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- PDB-1h8p: Bull seminal plasma PDC-109 fibronectin type II module -

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Basic information

Entry
Database: PDB / ID: 1h8p
TitleBull seminal plasma PDC-109 fibronectin type II module
ComponentsSEMINAL PLASMA PROTEIN PDC-109
KeywordsPHOSPHORYLCHOLINE-BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of sperm capacitation / phospholipid efflux / sperm capacitation / single fertilization / heparin binding / cell surface / extracellular space
Similarity search - Function
Seminal plasma protein, PDC-109-like / Fibronectin, type II, collagen-binding / Seminal Fluid Protein PDC-109 (Domain B) / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Kringle-like fold ...Seminal plasma protein, PDC-109-like / Fibronectin, type II, collagen-binding / Seminal Fluid Protein PDC-109 (Domain B) / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Kringle-like fold / Ribbon / Mainly Beta
Similarity search - Domain/homology
PHOSPHOCHOLINE / Seminal plasma protein PDC-109
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.82 Å
AuthorsWah, D.A. / Fernandez-Tornero, C. / Calvete, J.J. / Romero, A.
Citation
Journal: Structure / Year: 2002
Title: Sperm Coating Mechanism from the 1.8 A Crystal Structure of Pdc-109-Phosphorylcholine Complex
Authors: Wah, D.A. / Fernandez-Tornero, C. / Sanz, L. / Romero, A. / Calvete, J.J.
#1: Journal: Proteins: Struct.,Funct., Genet. / Year: 1997
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Bovine Seminal Plasma Pdc-109, a Protein Composed of Two Fibronectin Type II Domains
Authors: Romero, A. / Varela, P.F. / Topfer-Petersen, E. / Calvete, J.J.
History
DepositionFeb 14, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2002Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SEMINAL PLASMA PROTEIN PDC-109
B: SEMINAL PLASMA PROTEIN PDC-109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3596
Polymers25,6232
Non-polymers7374
Water3,693205
1
A: SEMINAL PLASMA PROTEIN PDC-109
B: SEMINAL PLASMA PROTEIN PDC-109
hetero molecules

A: SEMINAL PLASMA PROTEIN PDC-109
B: SEMINAL PLASMA PROTEIN PDC-109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,71912
Polymers51,2454
Non-polymers1,4738
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)90.881, 90.881, 52.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.93464, -0.35469, -0.02529), (0.35552, 0.93354, 0.04599), (0.0073, -0.05198, 0.99862)
Vector: 44.11178, -15.60781, 9.35187)
DetailsTHE PROTEIN IS ACTIVE AS HOMODIMER.

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Components

#1: Protein SEMINAL PLASMA PROTEIN PDC-109


Mass: 12811.352 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-134 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Tissue: SPERM / References: UniProt: P02784
#2: Chemical
ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H15NO4P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SWS ENTRY INCLUDES A PEPTIDE SIGNAL OF 25 AA.

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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: 2.43 Å3/Da / Density % sol: 49.1 %
Description: MAD EXPERIMENT WAS UNDERTAKEN AT DESY-HAMBURG (X31). A NATIVE DATA SET WAS COLLECTED AT ELETTRA (BEAMLINE 5.2 R).
Crystal growpH: 7.2
Details: CRYSTALS WERE OBTAINED IN 30% ISOPROPANOL, 5% PEG 4000, 0.1 M HEPES, PH 7.2.
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
250 mg/mlo-phosphorylcholine1drop
330 %(v/v)isopropanol1reservoir
48 %(w/v)PEG40001reservoir
50.1 Mimidazole1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.07466,1.07516,0.8856, 1.05271
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 2000 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.074661
21.075161
30.88561
41.052711
ReflectionResolution: 1.82→30 Å / Num. obs: 275885 / % possible obs: 99 % / Redundancy: 5.3 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 11.7
Reflection shellResolution: 1.82→1.92 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 5.3 / % possible all: 96.3
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 22445 / % possible obs: 99 % / Num. measured all: 275885 / Rmerge(I) obs: 0.032
Reflection shell
*PLUS
% possible obs: 96.3 % / Rmerge(I) obs: 0.119

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.82→16.32 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1454528.39 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE FIRST 21 RESIDUES (ASP 1-ASP 21) WERE NOT VISIBLE IN THE ELECTRON DENSITY MAPS AT 1.82 A RESOLUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1537 6.9 %RANDOM
Rwork0.207 ---
obs0.207 22379 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.4559 Å2 / ksol: 0.503596 e/Å3
Displacement parametersBiso mean: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.64 Å20.54 Å20 Å2
2--2.64 Å20 Å2
3----5.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.04 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.82→16.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 44 205 1737
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.932.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.211 173 5.7 %
Rwork0.202 2859 -
obs--79.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PCH_PAR.TXTPCH_TOP.TXT
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.69
LS refinement shell
*PLUS
Rfactor obs: 0.202

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