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- PDB-6z2c: Engineered lipocalin C3A5 in complex with a transition state analog -

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Basic information

Entry
Database: PDB / ID: 6z2c
TitleEngineered lipocalin C3A5 in complex with a transition state analog
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsPROTEIN BINDING / ANTICALIN / BETA-BARREL / CATALYSIS / DIELS-ALDER REACTION / LCN2 / LIPOCALIN / NGAL / PROTEIN ENGINEERING / TRANSITION STATE ANALOG
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 / response to blue light ...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 / response to blue light / cellular response to increased oxygen levels / response to fructose / cellular response to X-ray / short-term memory / cellular response to interleukin-6 / iron ion sequestering activity / enterobactin binding / 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 / Lipocalin signature.
Similarity search - Domain/homology
Chem-Q5E / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSkerra, A. / Eichinger, A.
CitationJournal: To be published
Title: Structure of an engineered lipocalin that catalyzes a Diels-Alder reaction
Authors: Eichinger, A. / Skerra, A.
History
DepositionMay 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 20, 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
B: Neutrophil gelatinase-associated lipocalin
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9116
Polymers65,4603
Non-polymers1,4523
Water4,900272
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3042
Polymers21,8201
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3042
Polymers21,8201
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3042
Polymers21,8201
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.385, 39.034, 96.385
Angle α, β, γ (deg.)90.000, 120.000, 90.000
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYAA3 - 1783 - 178
21GLYGLYBB3 - 1783 - 178
12ASPASPAA3 - 1773 - 177
22ASPASPCC3 - 1773 - 177
13ASPASPBB3 - 1773 - 177
23ASPASPCC3 - 1773 - 177

NCS ensembles :
ID
1
2
3

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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: 21819.842 Da / Num. of mol.: 3
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-Q5E / 1,7,8,9,10,10-hexachloro-4-carboxypentyl-4-aza-tricyclo[5.2.1.0(2,6)]dec-8-ene-3,5-dione / 6-[(1~{R},2~{S},6~{R},7~{S})-1,7,8,9,10,10-hexakis(chloranyl)-3,5-bis(oxidanylidene)-4-azatricyclo[5.2.1.0^{2,6}]dec-8- en-4-yl]hexanoic acid


Mass: 483.986 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H13Cl6NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 3350, ammonium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 22, 2018 / 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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.387
11-L, -K, -H20.053
11-H, -K, H+L30.039
11L, K, -H-L40.143
11-H-L, K, H50.243
11-H-L, -K, L60.135
ReflectionResolution: 1.294→83.472 Å / Num. obs: 55375 / % possible obs: 95.3 % / Redundancy: 6.2 % / Rpim(I) all: 0.1 / Rrim(I) all: 0.256 / Net I/av σ(I): 1.8 / Net I/σ(I): 4.9
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
1.8-1.95.70.391.44518979920.1780.4310.392.595.2
1.9-2.015.30.3291.63619968310.1540.3650.3293.385.7
2.01-2.156.50.3011.94816973700.1260.3270.3014.698.6
2.15-2.326.60.28624545469100.1180.310.2865.198.8
2.32-2.556.60.2632.14225963970.1090.2860.2635.698.9
2.55-2.856.30.2442.33557156390.1030.2650.244697.3
2.85-3.295.90.2312.42929749980.1020.2540.2315.996.4
3.29-4.025.70.2042.72172138340.0920.2240.2045.986.7
4.02-5.697.20.212.72475834470.0840.2260.216.9100
5.69-41.7366.90.1932.81341619570.080.2090.193899.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.548
Highest resolutionLowest resolution
Rotation41.74 Å1.89 Å

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Processing

Software
NameVersionClassification
MOSFLM7.2.1data reduction
SCALA3.3.22data scaling
MOLREP11.6.02phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N47

5n47


Resolution: 1.8→41.74 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.829 / SU ML: 0.058 / SU R Cruickshank DPI: 0.0237 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1899 2681 4.8 %RANDOM
Rwork0.1608 ---
obs0.1622 52693 94.83 %-
Solvent computationIon probe radii: 1.2 Å / Shrinkage radii: 1.2 Å / VDW probe radii: 1.5 Å / Solvent model: MASK
Displacement parametersBiso max: 59.99 Å2 / Biso mean: 19.936 Å2 / Biso min: 3.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.47 Å20 Å2-4.5 Å2
2--3.91 Å20 Å2
3----1.43 Å2
Refinement stepCycle: final / Resolution: 1.8→41.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4334 0 78 272 4684
Biso mean--15.76 18.94 -
Num. residues----531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134582
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174140
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.6876249
X-RAY DIFFRACTIONr_angle_other_deg1.1371.5929667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5995536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.57922.979235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.72115770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6571521
X-RAY DIFFRACTIONr_chiral_restr0.070.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025028
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02965
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A51600.12
12B51600.12
21A52690.1
22C52690.1
31B51310.11
32C51310.11
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 218 -
Rwork0.213 3935 -
all-4153 -
obs--95.87 %
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)
10.64550.09260.21890.7577-0.14020.95470.0175-0.015-0.00020.0017-0.0579-0.0332-0.05050.02790.04040.112-0.0091-0.11540.00580.00310.3453-5.6391.52724.049
21.0021-0.2235-0.12811.0017-0.19950.60390.01550.05640.06850.0026-0.02280.01720.0340.02740.00720.1047-0.0049-0.12020.00590.01360.3295-24.6271.568-7.254
30.90620.12980.21070.71730.17460.7248-0.00210.02010.02680.0414-0.00610.0193-0.0159-0.06420.00820.10710.0017-0.10940.00750.00120.3457-42.1171.65124.888
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 180
2X-RAY DIFFRACTION2B3 - 179
3X-RAY DIFFRACTION3C3 - 178

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