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- PDB-3u9p: Crystal Structure of Murine Siderocalin in Complex with an Fab Fr... -

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Basic information

Entry
Database: PDB / ID: 3u9p
TitleCrystal Structure of Murine Siderocalin in Complex with an Fab Fragment
Components
  • Monoclonal Fab Fragment Heavy Chain
  • Monoclonal Fab Fragment Light Chain
  • Neutrophil gelatinase-associated lipocalin
KeywordsIMMUNE SYSTEM / Beta Barrel / Transport Protein
Function / homology
Function and homology information


positive regulation of hippocampal neuron apoptotic process / Metal sequestration by antimicrobial proteins / positive regulation of iron ion import across plasma membrane / positive regulation of endothelial tube morphogenesis / negative regulation of hippocampal neuron apoptotic process / positive regulation of cell projection organization / cytoplasmic vesicle lumen / Iron uptake and transport / siderophore transport / short-term memory ...positive regulation of hippocampal neuron apoptotic process / Metal sequestration by antimicrobial proteins / positive regulation of iron ion import across plasma membrane / positive regulation of endothelial tube morphogenesis / negative regulation of hippocampal neuron apoptotic process / positive regulation of cell projection organization / cytoplasmic vesicle lumen / Iron uptake and transport / siderophore transport / short-term memory / iron ion sequestering activity / enterobactin binding / response to herbicide / positive regulation of reactive oxygen species biosynthetic process / long-term memory / extrinsic apoptotic signaling pathway in absence of ligand / Neutrophil degranulation / positive regulation of endothelial cell migration / response to bacterium / response to virus / cellular response to hydrogen peroxide / positive regulation of neuron apoptotic process / positive regulation of reactive oxygen species metabolic process / positive regulation of cold-induced thermogenesis / protease binding / defense response to bacterium / iron ion binding / positive regulation of apoptotic process / response to xenobiotic stimulus / innate immune response / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding / cytosol
Similarity search - Function
Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Immunoglobulins ...Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCorrenti, C. / Strong, R.K.
CitationJournal: Plos One / Year: 2012
Title: Siderocalin/Lcn2/NGAL/24p3 does not drive apoptosis through gentisic acid mediated iron withdrawal in hematopoietic cell lines.
Authors: Correnti, C. / Richardson, V. / Sia, A.K. / Bandaranayake, A.D. / Ruiz, M. / Suryo Rahmanto, Y. / Kovacevic, Z. / Clifton, M.C. / Holmes, M.A. / Kaiser, B.K. / Barasch, J. / Raymond, K.N. / ...Authors: Correnti, C. / Richardson, V. / Sia, A.K. / Bandaranayake, A.D. / Ruiz, M. / Suryo Rahmanto, Y. / Kovacevic, Z. / Clifton, M.C. / Holmes, M.A. / Kaiser, B.K. / Barasch, J. / Raymond, K.N. / Richardson, D.R. / Strong, R.K.
History
DepositionOct 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Neutrophil gelatinase-associated lipocalin
D: Neutrophil gelatinase-associated lipocalin
H: Monoclonal Fab Fragment Heavy Chain
K: Monoclonal Fab Fragment Heavy Chain
L: Monoclonal Fab Fragment Light Chain
M: Monoclonal Fab Fragment Light Chain


Theoretical massNumber of molelcules
Total (without water)135,4616
Polymers135,4616
Non-polymers00
Water1,09961
1
C: Neutrophil gelatinase-associated lipocalin
K: Monoclonal Fab Fragment Heavy Chain
M: Monoclonal Fab Fragment Light Chain


Theoretical massNumber of molelcules
Total (without water)67,7313
Polymers67,7313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-32 kcal/mol
Surface area24740 Å2
MethodPISA
2
D: Neutrophil gelatinase-associated lipocalin
H: Monoclonal Fab Fragment Heavy Chain
L: Monoclonal Fab Fragment Light Chain


