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- PDB-4nyr: In-vivo crystallisation (midguts of a viviparous cockroach) and s... -

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Basic information

Entry
Database: PDB / ID: 4nyr
TitleIn-vivo crystallisation (midguts of a viviparous cockroach) and structure at 2.5 A resolution of a glycosylated, lipid-binding, lipocalin-like protein
ComponentsMilk proteinMilk
KeywordsLIPID BINDING PROTEIN / In-vivo crystallization / cockroach / SAD phasing / lipocalin / Lipocalin fold / Fatty acid binding protein
Function / homologyCalycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta / Milk protein
Function and homology information
Biological speciesDiploptera punctata (Pacific beetle cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.49 Å
AuthorsCoussens, N.P. / Gallat, F.-X. / Ramaswamy, S. / Yagi, K. / Tobe, S.S. / Stay, B. / Chavas, L.M.G.
CitationJournal: Iucrj / Year: 2016
Title: Structure of a heterogeneous, glycosylated, lipid-bound, in vivo-grown protein crystal at atomic resolution from the viviparous cockroach Diploptera punctata.
Authors: Banerjee, S. / Coussens, N.P. / Gallat, F.X. / Sathyanarayanan, N. / Srikanth, J. / Yagi, K.J. / Gray, J.S. / Tobe, S.S. / Stay, B. / Chavas, L.M. / Ramaswamy, S.
History
DepositionDec 11, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Jan 1, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
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: Milk protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9115
Polymers18,7491
Non-polymers1,1624
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.280, 33.220, 40.180
Angle α, β, γ (deg.)99.50, 100.28, 104.11
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Milk protein / Milk / Lili-Mip


Mass: 18749.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Diploptera punctata (Pacific beetle cockroach)
References: UniProt: Q6SVB6
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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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: 300 K / Method: in-vivo crystallization / pH: 6
Details: Spontaneous crystallization inside the midguts of a living viviparous cockroach, pH 6.0, In-vivo crystallization, temperature 300K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 2.7 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 13, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. all: 5421 / Num. obs: 5421 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20 % / Net I/σ(I): 38.07
Reflection shellResolution: 2.49→2.56 Å / Mean I/σ(I) obs: 22.43 / Num. unique all: 820 / % possible all: 96.7

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.49→38.58 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.886 / SU B: 9.127 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23262 546 10.1 %RANDOM
Rwork0.15368 ---
all0.16159 ---
obs0.16159 4876 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.473 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20.17 Å2-0.05 Å2
2---0.22 Å20.38 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.49→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1248 0 76 88 1412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191369
X-RAY DIFFRACTIONr_angle_refined_deg1.9062.0211867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5155152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73723.54862
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.43315205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.681156
X-RAY DIFFRACTIONr_chiral_restr0.1220.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211042
X-RAY DIFFRACTIONr_mcbond_it1.1811.532611
X-RAY DIFFRACTIONr_mcangle_it2.0312.29762
X-RAY DIFFRACTIONr_scbond_it1.8361.842758
X-RAY DIFFRACTIONr_long_range_B_refined5.67813.7912089
LS refinement shellResolution: 2.491→2.556 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 41 -
Rwork0.184 357 -
obs-793 97.79 %

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