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- PDB-4yxh: Crystal structure of Deer prion protein complexed with POM1 FAB -

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Basic information

Entry
Database: PDB / ID: 4yxh
TitleCrystal structure of Deer prion protein complexed with POM1 FAB
Components
  • Major prion protein
  • POM1 FAB HEAVY CHAIN
  • POM1 FAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM / prion / antibody / Immune system complex
Function / homology
Function and homology information


side of membrane / protein homooligomerization / copper ion binding / Golgi apparatus / plasma membrane
Similarity search - Function
Prion protein signature 1. / Prion protein signature 2. / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain / Immunoglobulins ...Prion protein signature 1. / Prion protein signature 2. / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesOdocoileus hemionus (mule deer)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBaral, P.K. / Swayampakula, M. / James, M.N.G.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: X-ray structural and molecular dynamical studies of the globular domains of cow, deer, elk and Syrian hamster prion proteins.
Authors: Baral, P.K. / Swayampakula, M. / Aguzzi, A. / James, M.N.
History
DepositionMar 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major prion protein
H: POM1 FAB HEAVY CHAIN
L: POM1 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8884
Polymers62,8653
Non-polymers231
Water1,38777
1
A: Major prion protein


Theoretical massNumber of molelcules
Total (without water)15,9581
Polymers15,9581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6550 Å2
MethodPISA
2
H: POM1 FAB HEAVY CHAIN
L: POM1 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9303
Polymers46,9072
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-30 kcal/mol
Surface area20780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.282, 106.580, 75.775
Angle α, β, γ (deg.)90.00, 95.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Major prion protein / PrP


Mass: 15957.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Odocoileus hemionus (mule deer) / Gene: PRNP, PRP / Production host: Escherichia coli (E. coli) / References: UniProt: P47852
#2: Antibody POM1 FAB HEAVY CHAIN


Mass: 23397.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody POM1 FAB LIGHT CHAIN


Mass: 23509.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350, 0.1 M BIS-TRIS, 0.2 M lithium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 18203 / % possible obs: 98.4 % / Redundancy: 3.8 % / Rsym value: 0.12 / Net I/σ(I): 10
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H88, 4DGI

4h88

4dgi


Resolution: 2.7→38.326 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 31.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2879 920 5.1 %
Rwork0.2425 --
obs0.2449 18042 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→38.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4145 0 1 77 4223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0194250
X-RAY DIFFRACTIONf_angle_d2.6525774
X-RAY DIFFRACTIONf_dihedral_angle_d14.8171532
X-RAY DIFFRACTIONf_chiral_restr0.12635
X-RAY DIFFRACTIONf_plane_restr0.014744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.84240.39661360.31212438X-RAY DIFFRACTION99
2.8424-3.02050.30971130.27512439X-RAY DIFFRACTION98
3.0205-3.25360.27951270.2552419X-RAY DIFFRACTION97
3.2536-3.58080.31191330.2352458X-RAY DIFFRACTION99
3.5808-4.09840.29351420.23562446X-RAY DIFFRACTION99
4.0984-5.16150.26111360.21412415X-RAY DIFFRACTION97
5.1615-38.32940.2731330.25072507X-RAY DIFFRACTION99

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