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- PDB-3ppd: GGVLVN segment from Human Prostatic Acid Phosphatase Residues 260... -

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Basic information

Entry
Database: PDB / ID: 3ppd
TitleGGVLVN segment from Human Prostatic Acid Phosphatase Residues 260-265, involved in Semen-Derived Enhancer of Viral Infection
ComponentsGGVLVN peptide, amyloid forming segment
KeywordsPROTEIN FIBRIL / amyloid-like protofibril / amyloid fibrils
Function / homology
Function and homology information


thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / regulation of sensory perception of pain / acid phosphatase / lysophosphatidic acid phosphatase activity / acid phosphatase activity / XMP 5'-nucleosidase activity ...thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / regulation of sensory perception of pain / acid phosphatase / lysophosphatidic acid phosphatase activity / acid phosphatase activity / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / choline binding / nucleotide metabolic process / vesicle membrane / azurophil granule membrane / dephosphorylation / lysosome organization / phosphatase activity / purine nucleobase metabolic process / multivesicular body / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / filopodium / lipid metabolic process / apical part of cell / molecular adaptor activity / lysosome / lysosomal membrane / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Histidine acid phosphatases active site signature. / : / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily
Similarity search - Domain/homology
ACETIC ACID / Prostatic acid phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsZhao, A. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Nature / Year: 2011
Title: Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation.
Authors: Sievers, S.A. / Karanicolas, J. / Chang, H.W. / Zhao, A. / Jiang, L. / Zirafi, O. / Stevens, J.T. / Munch, J. / Baker, D. / Eisenberg, D.
History
DepositionNov 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GGVLVN peptide, amyloid forming segment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6833
Polymers5581
Non-polymers1252
Water181
1
A: GGVLVN peptide, amyloid forming segment
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)4,09918
Polymers3,3466
Non-polymers75312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
crystal symmetry operation4_645x+3/2,-y-1/2,-z1
Unit cell
Length a, b, c (Å)4.834, 17.682, 40.322
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide GGVLVN peptide, amyloid forming segment


Mass: 557.641 Da / Num. of mol.: 1 / Fragment: Residue 260-265 / Source method: obtained synthetically
Details: GGVLVN from human Prostatic Acid Phosphatase Residue 260-265, Amyloid forming segment, synthesized
Source: (synth.) Homo sapiens (human) / References: UniProt: P15309
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.55 Å3/Da / Density % sol: 20.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES pH6.0, 0.2M Zn(OAc)2, 10%(w/v)PEG-8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.5→80 Å / Num. all: 621 / Num. obs: 621 / % possible obs: 86.4 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.149 / Χ2: 0.999 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.552.60.256541.01174
1.55-1.623.40.334481.002164.9
1.62-1.694.40.295480.999182.8
1.69-1.784.20.186530.982185.5
1.78-1.894.40.206541.002190
1.89-2.046.60.231671.01189.3
2.04-2.246.10.177770.994197.5
2.24-2.565.90.192671.012190.5
2.56-3.235.80.118620.995196.9
3.23-804.70.09910.985191

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→20.16 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2026 / WRfactor Rwork: 0.1874 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8347 / SU B: 1.946 / SU ML: 0.066 / SU R Cruickshank DPI: 0.1011 / SU Rfree: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 61 10 %RANDOM
Rwork0.1779 ---
all0.1818 609 --
obs0.1818 609 87.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 17.52 Å2 / Biso mean: 9.4571 Å2 / Biso min: 5.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20.16 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms39 0 5 1 45
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.02241
X-RAY DIFFRACTIONr_bond_other_d0.0010.0220
X-RAY DIFFRACTIONr_angle_refined_deg1.2912.10954
X-RAY DIFFRACTIONr_angle_other_deg0.755351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.61755
X-RAY DIFFRACTIONr_dihedral_angle_2_deg57.108301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.476155
X-RAY DIFFRACTIONr_chiral_restr0.060.27
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0247
X-RAY DIFFRACTIONr_gen_planes_other00.025
X-RAY DIFFRACTIONr_mcbond_it0.7251.531
X-RAY DIFFRACTIONr_mcbond_other0.1681.513
X-RAY DIFFRACTIONr_mcangle_it1.266245
X-RAY DIFFRACTIONr_scbond_it1.593310
X-RAY DIFFRACTIONr_scangle_it2.7394.59
LS refinement shellResolution: 1.501→1.677 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.158 12 -
Rwork0.23 129 -
all-141 -
obs--73.44 %

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