- PDB-4l3u: Crystal structure of a DUF3571 family protein (ABAYE3784) from Ac... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4l3u
Title
Crystal structure of a DUF3571 family protein (ABAYE3784) from Acinetobacter baumannii AYE at 1.95 A resolution
Components
Uncharacterized protein
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF1209 family protein / DUF 3571 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Uncharacterised protein PF16133, DUF4844 / Protein of unknown function DUF4844 / DUF4844 superfamily / Domain of unknown function (DUF4844) / hypothetical protein mp506/mpn330, domain 1 / Up-down Bundle / Mainly Alpha / Uncharacterized protein
Function and homology information
Biological species
Acinetobacter baumannii (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 20-157 OF THE TARGET SEQUENCE.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 2
Resolution: 1.95→47.443 Å / Num. all: 12983 / Num. obs: 12983 / % possible obs: 100 % / Redundancy: 7.3 % / Rsym value: 0.075 / Net I/σ(I): 15.9
Reflection shell
Diffraction-ID: 1,2
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.95-2
7.4
0.699
1.1
7085
963
0.699
100
2-2.06
7.4
0.462
1.6
6848
924
0.462
100
2.06-2.12
7.4
0.349
2.1
6594
893
0.349
100
2.12-2.18
7.4
0.279
2.7
6539
887
0.279
100
2.18-2.25
7.2
0.262
2.7
6211
857
0.262
100
2.25-2.33
7.4
0.202
3.6
6049
821
0.202
100
2.33-2.42
7.4
0.145
5.1
6016
817
0.145
100
2.42-2.52
7.3
0.127
5.6
5549
757
0.127
100
2.52-2.63
7.3
0.112
6.4
5333
728
0.112
100
2.63-2.76
7.3
0.105
6.7
5214
711
0.105
100
2.76-2.91
7.2
0.091
7.1
4923
682
0.091
100
2.91-3.08
7.2
0.08
8.3
4580
633
0.08
100
3.08-3.3
7.1
0.069
9.1
4201
591
0.069
100
3.3-3.56
7.1
0.058
11.4
3937
555
0.058
100
3.56-3.9
6.7
0.049
13.4
3443
515
0.049
100
3.9-4.36
7.1
0.047
12.8
3339
470
0.047
100
4.36-5.04
7.6
0.052
11.5
3080
403
0.052
100
5.04-6.17
7.6
0.049
12.3
2686
353
0.049
100
6.17-8.72
7.5
0.045
13
2026
271
0.045
100
8.72-47.443
6.8
0.042
15.2
1040
152
0.042
98
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
PDB_EXTRACT
3.1
dataextraction
SHELX
phasing
SHARP
phasing
SCALA
3.3.20
datascaling
PHENIX
1.8.2
refinement
MOSFLM
datareduction
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.95→47.443 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 1.76 / Phase error: 30.5 / Stereochemistry target values: TWIN_LSQ_F Details: 1. RIDING HYDROGENS WERE BUILT TO IMPROVE THE ANTIBUMPING RESTRAINTS BUT WERE EXCLUDED FROM F_CALC. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. RIDING HYDROGENS WERE BUILT TO IMPROVE THE ANTIBUMPING RESTRAINTS BUT WERE EXCLUDED FROM F_CALC. 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.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.5. DATA ARE MEROHEDRALLY TWINNED WITH TWIN LAW (H, -K, -L).THE REFINED TWIN FRACTION WAS 0.28. THE R-FREE TEST SET REFLECTIONS WERE CHOSEN IN THIN RESOLUTION SHELLS.
Rfactor
Num. reflection
% reflection
Rfree
0.2055
753
5.81 %
Rwork
0.1735
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obs
0.1804
12959
99.87 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
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