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- PDB-8j8t: Crystal structure of calcium-saturated SRCR domain 11 of DMBT1 -

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Basic information

Entry
Database: PDB / ID: 8j8t
TitleCrystal structure of calcium-saturated SRCR domain 11 of DMBT1
ComponentsDeleted in malignant brain tumors 1 protein
KeywordsMETAL BINDING PROTEIN / Calcium-binding / scavenger receptor / SRCR domain / SALSA / DMBT1
Function / homology
Function and homology information


induction of bacterial agglutination / zymogen granule membrane / Surfactant metabolism / zymogen binding / scavenger receptor activity / pattern recognition receptor activity / epithelial cell differentiation / extracellular matrix / defense response / phagocytic vesicle membrane ...induction of bacterial agglutination / zymogen granule membrane / Surfactant metabolism / zymogen binding / scavenger receptor activity / pattern recognition receptor activity / epithelial cell differentiation / extracellular matrix / defense response / phagocytic vesicle membrane / calcium-dependent protein binding / protein transport / defense response to Gram-negative bacterium / defense response to virus / defense response to Gram-positive bacterium / innate immune response / extracellular space / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
SRCR domain signature. / Zona pellucida domain, conserved site / ZP domain signature. / : / : / ZP-N domain / Zona pellucida, ZP-C domain / ZP-C domain / Zona pellucida (ZP) domain / Scavenger receptor cysteine-rich domain ...SRCR domain signature. / Zona pellucida domain, conserved site / ZP domain signature. / : / : / ZP-N domain / Zona pellucida, ZP-C domain / ZP-C domain / Zona pellucida (ZP) domain / Scavenger receptor cysteine-rich domain / ZP domain profile. / Zona pellucida domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily
Similarity search - Domain/homology
Scavenger receptor cysteine-rich domain-containing protein DMBT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsZhang, C. / Lu, P. / Nagata, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP18H02151 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05771 Japan
Japan Society for the Promotion of Science (JSPS)JP19H03045 Japan
CitationJournal: To Be Published
Title: Crystal structure of Calcium-saturated SRCR domain 11 of SALSA
Authors: Zhang, C. / Lu, P. / Nagata, K.
History
DepositionMay 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deleted in malignant brain tumors 1 protein
B: Deleted in malignant brain tumors 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8628
Polymers25,6222
Non-polymers2406
Water4,252236
1
A: Deleted in malignant brain tumors 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9314
Polymers12,8111
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Deleted in malignant brain tumors 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9314
Polymers12,8111
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.197, 47.305, 69.833
Angle α, β, γ (deg.)90.00, 101.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Deleted in malignant brain tumors 1 protein / Glycoprotein 340 / Gp-340 / Hensin / Salivary agglutinin / SAG / Surfactant pulmonary-associated D- ...Glycoprotein 340 / Gp-340 / Hensin / Salivary agglutinin / SAG / Surfactant pulmonary-associated D-binding protein


Mass: 12810.994 Da / Num. of mol.: 2 / Fragment: SRCR domain 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DMBT1, GP340 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UGM3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.2 Å3/Da / Density % sol: 44.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Calcium acetate hydrate, 20% Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→38.9 Å / Num. obs: 35273 / % possible obs: 92.5 % / Redundancy: 1.79 % / CC1/2: 0.997 / Net I/σ(I): 10.61
Reflection shellResolution: 1.81→5.37 Å / Num. unique obs: 5540 / CC1/2: 0.933

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8J8D

8j8d


Resolution: 1.81→38.9 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.924 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23341 912 4.7 %RANDOM
Rwork0.16633 ---
obs0.16952 18416 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.502 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.01 Å2
2---0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.81→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 6 236 1946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0111746
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161418
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.6312374
X-RAY DIFFRACTIONr_angle_other_deg0.4751.5713308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4115226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.052514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41710242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022112
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02376
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_it1.7282.221910
X-RAY DIFFRACTIONr_mcbond_other1.722.222910
X-RAY DIFFRACTIONr_mcangle_it2.5553.3191134
X-RAY DIFFRACTIONr_mcangle_other2.5543.3231135
X-RAY DIFFRACTIONr_scbond_it2.2372.451836
X-RAY DIFFRACTIONr_scbond_other2.2262.446835
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2093.5891241
X-RAY DIFFRACTIONr_long_range_B_refined20.82547.3022699
X-RAY DIFFRACTIONr_long_range_B_other20.43943.5592519
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.853 Å
RfactorNum. reflection% reflection
Rfree0.272 78 -
Rwork0.267 1326 -
obs--97.23 %

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