- PDB-3s5t: Crystal structure of a member of duf3298 family (BF2082) from bac... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3s5t
Title
Crystal structure of a member of duf3298 family (BF2082) from bacteroides fragilis nctc 9343 at 2.30 A resolution
Components
DUF3298 family protein
Keywords
Structural Genomics / unknown function / PEPTIDOGLYCAN DEACETYLASE N-TERMINAL NONCATALYTIC REGION / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information
Fervidobacterium nodosum Rt17-B1 like / Heat-shock cognate protein, ATPase / Deacetylase PdaC / Deacetylase PdaC / Domain of unknown function DUF3298 / PdaC/RsiV-like superfamily / Protein of unknown function (DUF3298) / Actin; Chain A, domain 4 / Heat Shock Protein 90 / Alpha-Beta Complex ...Fervidobacterium nodosum Rt17-B1 like / Heat-shock cognate protein, ATPase / Deacetylase PdaC / Deacetylase PdaC / Domain of unknown function DUF3298 / PdaC/RsiV-like superfamily / Protein of unknown function (DUF3298) / Actin; Chain A, domain 4 / Heat Shock Protein 90 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT (RESIDUES 21-284) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 21-284) 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
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 10.0% 2-methyl-2,4-pentanediol, 0.2M lithium sulfate, 0.1M phosphate-citrate pH 4.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution: 2.3→29.298 Å / Num. all: 15972 / Num. obs: 15972 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rsym value: 0.065 / Net I/σ(I): 16.1
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2.3-2.36
7.3
0.731
1.1
8333
1138
0.731
100
2.36-2.42
7.3
0.611
1.3
8221
1127
0.611
100
2.42-2.49
7.3
0.51
1.5
7956
1092
0.51
100
2.49-2.57
7.3
0.376
2
7766
1065
0.376
100
2.57-2.66
7.2
0.33
2.3
7525
1041
0.33
100
2.66-2.75
7.3
0.254
3
7340
1011
0.254
100
2.75-2.85
7.3
0.184
4
6862
945
0.184
100
2.85-2.97
7.2
0.128
5.8
6810
941
0.128
100
2.97-3.1
7.2
0.112
6.6
6434
893
0.112
100
3.1-3.25
7.2
0.086
7.7
6316
873
0.086
100
3.25-3.43
7.1
0.075
8.4
5856
821
0.075
100
3.43-3.64
7.1
0.07
7.7
5632
788
0.07
100
3.64-3.89
7.1
0.059
9.8
5266
741
0.059
100
3.89-4.2
7.1
0.049
12.1
4862
688
0.049
100
4.2-4.6
7
0.043
12.8
4516
646
0.043
100
4.6-5.14
6.9
0.039
13.6
4099
591
0.039
100
5.14-5.94
6.8
0.047
12.5
3549
525
0.047
100
5.94-7.27
6.4
0.051
11.9
2959
459
0.051
100
7.27-10.29
6.2
0.04
14.3
2297
373
0.04
100
10.29-29.298
5.3
0.042
13.3
1135
214
0.042
93.6
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
PDB_EXTRACT
3.1
dataextraction
SHELX
phasing
SHARP
phasing
SCALA
3.3.15
datascaling
BUSTER-TNT
2.8.0
refinement
MOSFLM
datareduction
SHELXD
phasing
BUSTER
2.8.0
refinement
Refinement
Method to determine structure: MAD / Resolution: 2.3→29.298 Å / Cor.coef. Fo:Fc: 0.9571 / Cor.coef. Fo:Fc free: 0.9484 / Occupancy max: 1 / Occupancy min: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 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. MPD,CL, PO4 MODELED ARE PRESENT IN PROTEIN/CRYSTALLIZATION/ CRYO CONDITIONS. 4. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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