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- PDB-1x8u: Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed wi... -

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Basic information

Entry
Database: PDB / ID: 1x8u
TitleCrystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Carboxymycobactin T
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsANTIMICROBIAL PROTEIN / lipocalin / siderophore
Function / homologyBacteriophage P22, Gp10, DNA-stabilising / Phage stabilisation protein / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin / Beta Barrel / Mainly Beta / CARBOXYMYCOBACTIN T / Gene 8 protein
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Used previously-determined structure / Resolution: 2.2 Å
AuthorsHolmes, M.A. / Paulsene, W. / Jide, X. / Ratledge, C. / Strong, R.K.
CitationJournal: Structure / Year: 2005
Title: Siderocalin (Lcn 2) Also Binds Carboxymycobactins, Potentially Defending against Mycobacterial Infections through Iron Sequestration
Authors: Holmes, M.A. / Paulsene, W. / Jide, X. / Ratledge, C. / Strong, R.K.
History
DepositionAug 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neutrophil gelatinase-associated lipocalin
B: Neutrophil gelatinase-associated lipocalin
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0326
Polymers61,6693
Non-polymers2,3633
Water1,892105
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3442
Polymers20,5561
Non-polymers7881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3442
Polymers20,5561
Non-polymers7881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3442
Polymers20,5561
Non-polymers7881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.800, 114.800, 119.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a monomer.

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Components

#1: Protein Neutrophil gelatinase-associated lipocalin / siderocalin / NGAL / P25 / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin 2 / Oncogene 24p3


Mass: 20556.438 Da / Num. of mol.: 3 / Mutation: C87S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, NGAL, HNL / Plasmid: pGEX-4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-RIL / References: UniProt: P80188
#2: Chemical ChemComp-CM2 / CARBOXYMYCOBACTIN T


Mass: 787.635 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C35H49FeN5O12
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 3.2 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Ammonium sulfate, sodium chloride, acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorDetector: CCD / Date: Jun 23, 2003
RadiationMonochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 40019 / % possible obs: 97.6 % / Redundancy: 10.5 % / Biso Wilson estimate: 36.4 Å2 / Rsym value: 0.068 / Net I/σ(I): 14.6
Reflection shellResolution: 2.2→2.24 Å / Mean I/σ(I) obs: 2.6 / Num. unique all: 1996 / Rsym value: 0.375 / % possible all: 99.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
RefinementMethod to determine structure: Used previously-determined structure
Starting model: Previously-determined structure

Resolution: 2.2→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.253 3703 Used same set as previously-determined structure
Rwork0.22 --
all-38696 -
obs-38696 -
Displacement parametersBiso mean: 37.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4110 0 159 105 4374
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.024
X-RAY DIFFRACTIONc_angle_deg2.2
LS refinement shellResolution: 2.2→2.28 Å
RfactorNum. reflection% reflection
Rfree0.293 364 -
Rwork0.252 --
obs-3647 91 %

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