- PDB-4n0r: Crystal structure of a putative glycoside hydrolase (BVU_0362) fr... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4n0r
Title
Crystal structure of a putative glycoside hydrolase (BVU_0362) from Bacteroides vulgatus ATCC 8482 at 1.80 A resolution
Components
putative glycoside hydrolase
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Three domains protein / putative glycoside hydrolase domain (PF13204) / with N-terminal and C-terminal Ig-like domains / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information
Immunoglobulin-like - #3950 / Domain of unknown function DUF5060 / Domain of unknown function DUF5605 / Domain of unknown function (DUF5060) / Domain of unknown function (DUF5605) / Putative glycohydrolase domain DUF4038 / Protein of unknown function (DUF4038) / Glycosidases / Glycoside hydrolase superfamily / Immunoglobulins ...Immunoglobulin-like - #3950 / Domain of unknown function DUF5060 / Domain of unknown function DUF5605 / Domain of unknown function (DUF5060) / Domain of unknown function (DUF5605) / Putative glycohydrolase domain DUF4038 / Protein of unknown function (DUF4038) / Glycosidases / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 1264 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT (RESIDUES 23-534) WAS EXPRESSED WITH A PURIFICATION TAG. MGSDKIHHHHHHENLYFQG. THE ...THIS CONSTRUCT (RESIDUES 23-534) 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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.67 Details: 0.01M nickel (II) chloride, 22.0% polyethylene glycol monomethyl ether 2000, 0.2M NDSB-256, 0.1M TRIS pH 8.67, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2013 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
Radiation
Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.9792
1
3
0.97868
1
Reflection
Resolution: 1.8→29.211 Å / Num. obs: 127394 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 3.74 % / Biso Wilson estimate: 21.082 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 7.89
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.8-1.86
0.563
1.5
41606
20958
1
89.8
1.86-1.94
0.435
1.9
48515
25370
1
94.4
1.94-2.03
0.308
2.6
50128
24719
1
97.9
2.03-2.13
0.232
3.5
46254
22839
1
97.5
2.13-2.27
0.177
4.5
50272
25123
1
96
2.27-2.44
0.139
5.6
45195
23025
1
95.1
2.44-2.69
0.111
7.1
50509
24802
1
97.8
2.69-3.07
0.073
10.3
45936
23061
1
94.3
3.07-3.87
0.04
17.7
50510
24455
1
97.2
3.87-29.21
0.028
23.8
47908
23515
1
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
XSCALE
datascaling
REFMAC
5.7.0032
refinement
XDS
datareduction
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.8→29.211 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 4.109 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.095 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 SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. WATERS AND LIGANDS WERE EXCLUDED FROM TLS ASSIGNMENT. 4. NICKEL (NI) AND GLYCEROL(GOL) FROM THE CRYSTALLIZATION AND CRYOPROTECTANT SOLUTION HAVE BEEN MODELED. THE MODELING OF NI IS SUPPORTED BY ANOMALOUS DIFFERENCE FOURIER MAPS. 5. AN UNIDENTIFIED LIGAND (UNL) HAS BEEN MODELED INTO ELECTRON DENSITY IN A POCKET LINED BY W402, Y173, E354, Q328 AND E276 IN EACH CHAIN. DUE TO THE PRESENCE OF AN ANOMALOUS DIFFERENCE FOURIER PEAK OVERLAPPING THIS REGION, A NICKEL ION WAS MODELED ADJACENT TO THE MODELED UNL. 6. THE N-TERMINUS OF BOTH CHAINS COME TOGETHER NEAR AN EXTENDED ANOMALOUS DIFFERENCE FOURIER PEAK, BUT THE DISORDER OF THE ANOMALOUS PEAK AND SURROUNDING ELECTRON DENSITY PREVENTED MODELING GLY-0 FROM BOTH CHAINS AND THE PRESUMED HYDRATED NICKEL ION.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1796
6400
5 %
RANDOM
Rwork
0.1501
-
-
-
obs
0.1516
127320
98.67 %
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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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