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- PDB-6gqz: Petrobactin-binding engineered lipocalin without ligand -

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Basic information

Entry
Database: PDB / ID: 6gqz
TitlePetrobactin-binding engineered lipocalin without ligand
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsTRANSPORT PROTEIN / ANTICALIN / BETA-BARREL / PETROBACTIN / LCN2 / LIPOCALIN / NGAL / PROTEIN ENGINEERING
Function / homology
Function and homology information


siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin 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 ...siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin 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 / Neutrophil degranulation / apoptotic process / 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
Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsSkerra, A. / Eichinger, A.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Reprogramming Human Siderocalin To Neutralize Petrobactin, the Essential Iron Scavenger of Anthrax Bacillus.
Authors: Dauner, M. / Eichinger, A. / Lucking, G. / Scherer, S. / Skerra, A.
History
DepositionJun 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 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 1.3Nov 13, 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


Theoretical massNumber of molelcules
Total (without water)40,2682
Polymers40,2682
Non-polymers00
Water6,107339
1
A: Neutrophil gelatinase-associated lipocalin


Theoretical massNumber of molelcules
Total (without water)20,1341
Polymers20,1341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neutrophil gelatinase-associated lipocalin


Theoretical massNumber of molelcules
Total (without water)20,1341
Polymers20,1341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.990, 65.950, 67.940
Angle α, β, γ (deg.)90.000, 96.770, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 5 - 178 / Label seq-ID: 1 - 174

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 / ...NGAL / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin-2 / Oncogene 24p3 / Siderocalin LCN2 / p25


Mass: 20133.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Production host: Escherichia coli (E. coli) / References: UniProt: P80188
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 1.8 M ammonium sulfate, 0.1 M bicine/NaOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 31, 2017
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: 1.181→67.466 Å / Num. obs: 64603 / % possible obs: 96.3 % / Redundancy: 6.1 % / Rpim(I) all: 0.028 / Rrim(I) all: 0.072 / Rsym value: 0.066 / Net I/av σ(I): 4.9 / Net I/σ(I): 13.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.4-1.486.20.3562.192410.1520.3880.35695.1
1.48-1.5760.248388600.1070.2710.24895.6
1.57-1.675.60.1784.282770.0820.1970.17895.7
1.67-1.815.40.1235.977930.0570.1360.12396.4
1.81-1.986.40.0877.572130.0370.0950.08796.7
1.98-2.216.70.066965370.0270.0720.06696.9
2.21-2.566.40.069.457900.0260.0660.0696.8
2.56-3.135.60.058948420.0280.0650.05896.4
3.13-4.436.50.04710.238830.020.0510.04798.8
4.43-33.7337.20.0597.721670.0230.0630.05998.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.26 Å33.39 Å
Translation6.26 Å33.39 Å

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Processing

Software
NameVersionClassification
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER2.6.1phasing
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MVI

4mvi


Resolution: 1.4→33.41 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.209 / SU ML: 0.039 / SU R Cruickshank DPI: 0.0638 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.061
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1812 3254 5 %RANDOM
Rwork0.1373 ---
obs0.1396 61308 96.02 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 98.72 Å2 / Biso mean: 18.003 Å2 / Biso min: 6.89 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å2-0 Å2-0.65 Å2
2---1.35 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 1.4→33.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2842 0 0 339 3181
Biso mean---28.94 -
Num. residues----348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0143051
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172710
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.6654173
X-RAY DIFFRACTIONr_angle_other_deg0.991.6316410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.695384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86123.333168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60215536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5141515
X-RAY DIFFRACTIONr_chiral_restr0.0880.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023433
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02587
X-RAY DIFFRACTIONr_rigid_bond_restr2.11735761
X-RAY DIFFRACTIONr_sphericity_free25.2155227
X-RAY DIFFRACTIONr_sphericity_bonded13.90455771
Refine LS restraints NCS

Ens-ID: 1 / Number: 5577 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 243 -
Rwork0.169 4424 -
all-4667 -
obs--94.8 %
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)
10.0093-0.008-0.00630.01350.01220.0251-0.00360.0013-0.00150.00080.00210.0005-0.00130.00120.00150.00330.00040.00150.00510.00060.00118.762510.667398.9765
20.0023-0.0032-0.00210.0177-0.00820.0112-0.0001-0.0005-0.00020.0012-0.0005-0.0006-0.00110.00110.00060.0015-0.00010.00130.005600.00130.3065-0.544867.509
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 178
2X-RAY DIFFRACTION2B5 - 178

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