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- PDB-3myx: Crystal structure of a PSPTO_0244 (Protein with unknown function ... -

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Basic information

Entry
Database: PDB / ID: 3myx
TitleCrystal structure of a PSPTO_0244 (Protein with unknown function which belongs to Pfam DUF861 family) from Pseudomonas syringae pv. tomato str. DC3000 at 1.30 A resolution
Componentsuncharacterized protein PSPTO_0244
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein of unknown function (DUF861) / Cupin_3 (PF05899) / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology(S)-ureidoglycine aminohydrolase, cupin domain / EutQ-like cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / (S)-ureidoglycine aminohydrolase cupin domain-containing protein
Function and homology information
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a PSPTO_0244 (Protein with unknown function which belongs to Pfam DUF861 family) from Pseudomonas syringae pv. tomato str. DC3000 at 1.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein PSPTO_0244
B: uncharacterized protein PSPTO_0244
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,10215
Polymers51,3482
Non-polymers75413
Water14,250791
1
A: uncharacterized protein PSPTO_0244
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9586
Polymers25,6741
Non-polymers2845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized protein PSPTO_0244
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1449
Polymers25,6741
Non-polymers4708
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.584, 48.396, 80.454
Angle α, β, γ (deg.)90.000, 108.210, 90.000
Int Tables number4
Space group name H-MP1211
DetailsCRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION. SIZE-EXCLUSION CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING SUGGEST A DIMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.

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Components

#1: Protein uncharacterized protein PSPTO_0244


Mass: 25674.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: DC3000 / Gene: PSPTO0244, PSPTO_0244 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q88AY9
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 791 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.07 Å3/Da / Density % sol: 40.69 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-MERGE, COMPLETENESS AND
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 0.2000M NH4Cl, 20.0000% PEG-3350, No Buffer pH 6.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97913,0.97879
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 3, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979131
30.978791
ReflectionResolution: 1.3→28.759 Å / Num. obs: 101752 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 8.663 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 12.07
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.3-1.350.3082.4246341736480.3
1.35-1.40.2453.2312371787695.1
1.4-1.460.2024356541904398.8
1.46-1.540.1525.2394572096999
1.54-1.640.1127393492084099.1
1.64-1.760.0878.9362971911999.1
1.76-1.940.05912.7392142054399
1.94-2.220.03818.6385482009798.7
2.22-2.80.0323.1388812013198.4
2.80.01933.6386191984397.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.3→28.759 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 1.296 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.043
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.CHLORIDE (CL) AND 1,2-ETHANEDIOL (EDO) FROM THE CRYSTALLIZATION AND CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED. 4.ELECTRON DENSITY FOR RESIDUES A201-A203 WERE POOR AND THIS REGION HAS BEEN MODELED BASED ON THE CORRESPONDING PORTION IN CHAIN B.
RfactorNum. reflection% reflectionSelection details
Rfree0.146 5084 5 %RANDOM
Rwork0.117 ---
obs0.119 101735 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 122.15 Å2 / Biso mean: 13.022 Å2 / Biso min: 3.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.06 Å2
2--0.34 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.3→28.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3504 0 46 791 4341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224050
X-RAY DIFFRACTIONr_bond_other_d0.0010.022788
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9825607
X-RAY DIFFRACTIONr_angle_other_deg0.8536881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0715594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.82222.911158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87115678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8321536
X-RAY DIFFRACTIONr_chiral_restr0.0880.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214614
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02816
X-RAY DIFFRACTIONr_mcbond_it1.6832557
X-RAY DIFFRACTIONr_mcbond_other0.97131016
X-RAY DIFFRACTIONr_mcangle_it2.46744243
X-RAY DIFFRACTIONr_scbond_it2.91661493
X-RAY DIFFRACTIONr_scangle_it4.0381299
X-RAY DIFFRACTIONr_rigid_bond_restr1.22436838
X-RAY DIFFRACTIONr_sphericity_free5.6683832
X-RAY DIFFRACTIONr_sphericity_bonded2.73936706
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 311 -
Rwork0.168 6082 -
all-6393 -
obs--84.54 %

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