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Basic information

Entry
Database: PDB / ID: 6b4m
TitleStructural characterization of a novel monotreme-specific protein from the milk of the platypus
ComponentsMonotreme lactation protein
KeywordsANTIMICROBIAL PROTEIN / Monotreme / Novel-fold
Function / homologyLeg1 / Leg1 / extracellular space / IODIDE ION / Monotreme lactation protein / Monotreme lactation protein
Function and homology information
Biological speciesOrnithorhynchus anatinus (platypus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPeat, T.S. / Newman, J. / Sharp, J.A. / Kumar, A. / Nicholas, K.R. / Adams, T.E.
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 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monotreme lactation protein
B: Monotreme lactation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,12610
Polymers81,9922
Non-polymers1,1348
Water1,56787
1
A: Monotreme lactation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5635
Polymers40,9961
Non-polymers5674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Monotreme lactation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5635
Polymers40,9961
Non-polymers5674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.893, 79.337, 98.373
Angle α, β, γ (deg.)90.00, 92.33, 90.00
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: VAL / Beg label comp-ID: VAL / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 19 - 360 / Label seq-ID: 19 - 360

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

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Components

#1: Protein Monotreme lactation protein


Mass: 40995.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ornithorhynchus anatinus (platypus) / Gene: MLP / Cell line (production host): Freestyle-293 / Production host: Homo sapiens (human) / References: UniProt: A0A088CNJ7, UniProt: F6UME2*PLUS
#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.: 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-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.71 Å3/Da / Density % sol: 54.54 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 4 mg/mL protein mixed with an equal volume (200 nL) of reservoir: 100 mM ammonium acetate, 100 mM bis-tris-chloride, 25.7% PEG 8000 and incubated at 8 C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.4586 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.5→48.4 Å / Num. obs: 28749 / % possible obs: 94.6 % / Redundancy: 7.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.045 / Net I/σ(I): 14.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3250 / CC1/2: 0.839 / Rpim(I) all: 0.292 / % possible all: 73.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4v00

4v00


Resolution: 2.5→48.4 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.498 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.523 / ESU R Free: 0.26 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22009 1458 5.1 %RANDOM
Rwork0.18401 ---
obs0.1859 27276 94.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.753 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20.72 Å2
2--0.94 Å20 Å2
3----0.28 Å2
Refinement stepCycle: 1 / Resolution: 2.5→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5427 0 44 87 5558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195715
X-RAY DIFFRACTIONr_bond_other_d0.0020.025163
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9547789
X-RAY DIFFRACTIONr_angle_other_deg1.009311998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8365.028707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.68324.235255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57315919
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2841524
X-RAY DIFFRACTIONr_chiral_restr0.0870.2857
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216378
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021192
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_it2.8593.6862796
X-RAY DIFFRACTIONr_mcbond_other2.8593.6842795
X-RAY DIFFRACTIONr_mcangle_it4.4065.5213509
X-RAY DIFFRACTIONr_mcangle_other4.4065.5233510
X-RAY DIFFRACTIONr_scbond_it3.383.9452919
X-RAY DIFFRACTIONr_scbond_other3.3793.9452919
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.265.7834281
X-RAY DIFFRACTIONr_long_range_B_refined8.02368.92824323
X-RAY DIFFRACTIONr_long_range_B_other8.02368.92524322
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 23354 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 69 -
Rwork0.29 1391 -
obs--65.12 %

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