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- PDB-2qsd: Crystal structure of a protein Il1583 from Idiomarina loihiensis -

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Basic information

Entry
Database: PDB / ID: 2qsd
TitleCrystal structure of a protein Il1583 from Idiomarina loihiensis
ComponentsUncharacterized conserved protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NYSGRC / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


protein il1583 fold / protein il1583 domain / Domain of unknown function DUF1543 / Domain of Unknown Function (DUF1543) / Ubiquitin-like (UB roll) - #10 / 3-Layer(bba) Sandwich / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Uncharacterized conserved protein
Similarity search - Component
Biological speciesIdiomarina loihiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsPatskovsky, Y. / Bonanno, J. / Sauder, J.M. / Romero, R. / Rutter, M. / Koss, J. / Mckenzie, C. / Gheyi, T. / Bain, K. / Wasserman, S.R. ...Patskovsky, Y. / Bonanno, J. / Sauder, J.M. / Romero, R. / Rutter, M. / Koss, J. / Mckenzie, C. / Gheyi, T. / Bain, K. / Wasserman, S.R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of a Protein Il1583 from Idiomarina loihiensis.
Authors: Patskovsky, Y. / Bonanno, J. / Sauder, J.M. / Romero, R. / Rutter, M. / Koss, J. / Mckenzie, C. / Gheyi, T. / Bain, K. / Wasserman, S.R. / Burley, S.K. / Almo, S.C.
History
DepositionJul 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized conserved protein
B: Uncharacterized conserved protein
C: Uncharacterized conserved protein
D: Uncharacterized conserved protein
E: Uncharacterized conserved protein
F: Uncharacterized conserved protein
G: Uncharacterized conserved protein
H: Uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,9619
Polymers170,8698
Non-polymers921
Water5,026279
1
A: Uncharacterized conserved protein
B: Uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)42,7172
Polymers42,7172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-8 kcal/mol
Surface area16020 Å2
MethodPISA
2
C: Uncharacterized conserved protein
G: Uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)42,7172
Polymers42,7172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-8 kcal/mol
Surface area16130 Å2
MethodPISA
3
D: Uncharacterized conserved protein
E: Uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8093
Polymers42,7172
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-6 kcal/mol
Surface area16140 Å2
MethodPISA
4
F: Uncharacterized conserved protein
H: Uncharacterized conserved protein


Theoretical massNumber of molelcules
Total (without water)42,7172
Polymers42,7172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-7 kcal/mol
Surface area16360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.401, 185.401, 185.401
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11D-204-

HOH

21F-190-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ASP / End label comp-ID: HOH / Refine code: 1 / Auth seq-ID: 5 - 200 / Label seq-ID: 7

Dom-IDAuth asym-IDLabel asym-ID
1AA - J
2BB - K
3CC - L
4DD - M
5EE - N
6FF - O
7GG - P
8HH - Q
Detailshomodimer, ASU contains 8 monomers assembled as 4 dimers, AB,ED,CG,FH

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Components

#1: Protein
Uncharacterized conserved protein


Mass: 21358.574 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Idiomarina loihiensis (bacteria) / Strain: L2-TR, DSM 15497 / Gene: IL1583 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5QU98
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 3.11 Å3/Da / Density % sol: 60.43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2M Ammonium sulfate, 0.1M Tris-HCl, 10% Glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9796
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 24, 2007 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 142014 / % possible obs: 99.8 % / Observed criterion σ(I): -0.5 / Redundancy: 5.7 % / Biso Wilson estimate: 70.85 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.059 / Net I/σ(I): 6.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.3.0034refinement
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.794 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Bijvoet differences were used for phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25318 2207 3 %RANDOM
Rwork0.21515 ---
obs0.21632 70754 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.717 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9382 0 6 279 9667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229674
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0931.93713134
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.93451142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.00624.297512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.383151465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7931542
X-RAY DIFFRACTIONr_chiral_restr0.0740.21391
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027566
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1380.33216
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.56225
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.5746
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0950.356
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.521
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.41925931
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.8639332
X-RAY DIFFRACTIONr_scbond_it7.34434232
X-RAY DIFFRACTIONr_scangle_it9.62953799
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1142 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.320.05
2Btight positional0.290
3Ctight positional0.220
4Dtight positional0.270
5Etight positional0.240
6Ftight positional0.250
7Gtight positional0.30
8Htight positional0.250
1Atight thermal4.532.5
2Btight thermal4.470
3Ctight thermal5.020
4Dtight thermal5.270
5Etight thermal4.810
6Ftight thermal4.070
7Gtight thermal4.390
8Htight thermal3.920
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 164 -
Rwork0.319 5127 -
obs--99.83 %

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