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- PDB-5mhh: Crystal structure of engineered human lipocalin 2 carrying p-boro... -

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Basic information

Entry
Database: PDB / ID: 5mhh
TitleCrystal structure of engineered human lipocalin 2 carrying p-boronophenylalanine at position 36
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsSUGAR BINDING PROTEIN / beta-barrel / p-boronophenylalanine / lipocalin / Strep-tag
Function / homologyBacteriophage P22, Gp10, DNA-stabilising / Phage stabilisation protein / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin / Beta Barrel / Mainly Beta / Gene 8 protein
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSkerra, A. / Eichinger, A.
Funding support Germany, 2items
OrganizationGrant numberCountry
European Molecular Biology OrganizationALTF number 858-2011 Germany
Helmholtz-Zentrum Berlin Germany
CitationJournal: ACS Synth Biol / Year: 2017
Title: Rational Design of an Anticalin-Type Sugar-Binding Protein Using a Genetically Encoded Boronate Side Chain.
Authors: Edwardraja, S. / Eichinger, A. / Theobald, I. / Sommer, C.A. / Reichert, A.J. / Skerra, A.
History
DepositionNov 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Apr 24, 2019Group: Data collection / Polymer sequence / Category: entity_poly / pdbx_seq_map_depositor_info
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code
Revision 2.1Jan 17, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1594
Polymers21,8711
Non-polymers2883
Water77543
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint-35 kcal/mol
Surface area10440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.857, 90.857, 44.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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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: 21870.545 Da / Num. of mol.: 1 / Mutation: L36BFP Y52F K125W K134N
Source method: isolated from a genetically manipulated source
Details: BFP: p-boronophenylalanine / Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Production host: Escherichia coli (E. coli) / References: UniProt: P80188
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 2.4 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91801 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2015
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91801 Å / Relative weight: 1
ReflectionResolution: 1.888→64.246 Å / Num. all: 12330 / Num. obs: 12330 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rpim(I) all: 0.052 / Rrim(I) all: 0.141 / Rsym value: 0.131 / Net I/av σ(I): 3.533 / Net I/σ(I): 8.7 / Num. measured all: 89836
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.117.30.3412199.5
2.11-2.2470.2572.8199.9
2.24-2.397.70.232.6199.9
2.39-2.587.10.1873.71100
2.58-2.837.20.1614.41100
2.83-3.167.70.1344.8199.8
3.16-3.6570.1235.41100
3.65-4.477.70.1135.51100
4.47-6.3270.1016.41100
6.32-32.1237.10.0974.5199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.89 Å32.12 Å
Translation1.89 Å32.12 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.22data scaling
PHASER2.5.6phasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I0A

3i0a


Resolution: 2→64.246 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.393 / SU ML: 0.124 / SU R Cruickshank DPI: 0.1961 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.172
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2326 605 4.9 %RANDOM
Rwork0.181 ---
obs0.1836 11723 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 118.83 Å2 / Biso mean: 34.564 Å2 / Biso min: 12.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å2-0 Å2
2--0.63 Å20 Å2
3----1.25 Å2
Refinement stepCycle: final / Resolution: 2→64.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1499 0 15 43 1557
Biso mean--62.96 34.37 -
Num. residues----182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191558
X-RAY DIFFRACTIONr_bond_other_d0.0020.021431
X-RAY DIFFRACTIONr_angle_refined_deg1.391.962112
X-RAY DIFFRACTIONr_angle_other_deg0.90833298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6355179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41624.13375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90615256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.365157
X-RAY DIFFRACTIONr_chiral_restr0.0860.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211731
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02378
X-RAY DIFFRACTIONr_mcbond_it6.1891.766727
X-RAY DIFFRACTIONr_mcbond_other6.0111.764726
X-RAY DIFFRACTIONr_mcangle_it7.2862.614903
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 53 -
Rwork0.182 850 -
all-903 -
obs--99.34 %
Refinement TLS params.Method: refined / Origin x: -9.353 Å / Origin y: -23.443 Å / Origin z: -12.686 Å
111213212223313233
T0.0562 Å20.005 Å20.0061 Å2-0.0678 Å2-0.0108 Å2--0.1597 Å2
L0.9314 °20.651 °2-0.2353 °2-0.837 °2-0.5746 °2--0.9024 °2
S0.174 Å °-0.0392 Å °-0.0701 Å °0.0976 Å °-0.1605 Å °-0.0159 Å °-0.0837 Å °0.0807 Å °-0.0136 Å °

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