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- PDB-6l77: Crystal structure of MS5 from Brassica napus -

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Basic information

Entry
Database: PDB / ID: 6l77
TitleCrystal structure of MS5 from Brassica napus
ComponentsMS5a
KeywordsUNKNOWN FUNCTION / cystatin-like
Function / homologyProtein MS5 / Protein MS5 / MS5a
Function and homology information
Biological speciesBrassica napus (rape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsWang, X. / Guan, Z.Y. / Yin, P.
CitationJournal: Febs Lett. / Year: 2020
Title: Structural analysis of the meiosis-related protein MS5 reveals non-canonical papain enhancement by cystatin-like folds.
Authors: Wang, X. / Gao, Y. / Guan, Z. / Xie, Z. / Zhang, D. / Yin, P. / Yang, G. / Hong, D. / Xin, Q.
History
DepositionOct 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MS5a


Theoretical massNumber of molelcules
Total (without water)28,4951
Polymers28,4951
Non-polymers00
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11270 Å2
Unit cell
Length a, b, c (Å)52.672, 52.672, 168.424
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein MS5a / MS5


Mass: 28494.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica napus (rape) / Gene: MS5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A193DU83
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Potassium sodium tartrate tetrahydrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→45.62 Å / Num. obs: 21999 / % possible obs: 98.9 % / Redundancy: 36 % / Biso Wilson estimate: 26.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.02 / Rrim(I) all: 0.122 / Net I/σ(I): 27.3
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 24 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 7.7 / Num. unique obs: 1217 / CC1/2: 0.972 / Rpim(I) all: 0.095 / Rrim(I) all: 0.482 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→45.62 Å / SU ML: 0.1982 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.4952
RfactorNum. reflection% reflection
Rfree0.2194 1120 5.11 %
Rwork0.1737 --
obs0.1761 21934 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.76 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 0 182 1930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631796
X-RAY DIFFRACTIONf_angle_d0.94912437
X-RAY DIFFRACTIONf_chiral_restr0.0627276
X-RAY DIFFRACTIONf_plane_restr0.0051310
X-RAY DIFFRACTIONf_dihedral_angle_d15.06811087
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.990.24171270.19022343X-RAY DIFFRACTION91.38
1.99-2.090.21711460.18012564X-RAY DIFFRACTION99.85
2.09-2.220.22221260.16952604X-RAY DIFFRACTION100
2.22-2.40.21121530.17152603X-RAY DIFFRACTION100
2.4-2.640.28141380.18872595X-RAY DIFFRACTION99.82
2.64-3.020.24921290.18782624X-RAY DIFFRACTION100
3.02-3.80.1971360.16672686X-RAY DIFFRACTION100
3.8-45.620.20491650.16652795X-RAY DIFFRACTION99.73
Refinement TLS params.Method: refined / Origin x: 31.0825271791 Å / Origin y: 21.1717543597 Å / Origin z: 183.096193504 Å
111213212223313233
T0.21828372473 Å20.042996456899 Å2-0.0376440570841 Å2-0.203997853607 Å20.0153152967477 Å2--0.185645919459 Å2
L1.59288667616 °2-1.34175593171 °20.321713184079 °2-1.95290291216 °2-0.476937401998 °2--1.27576933761 °2
S0.208127247995 Å °0.181964359683 Å °-0.207663095115 Å °-0.196965427933 Å °-0.155718659486 Å °0.126427773573 Å °0.265283089319 Å °0.0729833682299 Å °-0.0466523447625 Å °
Refinement TLS groupSelection details: all

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