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- PDB-6z6z: Crystal structure of an Anticalin directed towards colchicine wit... -

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Basic information

Entry
Database: PDB / ID: 6z6z
TitleCrystal structure of an Anticalin directed towards colchicine without ligand
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsTRANSPORT PROTEIN / ANTICALIN / BETA-BARREL / COLCHICINE / CONFORMATION CHANGE / INDUCED FIT / LCN2 / LIPOCALIN / NGAL / PROTEIN ENGINEERING
Function / homologyBacteriophage P22, Gp10, DNA-stabilising / Phage stabilisation protein / Gene 8 protein
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsSkerra, A. / Eichinger, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To be published
Title: Structural rearrangement in the ligand pocket of Colchicalin upon Colchicine binding
Authors: Ilyukhina, E. / Eichinger, A. / Skerra, A.
History
DepositionMay 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5352
Polymers21,4951
Non-polymers401
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-10 kcal/mol
Surface area9080 Å2
Unit cell
Length a, b, c (Å)38.557, 75.579, 116.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-357-

HOH

21A-360-

HOH

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Components

#1: Protein Neutrophil gelatinase-associated lipocalin / NGAL / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin-2 / Oncogene 24p3 / Siderocalin / p25


Mass: 21495.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: engineered protein / Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Production host: Escherichia coli (E. coli) / References: UniProt: P80188
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.97 Å3/Da / Density % sol: 37.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350, calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 29, 2019 / Details: Si mirror
RadiationMonochromator: Si 111 double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.779→63.343 Å / Num. all: 16656 / Num. obs: 16656 / % possible obs: 99.6 % / Redundancy: 10.5 % / Rpim(I) all: 0.019 / Rrim(I) all: 0.064 / Rsym value: 0.06 / Net I/av σ(I): 6.5 / Net I/σ(I): 17.6 / Num. measured all: 175641
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.78-1.8811.20.4181.82681623970.1290.4380.4184.999.8
1.88-1.9910.50.3082.42376822690.0980.3230.3086.199.7
1.99-2.1310.20.2173.32176221390.070.2290.2178.299.7
2.13-2.310.90.1444.82179320010.0450.1510.1441299.7
2.3-2.529.60.1125.91753718230.0370.1180.11214.299.3
2.52-2.8111.10.0788.21852516750.0240.0820.07820.699.7
2.81-3.2510.20.057101513914860.0190.0610.05728.399.3
3.25-3.9811.30.046111450012860.0140.0490.04641.3100
3.98-5.639.90.04313.198799940.0140.0450.04344.798.9
5.63-63.34310.10.03514.359225860.0110.0360.03545.299

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.88 Å63.34 Å
Translation4.88 Å63.34 Å

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Processing

Software
NameVersionClassification
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER2.8.2phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NKN

5nkn


Resolution: 1.78→63.34 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.17 / SU ML: 0.127 / SU R Cruickshank DPI: 0.1394 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 811 4.9 %RANDOM
Rwork0.2007 ---
obs0.2036 15844 99.35 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.89 Å2 / Biso mean: 42.129 Å2 / Biso min: 20.69 Å2
Baniso -1Baniso -2Baniso -3
1-1.97 Å2-0 Å2-0 Å2
2--0.1 Å2-0 Å2
3----2.07 Å2
Refinement stepCycle: final / Resolution: 1.78→63.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1393 0 1 61 1455
Biso mean--25.31 39.32 -
Num. residues----172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131445
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171322
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.6521962
X-RAY DIFFRACTIONr_angle_other_deg1.2341.5733091
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6695175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41223.83673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97715250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.974155
X-RAY DIFFRACTIONr_chiral_restr0.0550.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021597
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02298
LS refinement shellResolution: 1.78→1.825 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.371 56 -
Rwork0.34 1154 -
obs--99.59 %
Refinement TLS params.Method: refined / Origin x: 3.14 Å / Origin y: 16.24 Å / Origin z: 14.868 Å
111213212223313233
T0.4274 Å2-0.041 Å2-0.0065 Å2-0.1432 Å2-0.0164 Å2--0.0534 Å2
L0.0364 °20.0894 °2-0.213 °2-0.7854 °20.1365 °2--2.6184 °2
S0.0856 Å °-0.0032 Å °-0.0226 Å °0.2393 Å °-0.0652 Å °-0.055 Å °-0.7824 Å °0.1386 Å °-0.0205 Å °

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