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- PDB-8wzs: Crystal structure of SRCRD11 of human DMBT1 from needle-shape crystal -

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Basic information

Entry
Database: PDB / ID: 8wzs
TitleCrystal structure of SRCRD11 of human DMBT1 from needle-shape crystal
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
: / : / ZP-N domain / SRCR domain signature. / Zona pellucida domain, conserved site / ZP domain signature. / Zona pellucida, ZP-C domain / ZP-C domain / Zona pellucida (ZP) domain / Scavenger receptor cysteine-rich domain ...: / : / ZP-N domain / SRCR domain signature. / Zona pellucida domain, conserved site / ZP domain signature. / 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: 2.54 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
DepositionNov 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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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


Theoretical massNumber of molelcules
Total (without water)12,6801
Polymers12,6801
Non-polymers00
Water1,49583
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)71.114, 71.114, 55.387
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 3.19 Å3/Da / Density % sol: 61.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Lithium citrate tribasic tetrahydrate, 25% w/v Polyethylene glycol 3,350

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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, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.54→41.18 Å / Num. obs: 8237 / % possible obs: 99.73 % / Redundancy: 5.11 % / CC1/2: 0.998 / Net I/σ(I): 13.12
Reflection shellResolution: 2.54→7.51 Å / Num. unique obs: 1637 / CC1/2: 0.634

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AS5

6as5


Resolution: 2.54→41.18 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.105 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24292 257 4.6 %RANDOM
Rwork0.17593 ---
obs0.17923 5307 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.817 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å2-0 Å2
2--0.03 Å20 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.54→41.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms807 0 0 83 890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.011832
X-RAY DIFFRACTIONr_bond_other_d0.0010.016672
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.6331135
X-RAY DIFFRACTIONr_angle_other_deg0.6161.5731566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1315106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.75757
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.73510113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02181
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_it5.8186.194427
X-RAY DIFFRACTIONr_mcbond_other5.8146.192427
X-RAY DIFFRACTIONr_mcangle_it7.7979.275532
X-RAY DIFFRACTIONr_mcangle_other7.7949.289533
X-RAY DIFFRACTIONr_scbond_it6.7746.764405
X-RAY DIFFRACTIONr_scbond_other6.6836.755404
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.2949.956604
X-RAY DIFFRACTIONr_long_range_B_refined14.96994.2461037
X-RAY DIFFRACTIONr_long_range_B_other15.02792.0831018
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.54→2.606 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 24 -
Rwork0.231 358 -
obs--99.22 %

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