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- PDB-4a1y: Human myelin P2 protein, K65Q mutant -

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Basic information

Entry
Database: PDB / ID: 4a1y
TitleHuman myelin P2 protein, K65Q mutant
ComponentsMYELIN P2 PROTEIN
KeywordsTRANSPORT
Function / homology
Function and homology information


membrane organization / cholesterol binding / fatty acid transport / fatty acid binding / myelin sheath / extracellular exosome / nucleus / cytosol
Similarity search - Function
Myelin P2 protein / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PALMITIC ACID / Myelin P2 protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLehtimaki, M. / Kursula, P.
CitationJournal: To be Published
Title: Structure-Function Relationships in the Myelin Peripheral Membrane Protein P2
Authors: Lehtimaki, M. / Kursula, P.
History
DepositionSep 20, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Apr 8, 2020Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_sf
Revision 1.3Dec 20, 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 / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: MYELIN P2 PROTEIN
B: MYELIN P2 PROTEIN
C: MYELIN P2 PROTEIN
D: MYELIN P2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,09411
Polymers59,9624
Non-polymers1,1327
Water17,240957
1
A: MYELIN P2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2823
Polymers14,9901
Non-polymers2922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MYELIN P2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2472
Polymers14,9901
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MYELIN P2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2823
Polymers14,9901
Non-polymers2922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MYELIN P2 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2823
Polymers14,9901
Non-polymers2922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.030, 83.030, 77.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
MYELIN P2 PROTEIN / PERIPHERAL MYELIN PROTEIN 2


Mass: 14990.419 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTH27 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P02689
#2: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 957 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 66 TO GLN ENGINEERED RESIDUE IN CHAIN B, LYS 66 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, LYS 66 TO GLN ENGINEERED RESIDUE IN CHAIN B, LYS 66 TO GLN ENGINEERED RESIDUE IN CHAIN C, LYS 66 TO GLN ENGINEERED RESIDUE IN CHAIN D, LYS 66 TO GLN

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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: 2.24 Å3/Da / Density % sol: 45.07 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.03317
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
111.000H, 1.000K, L10.609
111.000K, 1.000H, -L20.391
ReflectionResolution: 1.2→20 Å / Num. obs: 154219 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.5
Reflection shellResolution: 1.2→1.23 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.4 / % possible all: 63.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WUT

2wut


Resolution: 1.2→20 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.508 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.008 / ESU R Free: 0.008 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.15382 1809 1.2 %RANDOM
Rwork0.13117 ---
obs0.13145 152369 93.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.485 Å2
Baniso -1Baniso -2Baniso -3
1-8.15 Å20 Å20 Å2
2--8.15 Å20 Å2
3----16.29 Å2
Refinement stepCycle: LAST / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4192 0 75 957 5224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224773
X-RAY DIFFRACTIONr_bond_other_d0.0010.023434
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9766432
X-RAY DIFFRACTIONr_angle_other_deg0.79938484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0525623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52525.079189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80115996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.821528
X-RAY DIFFRACTIONr_chiral_restr0.0810.2723
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025327
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02908
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_it2.20222919
X-RAY DIFFRACTIONr_mcbond_other0.56721202
X-RAY DIFFRACTIONr_mcangle_it3.28344792
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.98661854
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.81981640
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.5638207
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.201→1.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 84 -
Rwork0.249 7450 -
obs--62.47 %

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