- PDB-2r3b: CRYSTAL STRUCTURE OF a ribokinase-like superfamily protein (EF179... -
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Basic information
Entry
Database: PDB / ID: 2r3b
Title
CRYSTAL STRUCTURE OF a ribokinase-like superfamily protein (EF1790) FROM ENTEROCOCCUS FAECALIS V583 AT 1.80 A RESOLUTION
Components
YjeF-related protein
Keywords
TRANSFERASE / PUTATIVE KINASE IN THE RIBOKINASE-LIKE SUPERFAMILY / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information
ADP-dependent NAD(P)H-hydrate dehydratase / ADP-dependent NAD(P)H-hydrate dehydratase activity / nicotinamide nucleotide metabolic process / ATP binding Similarity search - Function
BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999
SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 30, 2007 / Details: Flat mirror (vertical focusing)
Radiation
Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.91837
1
2
0.97926
1
3
0.97895
1
Reflection
Resolution: 1.8→29.591 Å / Num. obs: 73792 / % possible obs: 99.4 % / Redundancy: 5 % / Biso Wilson estimate: 20.819 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 6.2
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.8-1.85
5.1
0.67
1.1
27161
5365
0.67
98.9
1.85-1.9
5
0.513
1.4
26257
5207
0.513
98.5
1.9-1.95
5.1
0.412
1.8
25889
5124
0.412
99
1.95-2.01
5.1
0.351
2.1
25008
4949
0.351
98.9
2.01-2.08
5.1
0.28
2.7
24348
4821
0.28
99.3
2.08-2.15
5
0.227
3.3
23532
4662
0.227
99.1
2.15-2.23
5
0.202
3.7
22832
4532
0.202
99.2
2.23-2.32
5
0.167
4.5
22036
4364
0.167
99.4
2.32-2.43
5
0.154
4.8
21078
4185
0.154
99.6
2.43-2.55
5
0.128
5.7
20066
3983
0.128
99.6
2.55-2.68
5
0.109
6.6
19285
3839
0.109
99.7
2.68-2.85
5
0.098
7.3
18237
3628
0.098
99.6
2.85-3.04
5
0.084
8.1
17135
3406
0.084
99.8
3.04-3.29
5
0.071
9.2
15935
3195
0.071
99.9
3.29-3.6
5
0.058
11.1
14656
2942
0.058
99.9
3.6-4.02
5
0.051
12
13311
2679
0.051
100
4.02-4.65
4.9
0.049
12.4
11764
2386
0.049
100
4.65-5.69
4.9
0.047
12.4
9894
2019
0.047
100
5.69-8.05
4.8
0.052
12
7670
1599
0.052
100
8.05-29.591
4.6
0.044
12.7
4128
907
0.044
97.8
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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
SCALA
datascaling
PDB_EXTRACT
2
dataextraction
MAR345
CCD
datacollection
MOSFLM
datareduction
SHARP
phasing
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.8→29.591 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.829 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.091 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. EDO, CL AND MG MODELED ARE PRESENT IN CRYO/CRYSTALLIZATION CONDITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.183
3709
5 %
RANDOM
Rwork
0.15
-
-
-
all
0.152
-
-
-
obs
0.152
73782
99.28 %
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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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