- PDB-3hwu: Crystal structure of Putative DNA-binding protein (YP_299413.1) f... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3hwu
Title
Crystal structure of Putative DNA-binding protein (YP_299413.1) from Ralstonia eutrophA JMP134 at 1.30 A resolution
Components
Putative DNA-binding protein
Keywords
Structural Genomics / Unknown function / YP_299413.1 / Putative DNA-binding protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Domain of unknown function (DUF296)
Function / homology
Predicted DNA-binding protein with PD1-like DNA-binding motif / PPC domain / Plants and Prokaryotes Conserved (PCC) domain / PPC domain profile profile. / Hypothetical protein, similar to alpha- acetolactate decarboxylase; domain 2 / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta / PPC domain-containing protein
Function and homology information
Biological species
Ralstonia eutropha (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
Mass: 18.015 Da / Num. of mol.: 155 / 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 28-173 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: 1.89 Å3/Da / Density % sol: 35.09 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.2000M NaCl, 20.0000% PEG-1000, 0.1M Na,K-Phosphate pH 6.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.3→26.948 Å / Num. obs: 29085 / % possible obs: 91.6 % / Observed criterion σ(I): -3 / Redundancy: 2.71 % / Biso Wilson estimate: 11.177 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 13.78
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.3-1.35
0.258
2.4
5315
4046
1
64
1.35-1.4
0.209
3.2
6909
4731
1
86.8
1.4-1.46
0.154
4.1
7911
5410
1
94.8
1.46-1.54
0.109
5.8
8557
5840
1
95.1
1.54-1.64
0.073
8
8607
5872
1
95.5
1.64-1.76
0.058
10.3
7857
5354
1
95.8
1.76-1.94
0.036
15.4
8560
5845
1
96.2
1.94-2.22
0.025
22.2
8334
5687
1
96.2
2.22-2.8
0.021
26.5
8406
5742
1
96.3
2.8-26.948
0.017
34.1
8447
5755
1
96.6
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
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: 1.3→26.948 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.308 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.042 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.UNKNOWN ELECTRON DENSITY IS OBSERVED NEAR RESIDUE 117, 119 AND 133 DURING REFINEMENT.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.14
1490
5.1 %
RANDOM
Rwork
0.119
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obs
0.121
29085
98.58 %
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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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