- PDB-4qan: Crystal structure of a cystatin-like protein (RUMGNA_02398) from ... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4qan
Title
Crystal structure of a cystatin-like protein (RUMGNA_02398) from Ruminococcus gnavus ATCC 29149 at 2.10 A resolution
Components
hypothetical protein
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Cystatin-like fold / divergent member of NTF2-like superfamily / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Uncharacterized protein
Function and homology information
Biological species
Ruminococcus gnavus (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 32-420 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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M magnesium formate, 20.0% polyethylene glycol 3350, The additive is 0.1 M Cesium Chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2014 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
0.9798
1
3
0.97917
1
Reflection
Resolution: 2.1→29.671 Å / Num. obs: 45198 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 35.714 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 11
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Highest resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
2.1-2.17
0.829
1.5
21028
7603
93.5
2.17-2.26
0.661
1.9
24336
8873
97.3
2.26-2.36
0.443
2.5
21122
8086
95.1
2.36-2.49
0.378
3.2
25572
8911
97.6
2.49-2.64
0.293
4.1
23500
8212
97.6
2.64-2.85
0.198
6.1
24845
8845
97.9
2.85-3.13
0.124
9
22113
8195
95.8
3.13-3.59
0.068
16.5
24984
8668
97.5
3.59-4.51
0.037
27.9
22605
8232
95.1
4.51
0.027
37.6
23851
8322
94.1
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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
5.7.0032
refinement
XDS
datareduction
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.1→29.671 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 13.469 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.198 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 6. MODELING OF MAGNESIUM (MG) ION IS SUPPORTED BY COORDINATION AND ITS PRESENCE IN CRYSTALLIZATION CONDITION.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2404
2271
5 %
RANDOM
Rwork
0.1913
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obs
0.1937
45054
98.05 %
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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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