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- PDB-6atu: Exploring Cystine Dense Peptide Space to Open a Unique Molecular ... -

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Basic information

Entry
Database: PDB / ID: 6atu
TitleExploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox
ComponentsElafin
KeywordsTOXIN / Knottins / Cystine knot / Toxins
Function / homology
Function and homology information


structural constituent of skin epidermis / copulation / Formation of the cornified envelope / peptide cross-linking / cornified envelope / Antimicrobial peptides / endopeptidase inhibitor activity / extracellular matrix / serine-type endopeptidase inhibitor activity / antibacterial humoral response ...structural constituent of skin epidermis / copulation / Formation of the cornified envelope / peptide cross-linking / cornified envelope / Antimicrobial peptides / endopeptidase inhibitor activity / extracellular matrix / serine-type endopeptidase inhibitor activity / antibacterial humoral response / innate immune response / extracellular space / extracellular region / cytosol
Similarity search - Function
Seminal vesicle protein I / Trappin protein transglutaminase-binding repeat / Trappin protein transglutaminase binding domain / Seminal vesicle protein I repeats signature. / Elafin-like / R-elafin / WAP-type 'four-disulfide core' domain / Elafin-like superfamily / WAP-type (Whey Acidic Protein) 'four-disulfide core' / WAP-type 'four-disulfide core' domain profile. ...Seminal vesicle protein I / Trappin protein transglutaminase-binding repeat / Trappin protein transglutaminase binding domain / Seminal vesicle protein I repeats signature. / Elafin-like / R-elafin / WAP-type 'four-disulfide core' domain / Elafin-like superfamily / WAP-type (Whey Acidic Protein) 'four-disulfide core' / WAP-type 'four-disulfide core' domain profile. / Four-disulfide core domains / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGewe, M.M. / Rupert, P. / Strong, R.K.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Screening, large-scale production and structure-based classification of cystine-dense peptides.
Authors: Correnti, C.E. / Gewe, M.M. / Mehlin, C. / Bandaranayake, A.D. / Johnsen, W.A. / Rupert, P.B. / Brusniak, M.Y. / Clarke, M. / Burke, S.E. / De Van Der Schueren, W. / Pilat, K. / Turnbaugh, S. ...Authors: Correnti, C.E. / Gewe, M.M. / Mehlin, C. / Bandaranayake, A.D. / Johnsen, W.A. / Rupert, P.B. / Brusniak, M.Y. / Clarke, M. / Burke, S.E. / De Van Der Schueren, W. / Pilat, K. / Turnbaugh, S.M. / May, D. / Watson, A. / Chan, M.K. / Bahl, C.D. / Olson, J.M. / Strong, R.K.
History
DepositionAug 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elafin
B: Elafin
C: Elafin
D: Elafin
E: Elafin
F: Elafin
G: Elafin
H: Elafin
I: Elafin
J: Elafin
K: Elafin
L: Elafin
M: Elafin
N: Elafin
O: Elafin
P: Elafin
Q: Elafin
R: Elafin


Theoretical massNumber of molelcules
Total (without water)110,85018
Polymers110,85018
Non-polymers00
Water5,621312
1
A: Elafin


Theoretical massNumber of molelcules
Total (without water)6,1581
Polymers6,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Elafin


Theoretical massNumber of molelcules
Total (without water)6,1581
Polymers6,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Elafin


Theoretical massNumber of molelcules
Total (without water)6,1581
Polymers6,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Elafin


Theoretical massNumber of molelcules
Total (without water)6,1581
Polymers6,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Elafin


Theoretical massNumber of molelcules
Total (without water)6,1581
Polymers6,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Elafin


Theoretical massNumber of molelcules
Total (without water)6,1581
Polymers6,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Elafin


Theoretical massNumber of molelcules
Total (without water)6,1581
Polymers6,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Elafin


Theoretical massNumber of molelcules
Total (without water)6,1581
Polymers6,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Elafin


Theoretical massNumber of molelcules
Total (without water)6,1581
Polymers6,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Elafin


Theoretical massNumber of molelcules
Total (without water)6,1581
Polymers6,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Elafin


Theoretical massNumber of molelcules
Total (without water)6,1581
Polymers6,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Elafin


Theoretical massNumber of molelcules
Total (without water)6,1581
Polymers6,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: Elafin


Theoretical massNumber of molelcules
Total (without water)6,1581
Polymers6,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: Elafin


Theoretical massNumber of molelcules
Total (without water)6,1581
Polymers6,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: Elafin


Theoretical massNumber of molelcules
Total (without water)6,1581
Polymers6,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
P: Elafin


Theoretical massNumber of molelcules
Total (without water)6,1581
Polymers6,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
17
Q: Elafin


Theoretical massNumber of molelcules
Total (without water)6,1581
Polymers6,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
18
R: Elafin


Theoretical massNumber of molelcules
Total (without water)6,1581
Polymers6,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
19
B: Elafin
C: Elafin
G: Elafin
I: Elafin
N: Elafin
O: Elafin
P: Elafin
Q: Elafin

M: Elafin

A: Elafin
D: Elafin
F: Elafin
J: Elafin
R: Elafin

E: Elafin
H: Elafin
K: Elafin
L: Elafin


Theoretical massNumber of molelcules
Total (without water)110,85018
Polymers110,85018
Non-polymers00
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation4_564y,-x+1,z-1/41
crystal symmetry operation4_464y-1,-x+1,z-1/41
Buried area22480 Å2
ΔGint-171 kcal/mol
Surface area41760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.333, 71.333, 214.444
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Elafin / / Elastase-specific inhibitor / ESI / Peptidase inhibitor 3 / PI-3 / Protease inhibitor WAP3 / Skin- ...Elastase-specific inhibitor / ESI / Peptidase inhibitor 3 / PI-3 / Protease inhibitor WAP3 / Skin-derived antileukoproteinase / SKALP / WAP four-disulfide core domain protein 14


Mass: 6158.354 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PI3, WAP3, WFDC14 / Cell line (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: P19957
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4M Na malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→71.33 Å / Num. obs: 41565 / % possible obs: 99.2 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.028 / Net I/σ(I): 29.91
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.491 / Num. unique obs: 2035 / CC1/2: 0.94 / Rpim(I) all: 0.196 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FLE

1fle


Resolution: 2.4→71.33 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / SU B: 8.379 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.343 / ESU R Free: 0.249 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24825 2051 4.9 %RANDOM
Rwork0.19649 ---
obs0.19915 39448 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.584 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.4→71.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6305 0 0 312 6617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196491
X-RAY DIFFRACTIONr_bond_other_d0.0010.026178
X-RAY DIFFRACTIONr_angle_refined_deg1.1972.038812
X-RAY DIFFRACTIONr_angle_other_deg0.707314599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7365861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.20124.465159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92151147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9871535
X-RAY DIFFRACTIONr_chiral_restr0.0690.2993
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0226916
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02983
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0865.5813498
X-RAY DIFFRACTIONr_mcbond_other5.0765.583497
X-RAY DIFFRACTIONr_mcangle_it7.1939.3724341
X-RAY DIFFRACTIONr_mcangle_other7.1939.3744342
X-RAY DIFFRACTIONr_scbond_it5.486.2882993
X-RAY DIFFRACTIONr_scbond_other5.4796.292994
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.07210.3114471
X-RAY DIFFRACTIONr_long_range_B_refined10.15651.8776302
X-RAY DIFFRACTIONr_long_range_B_other10.17151.8936262
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.396→2.458 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 158 -
Rwork0.278 2852 -
obs--96.07 %

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