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- PDB-9x64: Crystal structure of DKK4 CRD1 domain -

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Basic information

Entry
Database: PDB / ID: 9x64
TitleCrystal structure of DKK4 CRD1 domain
ComponentsDickkopf-related protein 4
KeywordsSIGNALING PROTEIN / Wnt signaling / Cystein-rich domain 1
Function / homology
Function and homology information


Signaling by LRP5 mutants / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / receptor antagonist activity / co-receptor binding / negative regulation of Wnt signaling pathway / TCF dependent signaling in response to WNT / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / :
Similarity search - Function
: / Dickkopf, N-terminal cysteine-rich / Dickkopf-like protein / : / : / Dickkopf N-terminal cysteine-rich region / Dickkopf-related protein 1/2/4, C-terminal subdomain 2 / Dickkopf-related protein 1/2/4, C-terminal subdomain 1
Similarity search - Domain/homology
NITRATE ION / Dickkopf-related protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsShibata, N.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H02420 Japan
Japan Society for the Promotion of Science (JSPS)24K09357 Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2026
Title: Crystal structure of human Dickkopf 4 cysteine-rich domain 1 and evaluation of conformational rigidity.
Authors: Shibata, N.
History
DepositionOct 14, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dickkopf-related protein 4
B: Dickkopf-related protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6915
Polymers15,5322
Non-polymers1593
Water1,42379
1
A: Dickkopf-related protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8633
Polymers7,7661
Non-polymers972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area4160 Å2
MethodPISA
2
B: Dickkopf-related protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8282
Polymers7,7661
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.170, 67.550, 32.790
Angle α, β, γ (deg.)90.000, 91.648, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Dickkopf-related protein 4 / Dickkopf-4 / Dkk-4 / hDkk-4


Mass: 7765.907 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKK4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UBT3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.65 Å3/Da / Density % sol: 25.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M Ammonium nitrate and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 31, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→33.78 Å / Num. obs: 8880 / % possible obs: 99.1 % / Redundancy: 4.6 % / Biso Wilson estimate: 18.79 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.18 / Rrim(I) all: 0.203 / Net I/σ(I): 5.77
Reflection shellResolution: 1.83→1.94 Å / Redundancy: 3.59 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 1.57 / Num. unique obs: 1421 / CC1/2: 0.682 / Rrim(I) all: 0.682 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→33.77 Å / SU ML: 0.2088 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.4358
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2457 881 9.97 %
Rwork0.1851 7957 -
obs0.1911 8838 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.58 Å2
Refinement stepCycle: LAST / Resolution: 1.83→33.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms848 0 9 79 936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066903
X-RAY DIFFRACTIONf_angle_d0.7731214
X-RAY DIFFRACTIONf_chiral_restr0.0412137
X-RAY DIFFRACTIONf_plane_restr0.0112165
X-RAY DIFFRACTIONf_dihedral_angle_d14.8902362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.940.29881400.24561303X-RAY DIFFRACTION97.3
1.94-2.090.29131470.19551329X-RAY DIFFRACTION99.73
2.09-2.310.2711520.19151341X-RAY DIFFRACTION99.6
2.31-2.640.22111470.19371318X-RAY DIFFRACTION99.52
2.64-3.320.25931500.19351336X-RAY DIFFRACTION99.13
3.33-33.770.21421450.15931330X-RAY DIFFRACTION97.88
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)
14.8393876311-2.49538573416-0.0173435656084.82284688271-0.5799436915861.97411324272-0.006834730837570.4702432894360.00761685553638-0.431708295634-0.0606269995024-0.3398448633810.04814642006640.08304726729660.06044748057180.340860650641-0.06538850370570.06900823160620.171798655462-0.013389110920.22915232275-2.27030439109-5.6769426516-9.14798427603
28.00076569267-0.9656693047-0.263683658457.698025650572.451475075335.809699250680.0583637391854-1.010834777070.4472937705530.755820015155-0.1378866952670.464598619423-0.71664374485-0.3606993885630.04826923264550.3739894857280.01275385872030.06926870806570.2771465867910.008562260675520.231880587864-8.60586437005-3.713276017610.208049649172
32.991545524390.5345849615230.4037294415451.46936619471-0.8057911027973.349545584260.0409077636498-0.0911468664249-0.2049816779340.0777826330924-0.0182110024481-0.0900529724821-0.02248153285920.142880319898-0.05281940237460.1079873108190.00986256181794-0.003998771588920.09683275452070.01360179351160.123766566319-6.59793178373-16.00953391-4.74787466233
45.893794618350.4187092600335.369238201333.07326132374-3.191471297279.103470269930.01129163857460.541617867588-0.406579841418-0.1358070415210.20535325324-0.3629988009820.205113136686-0.214635284584-0.2006177441090.170034780062-0.01222347729010.03091756289570.175020593431-0.04808492053350.181715099449-11.4562387859-22.7738440608-8.43205001158
53.5331537971.19848613978-0.06039069821253.574748811141.438611334162.190773330880.01548516363860.300956174727-0.18499053774-0.0321396364341-0.0207818616922-0.08760255227580.241975470989-0.18018674997-0.06594309980530.09894388256380.0184739897707-0.00444647957130.150923069978-0.02242661236790.132434274598-1.83110271438-25.1166739229.92189436603
61.21216703722-0.444514322916-1.171631870971.763139894890.68225881511.951026281310.001969488263240.01451695326560.08022055846630.000625682720673-0.01336162554140.0207480369399-0.041702817683-0.0155872840148-0.005053303375150.1028449693950.0220783753926-0.003713282620960.1643909409420.02327902103070.160044262731-11.5284237753-18.622967908611.1364971048
72.199960833490.4974229455892.500335776894.89295737675-3.238569742526.3325794283-0.131627133107-0.3590443502280.265619152121-0.167382839702-0.109784100114-0.477836972985-1.00142429872-0.2954384832830.2474933429260.2254273594580.05582158740570.02949863702850.2936226186360.01829732914880.166974919474-15.3338540821-10.86628550049.29169051339
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 39 through 50 )AA39 - 501 - 12
22chain 'A' and (resid 51 through 61 )AA51 - 6113 - 23
33chain 'A' and (resid 62 through 83 )AA62 - 8324 - 45
44chain 'A' and (resid 84 through 93 )AA84 - 9346 - 55
55chain 'B' and (resid 39 through 61 )BB39 - 611 - 23
66chain 'B' and (resid 62 through 82 )BB62 - 8224 - 44
77chain 'B' and (resid 83 through 93 )BB83 - 9345 - 55

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