- PDB-4qhb: Crystal structure of a putative hydrolase (BVU_2763) from Bactero... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4qhb
Title
Crystal structure of a putative hydrolase (BVU_2763) from Bacteroides vulgatus ATCC 8482 at 2.44 A resolution
Components
Uncharacterized protein
Keywords
HYDROLASE / two domain protein / N-glycanase_Nterm (PF09112) and N-glycanase_Cterm (PF09113) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen Similarity search - Function
Peptide-N-glycosidase F, N-terminal domain / Peptide-N-glycosidase F, N-terminal domain superfamily / Peptide-N-glycosidase F, N terminal / Peptide-N-glycosidase F, N-terminal / Peptide-N-glycosidase F, C-terminal / Peptide-N-glycosidase F, N terminal / Peptide-N-glycosidase F, C terminal / Jelly Rolls - #230 / PHM/PNGase F domain superfamily / Copper type II, ascorbate-dependent monooxygenase-like, C-terminal ...Peptide-N-glycosidase F, N-terminal domain / Peptide-N-glycosidase F, N-terminal domain superfamily / Peptide-N-glycosidase F, N terminal / Peptide-N-glycosidase F, N-terminal / Peptide-N-glycosidase F, C-terminal / Peptide-N-glycosidase F, N terminal / Peptide-N-glycosidase F, C terminal / Jelly Rolls - #230 / PHM/PNGase F domain superfamily / Copper type II, ascorbate-dependent monooxygenase-like, C-terminal / Jelly Rolls / Sandwich / Mainly Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 638 / Source method: isolated from a natural source / Formula: H2O
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Details
Sequence details
THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING GLY 0 FOLLOWED BY RESIDUES 23-416 OF 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: 2.62 Å3/Da / Density % sol: 53.1 %
Resolution: 2.44→47.852 Å / Num. obs: 69089 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 40.515 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 8.79
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
2.44-2.53
0.605
2.1
22442
7091
1
99.7
2.53-2.63
0.483
2.6
21576
6766
1
100
2.63-2.75
0.389
3.3
22023
6899
1
100
2.75-2.89
0.298
4.2
21206
6652
1
99.8
2.89-3.07
0.234
5.3
21977
6894
1
100
3.07-3.31
0.155
7.7
22264
7023
1
99.8
3.31-3.64
0.093
11.5
21681
6820
1
99.9
3.64-4.16
0.07
14.4
22100
6916
1
99.8
4.16-5.23
0.053
17.9
22098
6936
1
99.7
5.23-47.852
0.058
18.5
22404
7092
1
99.1
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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
XSCALE
datascaling
REFMAC
5.7.0029
refinement
XDS
datareduction
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.44→47.852 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 14.552 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.415 / ESU R Free: 0.238 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. 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 ...Details: 1. 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. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD (MOTION DETERMINATION) SERVER. 6. POLYETHYLENE GLYCOL FRAGMENTS (PEG, PGE,PG4), AND SULFATE (SO4) FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.215
3499
5.1 %
RANDOM
Rwork
0.17
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obs
0.1723
69063
99.79 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
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