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- PDB-2i8d: Crystal structure of an uncharacterized conserved protein of COG5... -

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Basic information

Entry
Database: PDB / ID: 2i8d
TitleCrystal structure of an uncharacterized conserved protein of COG5646 (ZP_00384875.1) from Lactobacillus casei ATCC 334 at 1.69 A resolution
ComponentsUncharacterized conserved protein of COG5646
KeywordsStructural Genomics/Unknown Function / ZP_00384875.1 / Uncharacterized conserved protein of COG5646 / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG / Structural Genomics-Unknown Function COMPLEX
Function / homology
Function and homology information


Aspartate Aminotransferase, domain 1 - #200 / Domain of unknown function DUF1801 / Domain of unknown function (DU1801) / Immunoglobulin FC, subunit C / Aspartate Aminotransferase, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / : / YdhG-like domain-containing protein
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.69 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an uncharacterized conserved protein of COG5646 (ZP_00384875.1) from Lactobacillus casei ATCC 334 at 1.69 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_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
Revision 1.6Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). ASSIGNMENT OF A DIMER AS THE BIOLOGICALLY RELEVENT OLIGOMERIZATION STATE IS SUPPORTED BY SIZE EXCLUSION CHROMATOGRAPHY AND STATIC LIGHT SCATTERING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized conserved protein of COG5646
B: Uncharacterized conserved protein of COG5646
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8739
Polymers29,4902
Non-polymers3837
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9870 Å2
ΔGint-76 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.946, 69.276, 90.872
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsASSIGNMENT OF A DIMER AS THE BIOLOGICALLY RELEVENT OLIGOMERIZATION STATE IS SUPPORTED BY SIZE EXCLUSION CHROMATOGRAPHY AND STATIC LIGHT SCATTERING.

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Components

#1: Protein Uncharacterized conserved protein of COG5646


Mass: 14745.034 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: 62513320, UniProt: Q035U5*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
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: 2.557158 Å3/Da / Density % sol: 51.899723 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4
Details: 1.0M LiCl, 20.0% PEG-6000, 0.1M Citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.94926,0.97925
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 11, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.949261
20.979251
ReflectionResolution: 1.6→29.775 Å / Num. obs: 34612 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 23.99 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 4.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.69-1.733.70.6621.1918625040.662100
1.73-1.783.70.5591.3903724710.559100
1.78-1.833.70.4271.7876523900.427100
1.83-1.893.70.3592846323140.359100
1.89-1.953.70.2752.5823322500.275100
1.95-2.023.70.2293.2807122020.229100
2.02-2.13.70.1773.9780421280.177100
2.1-2.183.70.1335.2748120420.133100
2.18-2.283.70.1135.9716219530.113100
2.28-2.393.70.0947693118880.094100
2.39-2.523.70.0936.8654017800.093100
2.52-2.673.60.0866.5616916940.086100
2.67-2.863.60.0797.7581116050.079100
2.86-3.093.60.0678.9540214850.067100
3.09-3.383.60.05810503613910.058100
3.38-3.783.60.0578.4452912590.057100
3.78-4.363.60.0569.2405211280.05699.9
4.36-5.343.50.04811.233659530.04899.6
5.34-7.563.50.0618.225897460.06199
7.56-29.783.20.0695.813694290.06995.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.69→29.775 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.719 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.092
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. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. UNKNOWN LIGAND MODELED NEAR A85. 5. UNMODELED DENSITY NEAR B37. 6. CHLORINE AND GLYCEROL MODELED BASED ON CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1740 5 %RANDOM
Rwork0.168 ---
obs0.169 34565 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.732 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2--0.13 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.69→29.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1998 0 31 307 2336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222164
X-RAY DIFFRACTIONr_bond_other_d0.0010.021502
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.9292953
X-RAY DIFFRACTIONr_angle_other_deg0.86633638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2515258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16123.391115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89215354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.391516
X-RAY DIFFRACTIONr_chiral_restr0.0820.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022402
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02474
X-RAY DIFFRACTIONr_nbd_refined0.240.2429
X-RAY DIFFRACTIONr_nbd_other0.1880.21555
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21025
X-RAY DIFFRACTIONr_nbtor_other0.0850.21055
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2193
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.215
X-RAY DIFFRACTIONr_mcbond_it2.07431388
X-RAY DIFFRACTIONr_mcbond_other0.5173482
X-RAY DIFFRACTIONr_mcangle_it2.57952050
X-RAY DIFFRACTIONr_scbond_it3.85381013
X-RAY DIFFRACTIONr_scangle_it5.2711893
LS refinement shellResolution: 1.69→1.734 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 118 -
Rwork0.27 2380 -
obs-2498 99.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.71140.0374-0.58050.99680.03891.16080.0617-0.11320.1189-0.03420.0799-0.0773-0.15620.1304-0.1416-0.082-0.0128-0.0113-0.1164-0.0375-0.021244.20932.7340.802
20.36830.0115-0.5660.96890.38071.61760.0656-0.03510.07920.07440.03810.0076-0.04520.0413-0.1037-0.08570.0017-0.0117-0.1111-0.0097-0.034438.01130.0138.654
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 2 - 122 / Label seq-ID: 3 - 123

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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