- PDB-3h8u: Crystal structure of uncharacterized conserved protein with doubl... -
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Basic information
Entry
Database: PDB / ID: 3h8u
Title
Crystal structure of uncharacterized conserved protein with double-stranded beta-helix domain (YP_001338853.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.80 A resolution
Components
uncharacterized conserved protein with double-stranded beta-helix domain
Keywords
structural genomics / unknown function / YP_001338853.1 / uncharacterized conserved protein with double-stranded beta-helix domain / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Cupin domain
Function / homology
Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / Cupin_2 domain-containing protein
Journal: To be published Title: Crystal structure of uncharacterized conserved protein with double-stranded beta-helix domain (YP_001338853.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.80 A resolution Authors: Joint Center for Structural Genomics (JCSG)
A: uncharacterized conserved protein with double-stranded beta-helix domain B: uncharacterized conserved protein with double-stranded beta-helix domain hetero molecules
Mass: 18.015 Da / Num. of mol.: 207 / 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.
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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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.7000M (NH4)2SO4, 15.0000% Glycerol, 1.7000% PEG-400, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.8→24.953 Å / Num. obs: 21525 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 2.86 % / Biso Wilson estimate: 19.864 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.1
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
0.491
1.44
5531
3759
1
92.7
1.86-1.94
0.36
2
6567
4438
1
95.8
1.94-2.03
0.234
2.9
6285
4251
1
96.4
2.03-2.13
0.18
3.7
5722
3870
1
96.3
2.13-2.27
0.133
4.9
6464
4374
1
96.6
2.27-2.44
0.104
5.8
6019
4088
1
96.9
2.44-2.69
0.082
7.3
6326
4295
1
97.7
2.69-3.07
0.055
10.3
6118
4146
1
98
3.07-3.87
0.04
14.5
6273
4258
1
97.7
3.87-24.953
0.033
17.3
6326
4311
1
98.1
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0005
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→24.953 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.999 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.115 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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. 4. A SULPHATE CATION, GLYCEROL AND PEG FRAGMNET (2PE) MOLECULES FROM THE CRYSTALLIZATION CONDITIONS HAVE BEEN MODELED IN THE STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.196
1044
4.9 %
RANDOM
Rwork
0.152
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obs
0.154
21489
99.74 %
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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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