- PDB-4ib2: Crystal structure of a putative lipoprotein (RUMGNA_00858) from R... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4ib2
Title
Crystal structure of a putative lipoprotein (RUMGNA_00858) from Ruminococcus gnavus ATCC 29149 at 1.76 A resolution
Components
Putative Lipoprotein
Keywords
TRANSPORT PROTEIN / putative methionine-bindning / NLPA lipoprotein / PF03180 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Mass: 18.015 Da / Num. of mol.: 342 / 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 28-278 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: 2.05 Å3/Da / Density % sol: 40.02 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 0.8M (NH4)2SO4, 0.1M Citrate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 9, 2010 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
Radiation
Monochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 1.76→40.876 Å / Num. obs: 41851 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.456 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.9
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
1.76-1.82
0.562
2.4
15284
3914
93.5
1.82-1.9
0.399
3.3
17710
4510
95.2
1.9-1.98
0.281
4.7
15055
3841
95.2
1.98-2.09
0.195
6.7
17216
4389
95.6
2.09-2.22
0.143
9
16231
4135
96
2.22-2.39
0.104
12
16309
4183
96.3
2.39-2.63
0.075
16.4
16345
4174
96.8
2.63-3.01
0.052
23.2
16452
4217
97.1
3.01-3.78
0.029
37.9
16136
4169
97
3.78
0.02
51.8
16823
4319
98
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Phasing
Phasing
Method: molecular replacement
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Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
PDB_EXTRACT
3.1
dataextraction
PHASER
2.3.0
phasing
XSCALE
January30, 2009
datascaling
BUSTER-TNT
2.10.0
refinement
XDS
datareduction
BUSTER
2.10.0
refinement
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→40.876 Å / Cor.coef. Fo:Fc: 0.9584 / Cor.coef. Fo:Fc free: 0.9502 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (- ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (-AUTONCS). 4. CHLORIDE (CL) AND GLYCEROL (GOL) FROM THE PURIFICATION AND CRYOPROTECTANT SOLUTION ARE MODELED. 5. ENDOGENOUS METHIONINE (MET) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE BASED ON ELECTRON DENSITY AND COMPARISON WITH OTHER SIMILAR PROTEIN STRUCTURES AND IS LIKELY THE NATURAL LIGAND.
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