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- PDB-1spp: THE CRYSTAL STRUCTURES OF TWO MEMBERS OF THE SPERMADHESIN FAMILY ... -

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Basic information

Entry
Database: PDB / ID: 1spp
TitleTHE CRYSTAL STRUCTURES OF TWO MEMBERS OF THE SPERMADHESIN FAMILY REVEAL THE FOLDING OF THE CUB DOMAIN
Components
  • MAJOR SEMINAL PLASMA GLYCOPROTEIN PSP-I
  • MAJOR SEMINAL PLASMA GLYCOPROTEIN PSP-II
KeywordsCOMPLEX (SEMINAL PLASMA PROTEIN/SPP) / SEMINAL PLASMA PROTEINS / SPERMADHESINS / CUB DOMAIN ARCHITECTURE / COMPLEX (SEMINAL PLASMA PROTEIN-SPP) / COMPLEX (SEMINAL PLASMA PROTEIN-SPP) complex
Function / homology
Function and homology information


single fertilization / extracellular region
Similarity search - Function
Spermadhesin / Spermadhesins family signature 1. / Spermadhesins family signature 2. / Spermadhesin, CUB domain / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Jelly Rolls ...Spermadhesin / Spermadhesins family signature 1. / Spermadhesins family signature 2. / Spermadhesin, CUB domain / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major seminal plasma glycoprotein PSP-I / Major seminal plasma glycoprotein PSP-II
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.4 Å
AuthorsRomero, A. / Romao, M.J. / Varela, P.F. / Kolln, I. / Dias, J.M. / Carvalho, A.L. / Sanz, L. / Topfer-Petersen, E. / Calvete, J.J.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: The crystal structures of two spermadhesins reveal the CUB domain fold.
Authors: Romero, A. / Romao, M.J. / Varela, P.F. / Kolln, I. / Dias, J.M. / Carvalho, A.L. / Sanz, L. / Topfer-Petersen, E. / Calvete, J.J.
#1: Journal: FEBS Lett. / Year: 1996
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Boar Seminal Plasma Spermadhesin Psp-I/Psp-II, a Heterodimer of Two Cub Domains
Authors: Romero, A. / Varela, P.F. / Sanz, L. / Topfer-Petersen, E. / Calvete, J.J.
#2: Journal: FEBS Lett. / Year: 1995
Title: Boar Spermadhesin Psp-II: Location of Posttranslational Modifications, Heterodimer Formation with Psp-I Glycoforms and Effect of Dimerization on the Ligand-Binding Capabilities of the Subunits
Authors: Calvete, J.J. / Mann, K. / Schafer, W. / Raida, M. / Sanz, L. / Topfer-Petersen, E.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: The Cub Domain. A Widespread Module in Developmentally Regulated Proteins
Authors: Bork, P. / Beckmann, G.
History
DepositionJun 19, 1997Processing site: BNL
Revision 1.0Jun 24, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAJOR SEMINAL PLASMA GLYCOPROTEIN PSP-I
B: MAJOR SEMINAL PLASMA GLYCOPROTEIN PSP-II


Theoretical massNumber of molelcules
Total (without water)24,6562
Polymers24,6562
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.370, 96.370, 71.320
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 MAJOR SEMINAL PLASMA GLYCOPROTEIN PSP-I


Mass: 11997.683 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PLASMA / Tissue: SPERM / References: UniProt: P35495
#2: Protein MAJOR SEMINAL PLASMA GLYCOPROTEIN PSP-II


Mass: 12658.431 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PLASMA / Tissue: SPERM / References: UniProt: P35496
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsANALYSIS OF CDNAS CODING FOR BOAR SEMINAL PLASMA PSP-I AND PSP-II INDICATED THAT THE FULL-LENGTH ...ANALYSIS OF CDNAS CODING FOR BOAR SEMINAL PLASMA PSP-I AND PSP-II INDICATED THAT THE FULL-LENGTH AMINO ACIDS SEQUENCES OF THE PROTEINS CONTAIN 112 AND 116 RESIDUES, RESPECTIVELY. HOWEVER, THE MATURE PSP-I/PSP-II HETERODIMER FORM ISOLATED FROM ITS NATURAL SOURCE, THE BOAR SEMINAL PLASMA, LACKS THE FIRST THREE N-TERMINAL RESIDUES OF THE PSP-I SUBUNIT. THIS WAS CONFIRMED BY N-TERMINAL AMINO ACID SEQUENCES ANALYSIS OF HEXAGONAL AND TRIGONAL CRYSTALLINE PSP-I/PSP-II COMPLEX. THUS THE CRYSTAL STRUCTURE OS PSP-I/PSP-II REPORTED HERE CORRESPONDS TO RESIDUES LEU 4 - GLN 112 AND ALA 1 - TYR 116 OF PSP-I AND PSP-II, RESPECTIVELY.

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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: 3.21 Å3/Da / Density % sol: 62 %
Description: HEAVY-ATOM DERIVATIVES FOR MIR WERE PREPARED BY USING HEXAGONAL CRYSTALS OF THE PSP-I/PSP-II (CRYSTALS DIFFRACTED UP TO 3.0 A). MIR PHASES WERE CALCULATED USING MLPHARE AFTER SCALING BY ...Description: HEAVY-ATOM DERIVATIVES FOR MIR WERE PREPARED BY USING HEXAGONAL CRYSTALS OF THE PSP-I/PSP-II (CRYSTALS DIFFRACTED UP TO 3.0 A). MIR PHASES WERE CALCULATED USING MLPHARE AFTER SCALING BY SCALEIT. THE MODEL OBTAINED FOR THE HEXAGONAL CRYSTAL FORM WAS USED AS A SEARCH MODEL FOR REFINING THE STRUCTURE IN THE TRIGONAL CRYSTALS TO 2.4 A RESOLUTION BY MOLECULAR REPLACEMENT USING AMORE
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 30% (W/V) PEG 2000, 100 MM AMMONIUM ACETATE, PH 6.5. THE INITIAL PROTEIN CONCENTRATION WAS 15 MG/ML
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
250 mMsodium phosphate1drop
330 %(w/v)PEG20001reservoir
40.1 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 285 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→28.94 Å / Num. obs: 14809 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 45.2 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.08 / Net I/σ(I): 7.1
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3 / Rsym value: 0.265 / % possible all: 98.4
Reflection
*PLUS
Num. measured all: 61270
Reflection shell
*PLUS
% possible obs: 98.4 % / Rmerge(I) obs: 0.265

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
CCP4model building
PROTEINmodel building
X-PLOR3.1refinement
CCP4(ROTAVATA)data scaling
CCP4phasing
PROTEINphasing
RefinementMethod to determine structure: MIR / Resolution: 2.4→8 Å / Data cutoff high absF: 735.54 / Data cutoff low absF: 3.29 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 -10 %RANDOM
Rwork0.2 ---
obs0.2 14291 97 %-
Displacement parametersBiso mean: 31.71 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 0 79 1767
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.657
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.39
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.195
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it22
X-RAY DIFFRACTIONx_mcangle_it2.52.5
X-RAY DIFFRACTIONx_scbond_it2.52.5
X-RAY DIFFRACTIONx_scangle_it33
LS refinement shellResolution: 2.4→2.51 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.345 --
Rwork0.331 1647 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAMCSDX.PROTOPHCSD.PRO
X-RAY DIFFRACTION2PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1F / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.39
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.195

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