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Entry
Database: PDB / ID: 4v00
TitleStructural and functional characterization of a novel monotreme- specific protein from the milk of the platypus
ComponentsMONOTREME LACTATING PROTEIN
KeywordsANTIMICROBIAL PROTEIN / NOVEL FOLD / MILK PROTEIN / ANTIBACTERIAL
Function / homologyLeg1 / Leg1 / extracellular space / Monotreme lactation protein
Function and homology information
Biological speciesORNITHORHYNCHUS ANATINUS (platypus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.82 Å
AuthorsEnjapoori, A.K. / 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
DepositionSep 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: 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 1.3Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / entity
Item: _audit_author.name / _citation_author.identifier_ORCID / _entity.formula_weight
Revision 1.4May 15, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Structure summary
Category: entity / exptl_crystal_grow / struct_conn
Item: _entity.formula_weight / _exptl_crystal_grow.method ..._entity.formula_weight / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Jul 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MONOTREME LACTATING PROTEIN
B: MONOTREME LACTATING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7107
Polymers81,9922
Non-polymers7195
Water8,071448
1
A: MONOTREME LACTATING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4014
Polymers40,9961
Non-polymers4053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MONOTREME LACTATING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3093
Polymers40,9961
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.152, 59.721, 63.074
Angle α, β, γ (deg.)80.15, 82.98, 89.27
Int Tables number1
Space group name H-MP1

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Components

#1: Protein MONOTREME LACTATING PROTEIN


Mass: 40995.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: A C-TERMINAL FLAG TAG WAS ADDED FOR PURIFICATION PURPOSES
Source: (gene. exp.) ORNITHORHYNCHUS ANATINUS (platypus) / 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-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC-TERMINAL FLAG TAG ADDED TO THE PROTEIN FOR PURIFICATION

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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: 2.73 Å3/Da / Density % sol: 54.9 % / Description: NONE
Crystal growTemperature: 281 K / Method: vapor diffusion / pH: 6.6
Details: THE PROTEIN WAS AT 4 MG/ML IN TRIS BUFFERED SALINE; THE RESERVOIR WAS 68 MM AMMONIUM ACETATE, 25.1% W/V PEG 8K, 100 MM SODIUM CACODYLATE BUFFER AT PH 6.6; DONE AT 8C.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.45861
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45861 Å / Relative weight: 1
ReflectionResolution: 1.82→46.75 Å / Num. obs: 72773 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.1
Reflection shellResolution: 1.82→1.86 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.2 / % possible all: 91.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing
PHASERphasing
REFMAC5.8.0073refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.82→61.68 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.594 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUE WITH TLS ADDED. THERE IS SOME EXTRA POSITIVE DIFFERENCE DENSITY IN A POCKET LINED BY MOSTLY AROMATIC RESIDUES BUT WE DON'T KNOW WHAT THIS REPRESENTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18786 3676 5.1 %RANDOM
Rwork0.16591 ---
obs0.16702 69095 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.003 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.53 Å20.39 Å2
2--0.24 Å2-0.24 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.82→61.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5425 0 46 448 5919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196014
X-RAY DIFFRACTIONr_bond_other_d0.0010.025591
X-RAY DIFFRACTIONr_angle_refined_deg1.1621.9568242
X-RAY DIFFRACTIONr_angle_other_deg0.7913.00112908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3075.026773
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.51924.453265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37615980
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1621525
X-RAY DIFFRACTIONr_chiral_restr0.0720.2903
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217025
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021412
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_it1.1252.0322964
X-RAY DIFFRACTIONr_mcbond_other1.1232.0312963
X-RAY DIFFRACTIONr_mcangle_it1.7713.4163775
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8172.3223050
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: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 259 -
Rwork0.311 4775 -
obs--92.71 %
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)
10.2553-0.10770.03070.45250.10590.82940.0180.0342-0.0180.01-0.00580.02090.0472-0.0566-0.01230.01760.0085-0.0010.026-0.00490.0036-41.3393-13.1571-17.7575
20.28520.0109-0.10820.7940.06110.43810.0089-0.0230.027-0.0147-0.0017-0.0525-0.03050.0358-0.00720.02170.0171-0.00380.0273-0.00770.0079-16.121220.81969.1012
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 400
2X-RAY DIFFRACTION2B18 - 400

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