- PDB-4h0a: Crystal structure of a cysteine-rich secretory protein (SAV1118) ... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4h0a
Title
Crystal structure of a cysteine-rich secretory protein (SAV1118) from Staphylococcus aureus subsp. aureus Mu50 at 1.90 A resolution
Components
Uncharacterized protein
Keywords
UNKNOWN FUNCTION / CAP protein family / cysteine-rich secretory proteins / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 24-345 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 1.00M LiCl, 10.00% PEG-6000, 0.1M Citrate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.9→29.181 Å / Num. obs: 52080 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 34.616 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 11.38
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.9-1.97
0.643
1.7
19008
10028
1
94.2
1.97-2.05
0.395
2.5
19688
10282
1
98
2.05-2.14
0.301
3.3
18340
9600
1
96.8
2.14-2.25
0.193
4.8
18899
9897
1
97.7
2.25-2.39
0.145
6.1
19021
9977
1
97.4
2.39-2.58
0.105
8
20011
10490
1
98
2.58-2.84
0.073
11.3
19135
10045
1
97
2.84-3.25
0.042
16.9
18809
9971
1
96.7
3.25-4.08
0.025
26.6
17843
9552
1
93.6
4.08-29.181
0.019
33.6
18960
9843
1
94
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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
December6, 2010
datascaling
BUSTER-TNT
2.10.0
refinement
XDS
datareduction
SHELXD
phasing
BUSTER
2.10.0
refinement
Refinement
Method to determine structure: MAD / Resolution: 1.9→29.181 Å / Cor.coef. Fo:Fc: 0.9542 / Cor.coef. Fo:Fc free: 0.9374 / Occupancy max: 1 / Occupancy min: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM ...Details: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. 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. 5. NCS RESTRAINTS WERE APPLIED DURING REFINEMENT USING LSSR (-AUTONCS) IN BUSTER. 6. MAD PHASE RESTRAINTS WERE USED DURING REFINEMENT. 7. 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYOPROTECTION SOLUTION ARE MODELED. 8. THERE IS SOME UNMODELED ELECTRON DENSITY IN THE REGION NEAR PHE-87, VAL-304 AND GLN-227 IN BOTH CHAINS. 9. THE N-TERMINAL REGIONS (A29-A34 AND B25-B37) HAVE POOR ELECTRON DENSITY AND MAY CONTAIN REGISTER ERRORS.
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