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- PDB-1l0q: Tandem YVTN beta-propeller and PKD domains from an archaeal surfa... -

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Basic information

Entry
Database: PDB / ID: 1l0q
TitleTandem YVTN beta-propeller and PKD domains from an archaeal surface layer protein
ComponentsSurface layer protein
KeywordsPROTEIN BINDING / surface layer protein / SLP / S-layer / 7-bladed beta-propeller / PKD superfamily
Function / homology
Function and homology information


YVTN beta-propeller repeat / : / YNCE-like beta-propeller / Lactonase, 7-bladed beta-propeller / Nitrous oxide reductase, N-terminal / PKD domain / : / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily ...YVTN beta-propeller repeat / : / YNCE-like beta-propeller / Lactonase, 7-bladed beta-propeller / Nitrous oxide reductase, N-terminal / PKD domain / : / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsJing, H. / Takagi, J. / Liu, J.-H. / Lindgren, S. / Zhang, R.-G. / Joachimiak, A. / Wang, J.-H. / Springer, T.A.
Citation
Journal: Structure / Year: 2002
Title: Archaeal Surface Layer Proteins Contain beta Propeller, PKD, and beta Helix Domains and Are Related to Metazoan Cell Surface Proteins.
Authors: Jing, H. / Takagi, J. / Liu, J. / Lindgren, S. / Zhang, R. / Joachimiak, A. / Wang, J. / Springer, T.
#1: Journal: Nat.Struct.Biol. / Year: 2001
Title: Implications for familial hypercholesterolemia from structure of the LDL receptor YWTD-EGF doman pair
Authors: Jeon, H. / Meng, W. / Takagi, J. / Eck, M.J. / Springer, T.A. / Blacklow, S.C.
#2: Journal: Embo J. / Year: 1999
Title: The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease
Authors: Bycroft, M. / Bateman, A. / Clarke, J. / Hamill, S.J. / Sandford, R. / Thomas, R.L. / Chothia, C.
#3: Journal: Arch.Microbiol. / Year: 1998
Title: Structure, organization, and expression of genes coding for envelope components in the archaeon Methanosarcina mazei S-6
Authors: Mayerhofer, L.E. / Conway de Macario, E. / Yao, R. / Macario, A.J.L.
#4: Journal: To be Published
Title: The genome of Methanosarcina acetivorans reveals extensive metabolic and physiological diversity
Authors: Galagan, J.E. / Nusbaum, C. / Roy, A. / Endrizzi, M.G. / Macdonald, P. / FitzHugh, W. / Calvo, S. / Engels, R. / Smirnov, S.
#5: Journal: J.Mol.Biol. / Year: 1998
Title: An extracellular beta-propeller module predicted in lipoprotein and scavenger receptors, tyrosine kinases, epidermal growth factor precursor, and extracellular matrix components
Authors: Springer, T.A.
History
DepositionFeb 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 26, 2025Group: 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 / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE WHOLE SURFACE LAYER PROTEIN MOLECULE HAS A DOMAIN ORGANIZATION OF YVTN-PKD-YVTN-(PKD)11. THE COORDINATES OF ANY ONE OF THE 4 MOLECULES IN THE ASYMMETRIC UNIT COULD CORRESPOND TO THE BIOLOGICAL CONFORMATION OF THE N-TERMINAL YVTN-PKD DOMAIN PAIR.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Surface layer protein
B: Surface layer protein
C: Surface layer protein
D: Surface layer protein


Theoretical massNumber of molelcules
Total (without water)163,1864
Polymers163,1864
Non-polymers00
Water24,5721364
1
A: Surface layer protein


Theoretical massNumber of molelcules
Total (without water)40,7971
Polymers40,7971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Surface layer protein


Theoretical massNumber of molelcules
Total (without water)40,7971
Polymers40,7971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Surface layer protein


Theoretical massNumber of molelcules
Total (without water)40,7971
Polymers40,7971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Surface layer protein


Theoretical massNumber of molelcules
Total (without water)40,7971
Polymers40,7971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)188.181, 65.885, 140.030
Angle α, β, γ (deg.)90.00, 124.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Surface layer protein


Mass: 40796.559 Da / Num. of mol.: 4 / Fragment: YVTN beta-propeller domain 1 and PKD domain 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: S-6 / Plasmid: pQE-60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q50245
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1364 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: PEG-8000, potassium chloride, sodium acetate, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
113 mg/mlprotein1drop
220 %PEG80001reservoir
30.3 M1reservoirKCl
40.1 M1reservoirNaAcpH3.8

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979067,0.979221,0.939270
DetectorType: SBC-2 / Detector: CCD / Date: Nov 24, 1999 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9790671
20.9792211
30.939271
ReflectionResolution: 2.4→100 Å / Num. all: 52881 / Num. obs: 52881 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 30.36 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 14.6
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3.1 / Num. unique all: 4965 / % possible all: 89
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 318719 / Rmerge(I) obs: 0.109
Reflection shell
*PLUS
% possible obs: 89 % / Rmerge(I) obs: 0.434

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→20 Å / Data cutoff high rms absF: 1000 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2642 5 %RANDOM
Rwork0.214 ---
all0.217 52357 --
obs0.217 52357 93.9 %-
Solvent computationBsol: 40.168 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso mean: 23.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11400 0 0 1364 12764
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.354
X-RAY DIFFRACTIONc_dihedral_angle_d28.428
X-RAY DIFFRACTIONc_improper_angle_d0.797
X-RAY DIFFRACTIONc_mcbond_it1.2211.5
X-RAY DIFFRACTIONc_mcangle_it2.2212
X-RAY DIFFRACTIONc_scbond_it2.0132
X-RAY DIFFRACTIONc_scangle_it3.0552.5
LS refinement shellResolution: 2.4→2.49 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3466 247 -
Rwork0.2897 4786 -
obs--90.49 %
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.217 / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg28.428
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.797
LS refinement shell
*PLUS
Rfactor Rfree: 0.3466 / Rfactor Rwork: 0.2897

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