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- PDB-6rwc: crystal structure of chicken beta-microseminoprotein-like 3 (MSMB3) -

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Basic information

Entry
Database: PDB / ID: 6rwc
Titlecrystal structure of chicken beta-microseminoprotein-like 3 (MSMB3)
Componentschicken beta-microseminoprotein-like 3
KeywordsUNKNOWN FUNCTION / beta-microseminoprotein / chicken egg white
Function / homologyN-terminal domain of TfIIb - #590 / N-terminal domain of TfIIb / Single Sheet / Mainly Beta / CITRIC ACID
Function and homology information
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.143 Å
AuthorsCoste, F. / Rehault-godbert, S.
CitationJournal: Febs Open Bio / Year: 2021
Title: Three-dimensional structures of avian beta-microseminoproteins: insight from the chicken egg-specific beta-microseminoprotein 3 paralog
Authors: Coste, F. / Moreau, T. / Labas, V. / Chesse, M. / Bregeon, M. / Meudal, H. / Loth, K. / Castaing, B. / Guyot, N. / Rehault-Godbert, S.
History
DepositionJun 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: chicken beta-microseminoprotein-like 3
B: chicken beta-microseminoprotein-like 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6648
Polymers19,8832
Non-polymers7816
Water82946
1
A: chicken beta-microseminoprotein-like 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6266
Polymers9,9421
Non-polymers6855
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: chicken beta-microseminoprotein-like 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0382
Polymers9,9421
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.176, 101.047, 36.907
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein chicken beta-microseminoprotein-like 3


Mass: 9941.726 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: white egg

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Non-polymers , 5 types, 52 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.7 / Details: Phosphate/citrate buffer, Li2SO4, PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97903 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.14→42.75 Å / Num. obs: 10095 / % possible obs: 98.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 38.05 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Net I/σ(I): 12
Reflection shellResolution: 2.14→2.18 Å / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 446 / CC1/2: 0.724 / % possible all: 91.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ix0

3ix0


Resolution: 2.143→42.747 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.16
RfactorNum. reflection% reflection
Rfree0.2429 470 4.66 %
Rwork0.2207 --
obs0.2218 10093 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114 Å2 / Biso mean: 47.4207 Å2 / Biso min: 20.86 Å2
Refinement stepCycle: final / Resolution: 2.143→42.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1283 0 48 46 1377
Biso mean--73.41 44.45 -
Num. residues----168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021360
X-RAY DIFFRACTIONf_angle_d0.421839
X-RAY DIFFRACTIONf_chiral_restr0.045199
X-RAY DIFFRACTIONf_plane_restr0.002224
X-RAY DIFFRACTIONf_dihedral_angle_d10.924833
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1428-2.45290.28761340.25443076321096
2.4529-3.09030.31471550.260732063361100
3.0903-42.75520.21511810.199433413522100
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)
19.6491-0.14966.16175.96551.36526.0652-0.6287-1.05120.52130.6590.3051-0.0576-1.7588-0.4330.50310.59040.0235-0.01140.4282-0.14260.533951.511843.011533.1817
24.75090.39284.56421.18850.33174.59360.0882-0.85580.57920.4235-0.15330.00850.0718-0.3731-0.02370.39840.0229-0.07520.4147-0.020.314348.57234.609934.9238
39.092-1.29063.09518.96640.99848.26160.28420.52960.63210.1166-0.2259-0.3133-0.02980.81230.0390.32960.004-0.05370.2775-0.0090.306350.946937.98928.6527
47.98624.61416.89762.94083.76726.4307-0.32750.2101-0.0596-0.36290.11980.2502-0.4267-0.1460.11850.2612-0.026-0.02080.24560.0140.242427.5231.13517.6317
58.1815-0.53836.28421.04891.11017.07250.2372-0.1031-0.566-0.16930.0123-0.25060.3294-0.036-0.33110.3169-0.054500.22620.05430.324130.852126.335522.672
68.2168-2.1869-1.32149.86040.23236.2138-0.0521-0.5848-0.2237-0.2599-0.08950.076-0.43190.99880.08470.3648-0.102-0.08360.3469-0.00370.203125.331324.042514.1046
76.65482.7243-1.17945.2343-4.87977.23140.6703-0.4059-1.25170.9941-1.3775-0.7271-1.08132.06950.80980.5142-0.21910.08240.5169-0.04830.623941.161150.986923.5856
87.35484.67834.54579.812-3.13218.0990.45231.5121-0.4597-1.62890.721-2.0002-0.75962.0033-0.75870.7517-0.01610.15580.5241-0.1190.532438.354556.185110.6605
93.9776-0.1506-0.58751.00192.63717.6569-0.43270.06780.2439-1.15850.3467-0.9167-0.0863-0.22150.0390.3775-0.00880.02360.26970.0240.422532.251350.064115.8805
103.3024-3.55540.96085.17780.74282.62160.0132-0.5552-0.21051.20250.459-0.5005-1.02380.2241-0.32510.531-0.00640.02070.2274-0.03030.42235.621853.687620.7359
117.44163.8635-4.67323.652-4.22116.08-0.0815-0.5250.24390.6027-0.0080.4515-0.16950.20410.04320.35480.0385-0.04040.2920.03290.28327.413231.116330.9289
128.51563.2249-4.09487.0625-4.78523.75940.2988-0.08461.5587-0.12270.25340.9187-0.3645-0.0038-0.80420.48590.0177-0.1020.2397-0.01290.465223.807935.872425.1124
135.9705-0.62753.61732.96342.80399.5581-0.4513-0.8701-0.0271-0.58610.0750.1302-0.3477-1.16630.29550.44090.05310.06610.52350.04030.331520.236530.223234.3448
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )A1 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 30 )A17 - 30
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 44 )A31 - 44
4X-RAY DIFFRACTION4chain 'A' and (resid 45 through 62 )A45 - 62
5X-RAY DIFFRACTION5chain 'A' and (resid 63 through 72 )A63 - 72
6X-RAY DIFFRACTION6chain 'A' and (resid 73 through 84 )A73 - 84
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 6 )B1 - 6
8X-RAY DIFFRACTION8chain 'B' and (resid 7 through 19 )B7 - 19
9X-RAY DIFFRACTION9chain 'B' and (resid 20 through 30 )B20 - 30
10X-RAY DIFFRACTION10chain 'B' and (resid 31 through 44 )B31 - 44
11X-RAY DIFFRACTION11chain 'B' and (resid 45 through 62 )B45 - 62
12X-RAY DIFFRACTION12chain 'B' and (resid 63 through 72 )B63 - 72
13X-RAY DIFFRACTION13chain 'B' and (resid 73 through 84 )B73 - 84

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