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- PDB-2i5i: CRYSTAL STRUCTURE OF A PUTATIVE CELLOBIOSE-PHOSPHATE CLEAVAGE PRO... -

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Basic information

Entry
Database: PDB / ID: 2i5i
TitleCRYSTAL STRUCTURE OF A PUTATIVE CELLOBIOSE-PHOSPHATE CLEAVAGE PROTEIN (EF3048) FROM ENTEROCOCCUS FAECALIS V583 AT 1.70 A RESOLUTION
ComponentsUPF0249 protein EF_3048
KeywordsHYDROLASE / PUTATIVE CELLOBIOSE-PHOSPHATE CLEAVAGE PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / polysaccharide catabolic process / metal ion binding
Similarity search - Function
Chitooligosaccharide deacetylase ChbG-like, bacteria / Carbohydrate deacetylase YdjC-like / YdjC-like protein / Glycoside hydrolase/deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Carbohydrate deacetylase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (EF3048) from ENTEROCOCCUS FAECALIS V583 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: 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: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...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). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A HEXAMER AS THE BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE.
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0249 protein EF_3048
B: UPF0249 protein EF_3048


Theoretical massNumber of molelcules
Total (without water)60,3962
Polymers60,3962
Non-polymers00
Water6,539363
1
A: UPF0249 protein EF_3048
B: UPF0249 protein EF_3048

A: UPF0249 protein EF_3048
B: UPF0249 protein EF_3048

A: UPF0249 protein EF_3048
B: UPF0249 protein EF_3048


Theoretical massNumber of molelcules
Total (without water)181,1896
Polymers181,1896
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area12390 Å2
ΔGint-64 kcal/mol
Surface area53790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)130.530, 130.530, 85.760
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-379-

HOH

21B-397-

HOH

31B-408-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A HEXAMER AS THE BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE

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Components

#1: Protein UPF0249 protein EF_3048


Mass: 30198.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF3048 / Production host: Escherichia coli (E. coli) / References: UniProt: P59745
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.25 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7
Details: 40.0% MPD, 0.1M HEPES pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.918370,0.978981,0.979291
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 7, 2006 / 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
20.9789811
30.9792911
ReflectionResolution: 1.7→29.45 Å / Num. obs: 59414 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Χ2: 1.016 / Net I/σ(I): 20.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.7-1.743.70.505242431.02100
1.74-1.793.70.40842791.004100
1.79-1.843.80.34742250.948100
1.84-1.93.70.28642791.04599.9
1.9-1.973.60.22942621.01599.7
1.97-2.053.70.17842381.039100
2.05-2.143.60.14942411.04899.5
2.14-2.253.50.12442400.93799.5
2.25-2.43.60.10542421.12499.9
2.4-2.583.50.09342641.02799.8
2.58-2.843.50.08842601.02999.7
2.84-3.253.40.07542591.06699.7
3.25-4.13.30.05742011.03598.9
4.1-503.50.05241810.88998.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXrefinement
SCALEPACKdata scaling
PDB_EXTRACT2data extraction
HKL-2000data reduction
SOLVEphasing
SHELXL-97refinement
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.45 Å / Num. parameters: 17818 / Num. restraintsaints: 22295 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. NCS RESTRAINTS WERE APPLIED BETWEEN RESIDUES 2-262 OF CHAINS A AND B. 3. REFINEMENT WAS AGAINST INTENSITY ...Details: OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. NCS RESTRAINTS WERE APPLIED BETWEEN RESIDUES 2-262 OF CHAINS A AND B. 3. REFINEMENT WAS AGAINST INTENSITY DATA. 4. REFINEMENT WAS CARRIED WITH THE TWIN LAW OF [K,H,-L] WITH THE TWIN FRACTION OF 0.3513. THE RFREE DECREASES FROM 0.27 TO 0.1888. 5. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.185 2883 4.9 %THIN SHELLS
Rwork0.144 ---
obs0.146 59414 99.6 %-
all-59414 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 27.904 Å2
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 3978 / Occupancy sum non hydrogen: 4426.48
Refinement stepCycle: LAST / Resolution: 1.7→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4069 0 0 363 4432
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0.049
X-RAY DIFFRACTIONs_from_restr_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.044
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.017
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.052
X-RAY DIFFRACTIONs_approx_iso_adps0

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