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- PDB-3nr3: Crystal Structure of Human Peripheral Myelin Protein 2 -

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Basic information

Entry
Database: PDB / ID: 3nr3
TitleCrystal Structure of Human Peripheral Myelin Protein 2
ComponentsPMP2 protein
KeywordsTRANSPORT PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC / Transport
Function / homology
Function and homology information


membrane organization / cholesterol binding / fatty acid transport / fatty acid binding / myelin sheath / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
Myelin P2 protein / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / PALMITIC ACID / Myelin P2 protein / Myelin P2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsUgochukwu, E. / Pilka, E. / Phillips, C. / Yue, W.W. / Krojer, T. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. ...Ugochukwu, E. / Pilka, E. / Phillips, C. / Yue, W.W. / Krojer, T. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Kavanagh, K.L. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Human Peripheral Myelin Protein 2
Authors: Ugochukwu, E. / Pilka, E. / Phillips, C. / Yue, W.W. / Krojer, T. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Kavanagh, K.L. / Oppermann, U.
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: PMP2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5099
Polymers17,4061
Non-polymers1,1038
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.190, 67.190, 100.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PMP2 protein / / Peripheral myelin protein 2 / cDNA / FLJ92018 / Homo sapiens peripheral myelin protein 2 (PMP2) / mRNA


Mass: 17406.086 Da / Num. of mol.: 1 / Fragment: UNP residues 3-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hCG_21300, PMP2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q6FHL4, UniProt: P02689*PLUS

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Non-polymers , 7 types, 121 molecules

#2: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 2.5M ammonium_sulfate, Citrate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→42.92 Å / Num. obs: 17365 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 10.7
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.938 / Mean I/σ(I) obs: 2 / Num. unique all: 15462 / Rsym value: 0.938 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.6.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PMP

1pmp


Resolution: 1.95→42.92 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.671 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 877 5.1 %RANDOM
Rwork0.20573 ---
all0.20793 16432 --
obs0.20793 16432 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.718 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å20 Å2
2--1.24 Å20 Å2
3----2.47 Å2
Refinement stepCycle: LAST / Resolution: 1.95→42.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1056 0 68 113 1237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221143
X-RAY DIFFRACTIONr_bond_other_d0.0020.02813
X-RAY DIFFRACTIONr_angle_refined_deg1.4592.0141531
X-RAY DIFFRACTIONr_angle_other_deg0.8623.0031977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6085138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3522544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59215221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.987156
X-RAY DIFFRACTIONr_chiral_restr0.0740.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021193
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02207
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 64 -
Rwork0.304 1189 -
obs--100 %

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