- PDB-3pjy: Crystal structure of a putative transcription regulator (R01717) ... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3pjy
Title
Crystal structure of a putative transcription regulator (R01717) from Sinorhizobium meliloti 1021 at 1.55 A resolution
Components
Hypothetical signal peptide protein
Keywords
TRANSCRIPTION REGULATOR / DUF192 FAMILY PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Protein of unknown function DUF192 / Protein of unknown function DUF192 / Saro_0823-like superfamily / Uncharacterized ACR, COG1430 / Jelly Rolls / Sandwich / Mainly Beta / Hypothetical signal peptide protein
Function and homology information
Biological species
Sinorhizobium meliloti (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 29-163 OF THE FULL LENGTH PROTEIN.
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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: 2.5 Å3/Da / Density % sol: 50.85 % Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
Resolution: 1.55→29.208 Å / Num. obs: 45713 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 4.797 % / Biso Wilson estimate: 20.821 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 13.56
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.55-1.61
0.576
1.7
22767
9108
1
97.2
1.61-1.67
0.415
2.3
20232
8035
1
99.5
1.67-1.75
0.305
3.1
22992
9060
1
99.4
1.75-1.84
0.193
4.9
21327
8383
1
99.2
1.84-1.95
0.131
7.1
21084
8198
1
98.4
1.95-2.1
0.083
11.1
22162
8526
1
97.5
2.1-2.31
0.057
15.8
22032
8345
1
95.9
2.31-2.65
0.042
21
22705
8427
1
94.3
2.65-3.33
0.028
30.4
21877
7908
1
91.3
3.33-29.208
0.02
42.7
22081
7748
1
87.9
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
SHELX
phasing
REFMAC
5.5.0110
refinement
XSCALE
datascaling
PDB_EXTRACT
3.1
dataextraction
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.55→29.208 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.381 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.073 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 6. SULPHATE AND CHLORIDE IONS FROM THE CRYSTALLIZATION AND PROTEIN BUFFERS ARE MODELED IN THE STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1903
2298
5 %
RANDOM
Rwork
0.1611
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-
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obs
0.1626
45642
98.09 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
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