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- PDB-1qqs: NEUTROPHIL GELATINASE ASSOCIATED LIPOCALIN HOMODIMER -

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Basic information

Entry
Database: PDB / ID: 1qqs
TitleNEUTROPHIL GELATINASE ASSOCIATED LIPOCALIN HOMODIMER
ComponentsNEUTROPHIL GELATINASE
KeywordsSUGAR BINDING PROTEIN / NEUTROPHIL LIPOCALIN / SIGNAL PROTEIN / GLYCOPROTEIN
Function / homology
Function and homology information


positive regulation of iron ion import across plasma membrane / positive regulation of hippocampal neuron apoptotic process / positive regulation of endothelial tube morphogenesis / negative regulation of hippocampal neuron apoptotic process / positive regulation of cell projection organization / Metal sequestration by antimicrobial proteins / siderophore transport / response to kainic acid / response to mycotoxin / cellular response to increased oxygen levels ...positive regulation of iron ion import across plasma membrane / positive regulation of hippocampal neuron apoptotic process / positive regulation of endothelial tube morphogenesis / negative regulation of hippocampal neuron apoptotic process / positive regulation of cell projection organization / Metal sequestration by antimicrobial proteins / siderophore transport / response to kainic acid / response to mycotoxin / cellular response to increased oxygen levels / response to blue light / response to fructose / cellular response to X-ray / short-term memory / cellular response to interleukin-6 / enterobactin binding / iron ion sequestering activity / response to herbicide / response to iron(II) ion / positive regulation of reactive oxygen species biosynthetic process / cellular response to interleukin-1 / long-term memory / cellular response to nutrient levels / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of endothelial cell migration / acute-phase response / Iron uptake and transport / cellular response to nerve growth factor stimulus / response to virus / specific granule lumen / cellular response to hydrogen peroxide / cellular response to amyloid-beta / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / cellular response to lipopolysaccharide / protease binding / Interleukin-4 and Interleukin-13 signaling / cellular response to hypoxia / defense response to bacterium / iron ion binding / response to xenobiotic stimulus / innate immune response / Neutrophil degranulation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DECANOIC ACID / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsGoetz, D.H. / Willie, S.T. / Armen, R. / Bratt, T. / Borregaard, N. / Strong, R.K.
CitationJournal: Biochemistry / Year: 2000
Title: Ligand preference inferred from the structure of neutrophil gelatinase associated lipocalin
Authors: Goetz, D.H. / Willie, S.T. / Armen, R.S. / Bratt, T. / Borregaard, N. / Strong, R.K.
History
DepositionJun 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.occupancy / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEUTROPHIL GELATINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7723
Polymers20,0131
Non-polymers7592
Water1,26170
1
A: NEUTROPHIL GELATINASE
hetero molecules

A: NEUTROPHIL GELATINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5436
Polymers40,0262
Non-polymers1,5184
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_564y+1/2,-x+3/2,z-1/41
Unit cell
Length a, b, c (Å)54.290, 54.290, 121.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-209-

HOH

21A-239-

HOH

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Components

#1: Protein NEUTROPHIL GELATINASE / NGAL


Mass: 20012.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: unidentified baculovirus / References: UniProt: P80188
#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 45.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 14 % W/W PEG 8K 15% V/V GLYCEROL 50MM ACETATE, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
218-22 %(w/w)PEG80001reservoir
315 %(v/v)glycerol1reservoir
4100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 25, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 7633 / Num. obs: 6110 / % possible obs: 80 % / Observed criterion σ(I): 0 / Redundancy: 6.48 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 10.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 1.04 % / Rmerge(I) obs: 0.019 / % possible all: 38.7
Reflection
*PLUS
Num. obs: 6872 / % possible obs: 88.1 %
Reflection shell
*PLUS
% possible obs: 38.7 % / Rmerge(I) obs: 0.109 / Mean I/σ(I) obs: 5.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS0.5refinement
RefinementResolution: 2.4→20 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 290473.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
Rfree0.287 668 10.9 %
Rwork0.219 --
obs0.219 6110 80.1 %
all-6110 -
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.25 Å2 / ksol: 0.3404 e/Å3
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2---0.56 Å20 Å2
3----0.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1392 0 51 70 1513
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.581.5
X-RAY DIFFRACTIONc_mcangle_it6.392
X-RAY DIFFRACTIONc_scbond_it6.542
X-RAY DIFFRACTIONc_scangle_it8.582.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.424 67 13.5 %
Rwork0.298 431 -
obs--40.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PCARBOHYDRATE.TOP
X-RAY DIFFRACTION4NCA.PARNCA.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.9 % / Rfactor obs: 0.216 / Rfactor Rfree: 0.285
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.424 / % reflection Rfree: 13.5 % / Rfactor Rwork: 0.298

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