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- PDB-1row: Structure of SSP-19, an MSP-domain protein like family member in ... -

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Basic information

Entry
Database: PDB / ID: 1row
TitleStructure of SSP-19, an MSP-domain protein like family member in Caenorhabditis elegans
ComponentsMSP-domain protein like family member
KeywordsSTRUCTURAL PROTEIN / BETA BARREL / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


protein homodimerization activity
Similarity search - Function
Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / PapD-like superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Sperm-specific class P protein 19
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchormann, N. / Symersky, J. / Carson, M. / Luo, M. / Lin, G. / Li, S. / Qiu, S. / Arabashi, A. / Bunzel, B. / Luo, D. ...Schormann, N. / Symersky, J. / Carson, M. / Luo, M. / Lin, G. / Li, S. / Qiu, S. / Arabashi, A. / Bunzel, B. / Luo, D. / Nagy, L. / Gray, R. / Luan, C.-H. / Zhang, J. / Lu, S. / DeLucas, L. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of sperm-specific protein SSP-19 from Caenorhabditis elegans.
Authors: Schormann, N. / Symersky, J. / Luo, M.
History
DepositionDec 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: 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: MSP-domain protein like family member
B: MSP-domain protein like family member


Theoretical massNumber of molelcules
Total (without water)22,0452
Polymers22,0452
Non-polymers00
Water2,828157
1
A: MSP-domain protein like family member


Theoretical massNumber of molelcules
Total (without water)11,0221
Polymers11,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MSP-domain protein like family member


Theoretical massNumber of molelcules
Total (without water)11,0221
Polymers11,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.354, 31.848, 55.577
Angle α, β, γ (deg.)90.00, 97.67, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsThe biological unit is a monomer

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Components

#1: Protein MSP-domain protein like family member / SSP-19 / Sperm-Specific family / class P SSP-19 / hypothetical protein C55C2.2


Mass: 11022.486 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Strain: BRISTOL N2 (Clone C55C2) / Cell: SPERM / Gene: SSP-19 / Plasmid: pET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O01829
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 1.96 Å3/Da / Density % sol: 36.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.7M lithium sulfate, 0.05M Mes, 0.1M magnesium chloride, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 295 K / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17 mg/mlprotein1drop
220 mg/mlHEPES1droppH7.5
30.5 %(v/v)octyl beta-D-glucopyranoside1drop
41.7 Mlithium sulfate1reservoir
550 mMMES1reservoirpH5.6
6100 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 24, 2003 / Details: OSMIC MIRRORS
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 11037 / Num. obs: 11037 / % possible obs: 88.2 % / Observed criterion σ(I): 0.5 / Redundancy: 3.3 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 33.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.066 / Num. unique all: 747 / Rsym value: 0.066 / % possible all: 60.5
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 8710 / % possible obs: 92.4 % / Num. measured all: 28027 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / % possible obs: 89.7 % / Redundancy: 3 % / Num. unique obs: 852 / Rmerge(I) obs: 0.087 / Mean I/σ(I) obs: 21.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model (Swiss Model)based on PDB Entry 1M1S

1m1s


Resolution: 2→19.56 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 525587.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: In initial stages restrained NCS was used, but later the two monomers were refined independently
RfactorNum. reflection% reflectionSelection details
Rfree0.274 560 5.2 %RANDOM
Rwork0.225 ---
all0.238 11037 --
obs0.225 11037 85.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.6843 Å2 / ksol: 0.363445 e/Å3
Displacement parametersBiso mean: 26.9 Å2
Baniso -1Baniso -2Baniso -3
1--8.1 Å20 Å2-4.09 Å2
2---8.84 Å20 Å2
3---16.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 0 157 1671
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d28.3
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.732
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it2.812.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 56 4.4 %
Rwork0.237 1214 -
obs-1214 65.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 24.79 Å / Num. reflection obs: 8637 / % reflection Rfree: 5 % / Rfactor obs: 0.219 / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg28.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.34 Å / Rfactor Rfree: 0.327 / Rfactor Rwork: 0.207 / Num. reflection Rwork: 1217 / Rfactor obs: 0.237

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