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- PDB-3q2u: Structure of Human Glioma Pathogenesis-related Protein 1 Reveals ... -

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Basic information

Entry
Database: PDB / ID: 3q2u
TitleStructure of Human Glioma Pathogenesis-related Protein 1 Reveals Unique loops and surface motifs.
ComponentsGlioma pathogenesis-related protein 1
KeywordsMEMBRANE PROTEIN / CRISP / human glioma pathogenesis-related protein 1 (GLIPR1) / RTVP1
Function / homology
Function and homology information


azurophil granule membrane / PPARA activates gene expression / Neutrophil degranulation / extracellular space / membrane / plasma membrane
Similarity search - Function
Glioma pathogenesis-related protein 1-like, SCP domain / Venom allergen 5-like / CRISP family signature 2. / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / Pathogenesis-related Protein p14a / CAP / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain ...Glioma pathogenesis-related protein 1-like, SCP domain / Venom allergen 5-like / CRISP family signature 2. / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / Pathogenesis-related Protein p14a / CAP / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / CAP superfamily / Cysteine-rich secretory protein family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glioma pathogenesis-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsAsojo, O.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structural studies of human glioma pathogenesis-related protein 1.
Authors: Asojo, O.A. / Koski, R.A. / Bonafe, N.
History
DepositionDec 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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: Glioma pathogenesis-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6925
Polymers23,3231
Non-polymers3684
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.077, 79.532, 38.849
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Glioma pathogenesis-related protein 1 / GliPR 1 / Protein RTVP-1


Mass: 23323.301 Da / Num. of mol.: 1 / Fragment: UNP residues 22-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLIPR, GLIPR1, RTVP1, synthesized / Plasmid: pPicZalpha / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: P48060
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.085M MES, 25.5% w/v PEG 5000 MME, 0.17M Ammonium sulfate 15% v/v glycerol, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.514 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: May 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 1.85→29.04 Å / Num. obs: 23229 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 16237 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CrysalisProdata collection
PHASERphasing
REFMAC5.5.0109refinement
CrysalisProdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q2R

3q2r


Resolution: 1.85→27.79 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.736 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18421 1187 5.1 %RANDOM
Rwork0.13402 ---
obs0.13662 21977 99.75 %-
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: 20.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2---3.5 Å20 Å2
3---4.25 Å2
Refinement stepCycle: LAST / Resolution: 1.85→27.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1532 0 24 190 1746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221607
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8881.9282186
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9225194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5724.34276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46315247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.186157
X-RAY DIFFRACTIONr_chiral_restr0.1510.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211238
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.1281.5968
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.29421571
X-RAY DIFFRACTIONr_scbond_it5.2873639
X-RAY DIFFRACTIONr_scangle_it7.6124.5614
X-RAY DIFFRACTIONr_rigid_bond_restr2.82431607
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 88 -
Rwork0.1 1524 -
obs--97.82 %

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