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- PDB-4v3j: Structural and functional characterization of a novel monotreme- ... -

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Basic information

Entry
Database: PDB / ID: 4v3j
TitleStructural and functional characterization of a novel monotreme- specific protein from the milk of the platypus
ComponentsMONOTREME LACTATING PROTEIN
KeywordsUNKNOWN FUNCTION / NOVEL MONOTREME SPECIFIC PROTEIN / ANTI-BACTERIAL
Function / homologyLeg1 / Leg1 / extracellular space / Monotreme lactation protein
Function and homology information
Biological speciesORNITHORHYNCHUS ANATINUS (platypus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsKumar, A. / Newman, J. / Polekina, G. / Adams, T.E. / Sharp, J.A. / Peat, T.S. / Nicholas, K.R.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Structural characterization of a novel monotreme-specific protein with antimicrobial activity from the milk of the platypus.
Authors: Newman, J. / Sharp, J.A. / Enjapoori, A.K. / Bentley, J. / Nicholas, K.R. / Adams, T.E. / Peat, T.S.
History
DepositionOct 20, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 15, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MONOTREME LACTATING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2172
Polymers40,9961
Non-polymers2211
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.351, 73.008, 56.732
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MONOTREME LACTATING PROTEIN


Mass: 40995.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FLAG-TAG AT THE C-TERMINUS / Source: (gene. exp.) ORNITHORHYNCHUS ANATINUS (platypus) / Tissue: MILK / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: F6UME2
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Description: STRUCTURE WAS INITIALLY SOLVED WITH A DIFFERENT DATA SET BY SIRAS, THEN MR TO SOLVE THIS STRUCTURE.
Crystal growTemperature: 281 K / Method: vapor diffusion / pH: 8.65
Details: PROTEIN WAS 4.7 MG/ML AND SET UP IN 200 PLUS 200 NL DROPS AT 8C WITH: 48 MM NACL, 28.3% PEG 8K, 10% MALONATE-IMIDAZOLE-BORATE BUFFER AT PH 8.65.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.06879
DetectorType: ADXV / Detector: CCD / Date: Oct 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06879 Å / Relative weight: 1
ReflectionResolution: 1.97→46.2 Å / Num. obs: 26295 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.2
Reflection shellResolution: 1.97→2.08 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.7 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→57.27 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.715 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED THERE IS SOME UNEXPLAINED DENSITY AROUND ASN295.
RfactorNum. reflection% reflectionSelection details
Rfree0.21148 1328 5.1 %RANDOM
Rwork0.17196 ---
obs0.17401 24961 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.666 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å2-0.24 Å2
2---1.04 Å20 Å2
3---1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.97→57.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2721 0 14 139 2874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192905
X-RAY DIFFRACTIONr_bond_other_d0.0050.022704
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.9533967
X-RAY DIFFRACTIONr_angle_other_deg0.88136232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0265364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34324.297128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63415474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2931512
X-RAY DIFFRACTIONr_chiral_restr0.1030.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213326
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02680
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9023.9371429
X-RAY DIFFRACTIONr_mcbond_other3.8743.9361428
X-RAY DIFFRACTIONr_mcangle_it4.8336.6081802
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.5014.3721476
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.974→2.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 98 -
Rwork0.29 1818 -
obs--96.38 %
Refinement TLS params.Method: refined / Origin x: 24.6671 Å / Origin y: 8.0809 Å / Origin z: 69.1825 Å
111213212223313233
T0.0244 Å2-0.0086 Å20.0136 Å2-0.0376 Å2-0.0058 Å2--0.0577 Å2
L0.5559 °2-0.041 °20.0334 °2-1.0724 °20.1839 °2--0.0447 °2
S0.0127 Å °-0.0002 Å °-0.0106 Å °0.1023 Å °-0.0615 Å °0.234 Å °0.0129 Å °0.0061 Å °0.0488 Å °

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