wilson estimate: 141.48 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 21.4
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.61 / Num. unique all: 1170 / % possible all: 100

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Processing

Software
NameVersionClassification
SHARPphasing
BUSTER2.9.1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 3.1→33.25 Å / SU R Cruickshank DPI: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 794 5 %RANDOM
Rwork0.1993 ---
obs0.2001 15869 99.88 %-
all-15888 --
Displacement parametersBiso mean: 141.07 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 1.266 Å
Refinement stepCycle: LAST / Resolution: 3.1→33.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 0 0 2438
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0124842
X-RAY DIFFRACTIONt_angle_deg1.233692
X-RAY DIFFRACTIONt_dihedral_angle_d8732
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes672
X-RAY DIFFRACTIONt_gen_planes3625
X-RAY DIFFRACTIONt_it248420
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.52
X-RAY DIFFRACTIONt_other_torsion20.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3425
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact29514
LS refinement shellResolution: 3.1→3.31 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3328 147 5.16 %
Rwork0.2767 2702 -
all0.2795 2849 -
obs--99.88 %

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