- PDB-3b5o: CRYSTAL STRUCTURE OF A CADD-LIKE PROTEIN OF UNKNOWN FUNCTION (NPU... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3b5o
Title
CRYSTAL STRUCTURE OF A CADD-LIKE PROTEIN OF UNKNOWN FUNCTION (NPUN_F6505) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.35 A RESOLUTION
Components
CADD-like protein of unknown function
Keywords
OXIDOREDUCTASE / CADD-LIKE PROTEIN OF UNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Protein of unknown function DUF3865, CADD-like / Domain of Unknown Function with PDB structure (DUF3865) / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha / CADD-like protein of unknown function
Function and homology information
Biological species
Nostoc punctiforme (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.35 Å
SEQUENCE 1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 1. 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. 2. THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. THE SEQUENCE INFORMATION IS AVAILABLE AT GENBANK WITH ACCESSION CODE ZP_00108531.1 AND FROM THE UNIPROT ARCHIVE (UNIPARC) UNDER ACCESSION ID UPI000038D4FF.
Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Sequence details
REMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 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: 2.93 Å3/Da / Density % sol: 57.95 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: NANODROP, 0.2M Mg(OAc)2, 20.0% PEG 8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.35→27.267 Å / Num. obs: 68962 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.08 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 12.58
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.35-1.4
0.823
1.6
48783
13076
1
91.5
1.4-1.45
0.684
2
44698
11789
1
95.9
1.45-1.52
0.468
3
53368
14084
1
96.2
1.52-1.6
0.313
4.5
50187
13243
1
96.6
1.6-1.7
0.224
6.1
50736
13340
1
97.2
1.7-1.83
0.142
9.2
50930
13384
1
97.5
1.83-2.02
0.085
14.1
52218
13847
1
98
2.02-2.31
0.05
21.9
50219
13404
1
98.4
2.31-2.91
0.038
27.5
50106
13578
1
98.9
2.91-27.267
0.027
33.9
49862
13608
1
98.9
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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
dataextraction
ADSC
Quantum
datacollection
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.35→27.267 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.608 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.044 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. RESIDUES 181-187 IN CHAIN A ARE DISORDERED AND NOT INCLUDED IN THE MODEL.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.174
3484
5.1 %
RANDOM
Rwork
0.155
-
-
-
obs
0.156
68952
98.97 %
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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
Displacement parameters
Biso mean: 17.133 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.34 Å2
0.17 Å2
0 Å2
2-
-
0.34 Å2
0 Å2
3-
-
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-0.51 Å2
Refinement step
Cycle: LAST / Resolution: 1.35→27.267 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1773
0
0
239
2012
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
2046
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1312
X-RAY DIFFRACTION
r_angle_refined_deg
1.259
1.954
2813
X-RAY DIFFRACTION
r_angle_other_deg
0.945
3
3245
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.025
5
277
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
41.535
25.667
90
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.127
15
345
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
12.559
15
6
X-RAY DIFFRACTION
r_chiral_restr
0.076
0.2
318
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
2410
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
408
X-RAY DIFFRACTION
r_nbd_refined
0.247
0.2
509
X-RAY DIFFRACTION
r_nbd_other
0.175
0.2
1372
X-RAY DIFFRACTION
r_nbtor_refined
0.184
0.2
1098
X-RAY DIFFRACTION
r_nbtor_other
0.086
0.2
927
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.177
0.2
190
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.564
0.2
12
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.334
0.2
35
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.16
0.2
29
X-RAY DIFFRACTION
r_mcbond_it
2.317
3
1388
X-RAY DIFFRACTION
r_mcbond_other
1.63
3
522
X-RAY DIFFRACTION
r_mcangle_it
2.948
5
2107
X-RAY DIFFRACTION
r_scbond_it
4.333
8
822
X-RAY DIFFRACTION
r_scangle_it
5.842
11
706
X-RAY DIFFRACTION
r_rigid_bond_restr
2.202
3
3803
X-RAY DIFFRACTION
r_sphericity_free
6.638
3
242
X-RAY DIFFRACTION
r_sphericity_bonded
4.1
3
3300
LS refinement shell
Resolution: 1.35→1.38 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.282
235
-
Rwork
0.264
4700
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all
-
4935
-
obs
-
-
96.03 %
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