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- PDB-8j8d: Crystal structure of SRCR domain 11 of DMBT1 -

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Basic information

Entry
Database: PDB / ID: 8j8d
TitleCrystal structure of SRCR domain 11 of DMBT1
ComponentsDeleted in malignant brain tumors 1 protein
KeywordsMETAL BINDING PROTEIN / scavenger receptor cysteine-rich domain / Salivary scavenger and agglutinin
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
Zona pellucida domain, conserved site / ZP domain signature. / : / : / ZP-N domain / SRCR domain signature. / Zona pellucida, ZP-C domain / ZP-C domain / Zona pellucida (ZP) domain / ZP domain profile. ...Zona pellucida domain, conserved site / ZP domain signature. / : / : / ZP-N domain / SRCR domain signature. / Zona pellucida, ZP-C domain / ZP-C domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain / Scavenger receptor cysteine-rich 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: 1.51 Å
AuthorsZhang, C. / Lu, P. / Nagata, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP18H02151 Japan
CitationJournal: Protein J. / Year: 2024
Title: Refolding, Crystallization, and Crystal Structure Analysis of a Scavenger Receptor Cysteine-Rich Domain of Human Salivary Agglutinin Expressed in Escherichia coli.
Authors: Zhang, C. / Lu, P. / Wei, S. / Hu, C. / Miyoshi, M. / Okamoto, K. / Itoh, H. / Okuda, S. / Suzuki, M. / Kawakami, H. / Nagata, K.
History
DepositionMay 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Dec 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7513
Polymers12,6801
Non-polymers712
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.802, 31.705, 35.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 12679.798 Da / Num. of mol.: 1 / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 1.96 Å3/Da / Density % sol: 37.32 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.2 M Ammonium iodide, 20% PEG3350

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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: 1.51→40.9 Å / Num. obs: 22788 / % possible obs: 98.7 % / Redundancy: 2.94 % / CC1/2: 0.999 / Net I/σ(I): 27.02
Reflection shellResolution: 1.51→4.49 Å / Num. unique obs: 3604 / CC1/2: 0.993

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S5A

6s5a


Resolution: 1.51→40.9 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.151 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17225 742 5.1 %RANDOM
Rwork0.13814 ---
obs0.13999 13685 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.012 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.51→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms813 0 2 154 969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.011834
X-RAY DIFFRACTIONr_bond_other_d0.0020.016676
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.6311135
X-RAY DIFFRACTIONr_angle_other_deg0.6611.5731576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1755107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.09257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82810114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1080.2115
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021010
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02182
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_it1.4721.089431
X-RAY DIFFRACTIONr_mcbond_other1.4421.088431
X-RAY DIFFRACTIONr_mcangle_it2.3371.624537
X-RAY DIFFRACTIONr_mcangle_other2.3361.632538
X-RAY DIFFRACTIONr_scbond_it2.0741.331403
X-RAY DIFFRACTIONr_scbond_other2.0331.319402
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0631.926599
X-RAY DIFFRACTIONr_long_range_B_refined27.27246.211500
X-RAY DIFFRACTIONr_long_range_B_other26.69730.8971252
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.51→1.545 Å
RfactorNum. reflection% reflection
Rfree0.194 31 -
Rwork0.175 687 -
obs--65.15 %

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