Theoretical massNumber of molelcules
Total (without water)67,7313
Polymers67,7313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-33 kcal/mol
Surface area24390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.133, 124.091, 147.487
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Neutrophil gelatinase-associated lipocalin / NGAL / Lipocalin-2 / SV-40-induced 24P3 protein / p25


Mass: 21040.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lcn2 / Production host: Escherichia coli (E. coli) / References: UniProt: P11672
#2: Antibody Monoclonal Fab Fragment Heavy Chain


Mass: 23205.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
#3: Antibody Monoclonal Fab Fragment Light Chain


Mass: 23484.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.77 Å3/Da / Density % sol: 55.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 20% PEG 8000, 0.1M sodium citrate, 0.2M sodium chloride, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2010
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 35241 / % possible obs: 93.1 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.071 / Χ2: 1.045 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.94.40.36135721.074195.8
2.9-3.024.50.26835621.064195.9
3.02-3.154.50.19635801.057195.7
3.15-3.324.50.14535481.07195.2
3.32-3.534.60.09935361.075194.6
3.53-3.84.60.07335321.076193.9
3.8-4.184.60.05635091.067193.2
4.18-4.794.70.04435031192
4.79-6.034.70.05134531.059190
6.03-504.70.03234460.916185.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49.51 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.852 / Occupancy max: 1 / Occupancy min: 1 / SU B: 34.899 / SU ML: 0.314 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2917 1759 5 %RANDOM
Rwork0.2193 ---
obs0.2229 35239 93.06 %-
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 max: 120.76 Å2 / Biso mean: 46.9157 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8278 0 0 61 8339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0218480
X-RAY DIFFRACTIONr_bond_other_d0.0010.025323
X-RAY DIFFRACTIONr_angle_refined_deg1.2841.94311602
X-RAY DIFFRACTIONr_angle_other_deg0.854312976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63951125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76923.311299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.195151111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5791534
X-RAY DIFFRACTIONr_chiral_restr0.0730.21344
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219672
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021782
X-RAY DIFFRACTIONr_mcbond_it0.59725685
X-RAY DIFFRACTIONr_mcbond_other0.09822287
X-RAY DIFFRACTIONr_mcangle_it1.12639017
X-RAY DIFFRACTIONr_scbond_it1.59642795
X-RAY DIFFRACTIONr_scangle_it2.50362585
LS refinement shellResolution: 2.801→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 141 -
Rwork0.304 2479 -
all-2620 -
obs--95.1 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.138-0.3884-0.25623.4710.21211.4916-0.0335-0.1185-0.11870.4417-0.13440.54490.1703-0.18390.16790.2271-0.07340.10650.1969-0.03180.1442-10.358-70.31263.671
21.7147-0.7830.35024.396-1.92543.3639-0.1279-0.2628-0.01660.82560.57160.6195-0.9287-0.6007-0.44370.38790.29620.24840.30220.13820.2768-28.25728.89344.636
33.1953-2.2254-1.68092.1392.01792.64590.10741.088-0.61860.1696-0.76850.67840.4922-1.27020.66110.1955-0.23630.06581.1576-0.2080.3973-30.768-9.92525.108
41.36311.7474-0.44732.7452-0.24771.04690.0834-0.3668-0.02450.1068-0.2162-0.0329-0.21850.04580.13290.06070.0299-0.04010.3534-0.01230.14649.948-29.69268.082
50.9641-1.5122-0.83813.32641.68822.8117-0.01150.1196-0.05560.2424-0.02010.12190.5525-0.27010.03160.1867-0.093-0.00120.2680.03760.1759-11.298-14.34726.929
61.6591.8593-0.06042.6987-0.04550.9721-0.26030.11310.1612-0.35530.21210.1459-0.17880.0050.04820.16870.0431-0.04890.188-0.00020.14589.586-26.71248.966
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1 - 174
2X-RAY DIFFRACTION2D1 - 173
3X-RAY DIFFRACTION3H1 - 212
4X-RAY DIFFRACTION4K1 - 215
5X-RAY DIFFRACTION5L1 - 212
6X-RAY DIFFRACTION6M1 - 211

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