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- PDB-6qmu: A tetrahedral boronic acid diester formed by a non-natural amino ... -

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Basic information

Entry
Database: PDB / ID: 6qmu
TitleA tetrahedral boronic acid diester formed by a non-natural amino acid in the ligand pocket of an engineered lipocalin
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsTRANSPORT PROTEIN / BETA-BARREL / P-BORONOPHENYLALANINE / LIPOCALIN / STREP-TAG / SUGAR
Function / homology
Function and homology information


siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin binding / small molecule binding / Iron uptake and transport / specific granule lumen / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / defense response to bacterium ...siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin binding / small molecule binding / Iron uptake and transport / specific granule lumen / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / defense response to bacterium / iron ion binding / innate immune response / apoptotic process / Neutrophil degranulation / 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 / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
3-nitrophenol / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsSkerra, A. / Eichinger, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGRK2062 Germany
CitationJournal: Chembiochem / Year: 2020
Title: A Tetrahedral Boronic Acid Diester Formed by an Unnatural Amino Acid in the Ligand Pocket of an Engineered Lipocalin.
Authors: Sommer, C.A. / Eichinger, A. / Skerra, A.
History
DepositionFeb 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _struct_conn.pdbx_leaving_atom_flag / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0194
Polymers43,7412
Non-polymers2782
Water1,72996
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0102
Polymers21,8711
Non-polymers1391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0102
Polymers21,8711
Non-polymers1391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.486, 44.150, 92.167
Angle α, β, γ (deg.)90.000, 133.470, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 5 - 188 / Label seq-ID: 5 - 188

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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: 21870.545 Da / Num. of mol.: 2 / Mutation: L36T2C Y52F K125W K134N
Source method: isolated from a genetically manipulated source
Details: Residues 179-188 correspond to the Strep-tag, which was used for affinity purification.
Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Production host: Escherichia coli (E. coli) / References: UniProt: P80188
#2: Chemical ChemComp-ZCQ / 3-nitrophenol / Nitrophenol


Mass: 139.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.6 M ammonium sulfate

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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 PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2018 / Details: Si mirror
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.975→66.889 Å / Num. obs: 26302 / % possible obs: 97.5 % / Redundancy: 5.8 % / CC1/2: 0.998 / Rpim(I) all: 0.032 / Rrim(I) all: 0.078 / Rsym value: 0.071 / Net I/av σ(I): 6.8 / Net I/σ(I): 12.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.98-2.0860.312.438590.1350.3390.3198.8
2.08-2.215.80.2353.136130.1040.2580.23597.4
2.21-2.365.70.1883.833380.0840.2070.18896.2
2.36-2.5560.1464.932050.0640.160.14698.7
2.55-2.795.40.1126.228480.0510.1230.11295.9
2.79-3.1260.0798.126990.0350.0870.07998.7
3.12-3.615.80.0629.523160.0280.0680.06297
3.61-4.426.10.04912.120090.0220.0540.04997.7
4.42-6.255.70.04512.115360.020.0490.04596.8
6.25-66.8895.80.04211.18790.0190.0470.04296.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.51 Å66.89 Å
Translation5.51 Å66.89 Å

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Processing

Software
NameVersionClassification
MOSFLM7.2.1data reduction
SCALA3.3.22data scaling
PHASER2.7.17phasing
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MHH

5mhh


Resolution: 1.98→66.89 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.886 / WRfactor Rfree: 0.2709 / WRfactor Rwork: 0.2079 / FOM work R set: 0.8275 / SU B: 9.011 / SU ML: 0.126 / SU R Cruickshank DPI: 0.2114 / SU Rfree: 0.1947 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2705 1283 4.9 %RANDOM
Rwork0.2068 ---
obs0.2098 25008 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 88.99 Å2 / Biso mean: 35.922 Å2 / Biso min: 21.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20.96 Å2
2---0.92 Å20 Å2
3----0.57 Å2
Refinement stepCycle: final / Resolution: 1.98→66.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3056 0 0 96 3152
Biso mean---38.57 -
Num. residues----368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0143154
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172766
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.6564288
X-RAY DIFFRACTIONr_angle_other_deg0.8351.6436492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1485366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90723.012166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.86615524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.371514
X-RAY DIFFRACTIONr_chiral_restr0.0690.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023646
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02636
Refine LS restraints NCS

Ens-ID: 1 / Number: 5805 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.975→2.026 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 90 -
Rwork0.217 1875 -
all-1965 -
obs--98.99 %
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)
11.04850.22930.07310.53240.37950.2852-0.0633-0.0603-0.0430.00290.0589-0.00580.00280.02560.00440.03360.0141-0.0320.09770.01910.0522-24.0243-13.165510.1212
20.9618-0.1328-0.71440.84940.28221.10020.2021-0.04690.0418-0.0038-0.0165-0.0698-0.0528-0.0112-0.18560.06350.0023-0.01560.07680.01750.045610.0509-12.930123.8806
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 188
2X-RAY DIFFRACTION2B5 - 188

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