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- PDB-3q2r: crystal structure of sGLIPR1 soaked with zinc chloride -

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Basic information

Entry
Database: PDB / ID: 3q2r
Titlecrystal structure of sGLIPR1 soaked with zinc chloride
ComponentsGlioma pathogenesis-related protein 1
KeywordsMEMBRANE PROTEIN / Glioma / 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: 2.2 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 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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_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

Downloads & links

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Assembly

Deposited unit
A: Glioma pathogenesis-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3892
Polymers23,3231
Non-polymers651
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.920, 79.720, 38.760
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.85 Å3/Da / Density % sol: 56.78 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 0.085M sodium cacodylate, 25.5%w/v PEG8000, 0.17M Ammonium sulfate, 15% glycerol 0.2mM Zinc Chloride, 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
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Dec 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2→27.79 Å / Num. obs: 18698 / % possible obs: 99.4 % / Observed criterion σ(I): 3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.179 / Net I/σ(I): 7.9
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2.5 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIXdev_777refinement
PHASERphasing
REFMAC5.5.0109refinement
CrysalisProdata reduction
SCALAdata scaling
CrysalisProdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RC9

1rc9


Resolution: 2.2→27.788 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.894 / SU ML: 0.35 / σ(F): 0 / Phase error: 16.09 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.192 703 5.01 %
Rwork0.1584 --
obs0.1601 14042 99.54 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.496 Å2 / ksol: 0.416 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.0529 Å2-0 Å2-0 Å2
2---1.0231 Å20 Å2
3----0.6412 Å2
Refinement stepCycle: LAST / Resolution: 2.2→27.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1527 0 1 208 1736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071588
X-RAY DIFFRACTIONf_angle_d0.9822157
X-RAY DIFFRACTIONf_dihedral_angle_d12.974569
X-RAY DIFFRACTIONf_chiral_restr0.071225
X-RAY DIFFRACTIONf_plane_restr0.004282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.36980.20471420.14622600X-RAY DIFFRACTION100
2.3698-2.60810.19661490.14052625X-RAY DIFFRACTION100
2.6081-2.98520.16581510.14212628X-RAY DIFFRACTION100
2.9852-3.75950.20131340.14682664X-RAY DIFFRACTION100
3.7595-27.79040.19271270.19892822X-RAY DIFFRACTION99

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