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- PDB-5fwt: Wnt modulator Kremen crystal form I at 2.10A -

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Basic information

Entry
Database: PDB / ID: 5fwt
TitleWnt modulator Kremen crystal form I at 2.10A
ComponentsKREMEN PROTEIN 1
KeywordsSIGNALING PROTEIN / WNT / CELL SURFACE / SIGNALLING / MEMBRANE PROTEIN
Function / homology
Function and homology information


Signaling by LRP5 mutants / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / negative regulation of axon regeneration / cell communication / negative regulation of ossification / regulation of canonical Wnt signaling pathway / limb development / TCF dependent signaling in response to WNT / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway ...Signaling by LRP5 mutants / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / negative regulation of axon regeneration / cell communication / negative regulation of ossification / regulation of canonical Wnt signaling pathway / limb development / TCF dependent signaling in response to WNT / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / neuronal cell body / apoptotic process / membrane / plasma membrane
Similarity search - Function
Kremen / : / Carbohydrate-binding WSC / WSC domain / WSC domain profile. / present in yeast cell wall integrity and stress response component proteins / Plasminogen Kringle 4 / Plasminogen Kringle 4 / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. ...Kremen / : / Carbohydrate-binding WSC / WSC domain / WSC domain profile. / present in yeast cell wall integrity and stress response component proteins / Plasminogen Kringle 4 / Plasminogen Kringle 4 / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Kremen protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å
AuthorsZebisch, M. / Jackson, V.A. / Jones, E.Y.
CitationJournal: Structure / Year: 2016
Title: Structure of the Dual-Mode Wnt Regulator Kremen1 and Insight Into Ternary Complex Formation with Lrp6 and Dickkopf
Authors: Zebisch, M. / Jackson, V.A. / Zhao, Y. / Jones, E.Y.
History
DepositionFeb 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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: KREMEN PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3506
Polymers44,5521
Non-polymers7995
Water1,02757
1
A: KREMEN PROTEIN 1
hetero molecules

A: KREMEN PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,70112
Polymers89,1042
Non-polymers1,59710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3800 Å2
ΔGint-27.4 kcal/mol
Surface area25250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.538, 50.538, 187.402
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein KREMEN PROTEIN 1


Mass: 44551.777 Da / Num. of mol.: 1 / Fragment: ECD, RESIDUES 1-473
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q96MU8
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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 Å3/Da / Density % sol: 38 % / Description: NONE
Crystal growpH: 5.6 / Details: 1.000 M (NH4)H2PO4 0.100 M NA3CITRATE PH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→62.47 Å / Num. obs: 17089 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.1→62.47 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / SU B: 14.385 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23223 864 5.1 %RANDOM
Rwork0.18222 ---
obs0.18466 16170 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.142 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20.65 Å20 Å2
2--1.29 Å20 Å2
3----4.19 Å2
Refinement stepCycle: LAST / Resolution: 2.1→62.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 48 57 2406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192434
X-RAY DIFFRACTIONr_bond_other_d0.0030.022098
X-RAY DIFFRACTIONr_angle_refined_deg2.0051.9433317
X-RAY DIFFRACTIONr_angle_other_deg1.15434839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5345292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03623.445119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35415335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.521513
X-RAY DIFFRACTIONr_chiral_restr0.130.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212802
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02617
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_it1.4892.511171
X-RAY DIFFRACTIONr_mcbond_other1.4882.5091170
X-RAY DIFFRACTIONr_mcangle_it2.3073.761462
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2952.8781261
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 59 -
Rwork0.314 1166 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.1843-1.28110.95817.7365-1.19063.49520.1708-0.119-0.47160.0862-0.1118-0.3990.30740.2212-0.0590.03590.0126-0.00950.0232-0.00430.333627.7749-21.7897-12.0908
23.3396-0.4149-1.24693.4359-0.56022.57140.15820.0710.316-0.1191-0.09230.1006-0.36590.2602-0.06590.0654-0.0393-0.00350.0422-0.00740.332123.31922.8178-17.0772
33.30350.10670.93451.84870.2243.82550.07530.2203-0.2876-0.07290.0174-0.04360.2757-0.0638-0.09270.0252-0.00240.00670.0262-0.00040.35150.6624-8.8363-11.4133
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 117
2X-RAY DIFFRACTION2A118 - 212
3X-RAY DIFFRACTION3A213 - 322

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