- PDB-3i09: CRYSTAL STRUCTURE OF A PERIPLASMIC BINDING PROTEIN (BMA2936) FROM... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3i09
Title
CRYSTAL STRUCTURE OF A PERIPLASMIC BINDING PROTEIN (BMA2936) FROM BURKHOLDERIA MALLEI AT 1.80 A RESOLUTION
Components
Periplasmic branched-chain amino acid-binding protein
Keywords
TRANSPORT PROTEIN / TYPE I PERIPLASMIC BINDING PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information
Leucine-binding protein domain / Periplasmic binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 715 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT (RESIDUES 25-398) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 25-398) 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: 2.11 Å3/Da / Density % sol: 41.73 % Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND .
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 20.0000% PEG-6000, 0.1M Citrate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.8→29.709 Å / Num. obs: 63635 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 19.194 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 11.41
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
0.324
2.7
21528
11335
1
95.9
1.86-1.94
0.245
3.6
25604
13331
1
98.4
1.94-2.03
0.181
4.7
24205
12600
1
98.8
2.03-2.13
0.136
6.2
22301
11590
1
98.3
2.13-2.27
0.106
7.9
25028
13010
1
98.7
2.27-2.44
0.083
9.7
23354
12096
1
99
2.44-2.69
0.067
11.7
24414
12623
1
98.7
2.69-3.07
0.046
16.1
23631
12220
1
98.6
3.07-3.87
0.028
22.7
24031
12405
1
97.9
3.87-29.709
0.023
28.9
23738
12214
1
96.4
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.5.0053
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3.006
dataextraction
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.8→29.709 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 4.473 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.107 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. RAMACHADRAN OUTLIERS A/B103 ARE SUPPORTED BY WELL-DEFINED DENSITY. 4. ACETOACETIC ACID (AAE) IS TENTATIVELY MODELED BASED ON DENSITY AND PROTEIN ENVIROMENT FOR LIGAND INTERACTION. CITRATE AND EDO MODELED IS PRESENT IN CRYTALLIZATION/CRYO SOLUTION.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.174
3224
5.1 %
RANDOM
Rwork
0.137
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obs
0.139
63613
99.38 %
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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: MASK
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