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- PDB-3ejv: Crystal structure of a cystatin-like protein (saro_2766) from nov... -

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Basic information

Entry
Database: PDB / ID: 3ejv
TitleCrystal structure of a cystatin-like protein (saro_2766) from novosphingobium aromaticivorans dsm at 1.40 A resolution
Componentsuncharacterized protein with cystatin-like fold
KeywordsUNKNOWN FUNCTION / Cystatin-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Unknown ligand / SnoaL-like domain-containing protein
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans DSM 12444 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of protein of unknown function with a cystatin-like fold (YP_498036.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 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 6, 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 with cystatin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5667
Polymers20,1681
Non-polymers3986
Water3,135174
1
A: uncharacterized protein with cystatin-like fold
hetero molecules

A: uncharacterized protein with cystatin-like fold
hetero molecules

A: uncharacterized protein with cystatin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,69821
Polymers60,5033
Non-polymers1,19518
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area11530 Å2
ΔGint-5 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.540, 79.540, 79.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-206-

HOH

21A-274-

HOH

31A-275-

HOH

41A-293-

HOH

51A-321-

HOH

61A-322-

HOH

71A-330-

HOH

DetailsAUTHORS STATE THAT CRYSTAL PACKING ANALYSIS SUGGESTS A TRIMER AS THE OLIGOMERIC FORM IN SOLUTION.

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Components

#1: Protein uncharacterized protein with cystatin-like fold


Mass: 20167.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans DSM 12444 (bacteria)
Gene: YP_498036.1, Saro_2766 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2G4M1
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0000M (NH4)2SO4, 2.0000% PEG-400, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97929
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 10, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979291
ReflectionResolution: 1.4→28.127 Å / Num. obs: 33205 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.35 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.99
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.4-1.450.55217275619897
1.45-1.510.3922.818394655899.5
1.51-1.580.2823.818154645799.6
1.58-1.660.2045.317415616199.6
1.66-1.760.147.417474615099.6
1.76-1.90.09610.618779658799.6
1.9-2.090.05816.318230637799.7
2.09-2.390.04222.118160631699.5
2.39-3.010.0328.718588641899.8
3.01-28.1270.02240.318692644399.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→28.127 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 1.605 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.051
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.PGE (PEG 400 FRAGMENT) AND 1,2-ETHANEDIOL (EDO) FROM THE CRYSTALLIZATION AND CRYOPROTECTANT RESPECTIVELY HAVE BEEN MODELED. 4.AN UNKNOWN LIGAND (UNL) RESEMBLING BENZOIC ACID (BEZ) HAS BEEN MODELED NEAR RESIDUE TYR16 BASED ON ELECTRON DENSITY. 5.THE ELECTRON DENSITY BETWEEN RESIDUES 72-75 IS POOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.161 1672 5 %RANDOM
Rwork0.142 ---
obs0.143 33165 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.96 Å2 / Biso mean: 16.11 Å2 / Biso min: 5.38 Å2
Refinement stepCycle: LAST / Resolution: 1.4→28.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1203 0 35 174 1412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221387
X-RAY DIFFRACTIONr_bond_other_d0.0080.02952
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.961900
X-RAY DIFFRACTIONr_angle_other_deg0.97132325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6245194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9732360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.8615228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.21513
X-RAY DIFFRACTIONr_chiral_restr0.1120.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021582
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02288
X-RAY DIFFRACTIONr_nbd_refined0.2230.2208
X-RAY DIFFRACTIONr_nbd_other0.2140.2957
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2646
X-RAY DIFFRACTIONr_nbtor_other0.0860.2761
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.278
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2950.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.226
X-RAY DIFFRACTIONr_mcbond_it1.992934
X-RAY DIFFRACTIONr_mcbond_other0.8592348
X-RAY DIFFRACTIONr_mcangle_it2.60631403
X-RAY DIFFRACTIONr_scbond_it2.1312569
X-RAY DIFFRACTIONr_scangle_it2.8883481
X-RAY DIFFRACTIONr_rigid_bond_restr1.36332641
X-RAY DIFFRACTIONr_sphericity_free6.2873187
X-RAY DIFFRACTIONr_sphericity_bonded3.05732301
LS refinement shellResolution: 1.401→1.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 118 -
Rwork0.202 2317 -
all-2435 -
obs--99.43 %

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