Journal: To be published Title: Crystal structure of hypothetical protein (JCVI_PEP_1096682647733) from an environmental metagenome (unidentified marine microbe), Sorcerer II Global Ocean Sampling experiment at 1.85 A resolution Authors: Joint Center for Structural Genomics (JCSG)
History
Deposition
Dec 21, 2006
Deposition site: RCSB / Processing site: RCSB
Revision 1.0
Jan 23, 2007
Provider: repository / Type: Initial release
Revision 1.1
May 1, 2008
Group: Version format compliance
Revision 1.2
Jul 13, 2011
Group: Advisory / Refinement description / Version format compliance
BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ...BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999
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 THE PROTEIN WAS NOT AVAILABLE IN THE UNP DATABASE AT THE TIME OF PROCESSING. (3) PRODUCT OF THE EXPRESSED SYNTHETIC GENE WAS BASED ON THE PREDICTED SEQUENCE OF ACCESSION ID JCVI_PEP_1096682647733 FROM THE J. CRAIG VENTER INSTITUTE.
Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: OHA / End label comp-ID: OHA / Refine code: 6 / Auth seq-ID: 3 - 300 / Label seq-ID: 4
Dom-ID
Auth asym-ID
Label asym-ID
1
A
A - E
2
B
B - G
3
C
C - K
4
D
D - O
Details
SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
-
Components
#1: Protein
hypotheticalprotein
Mass: 12978.046 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured marine organism (environmental samples) Description: SYNTHETIC GENE: The gene product was based on JCVI_PEP_1096682647733 from the Sorcerer II Global Ocean Sampling experiment Production host: Escherichia coli (E. coli)
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 19, 2006 / Details: Flat mirror (vertical focusing)
Radiation
Monochromator: Single crystal Si(111) bent monochromator (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
0.97944
1
3
0.97972
1
Reflection
Resolution: 1.8→29.086 Å / Num. obs: 42961 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 6.1
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
1.85-1.9
3.6
0.611
1.2
11297
3134
0.611
100
1.9-1.95
3.6
0.444
1.7
10997
3052
0.444
100
1.95-2.01
3.6
0.368
2
10751
2976
0.368
100
2.01-2.07
3.6
0.292
2.5
10395
2885
0.292
100
2.07-2.14
3.6
0.242
2.9
10152
2821
0.242
100
2.14-2.21
3.6
0.186
3.7
9725
2690
0.186
100
2.21-2.29
3.6
0.175
3.9
9419
2630
0.175
100
2.29-2.39
3.6
0.142
4.7
9153
2541
0.142
100
2.39-2.49
3.6
0.119
5.5
8722
2428
0.119
100
2.49-2.62
3.6
0.107
5.6
8422
2357
0.107
100
2.62-2.76
3.6
0.097
6.3
7899
2206
0.097
100
2.76-2.93
3.6
0.088
6
7475
2103
0.088
100
2.93-3.13
3.6
0.076
7.5
7113
2001
0.076
100
3.13-3.38
3.5
0.067
7.8
6556
1854
0.067
100
3.38-3.7
3.5
0.055
10.6
6111
1728
0.055
100
3.7-4.14
3.5
0.049
11.8
5464
1560
0.049
99.9
4.14-4.78
3.5
0.049
12.4
4814
1386
0.049
99.7
4.78-5.85
3.4
0.048
12.7
4095
1195
0.048
99.4
5.85-8.27
3.3
0.049
12.3
3087
932
0.049
98.8
8.27-29.09
2.9
0.042
14.9
1402
482
0.042
86.1
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
SOLVE
phasing
REFMAC
5.2.0019
refinement
SCALA
datascaling
PDB_EXTRACT
2
dataextraction
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
Refinement
Method to determine structure: MAD / Resolution: 1.85→29.086 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 9.082 / SU ML: 0.132 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.137 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: (1). HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS. (2). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (3). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING ...Details: (1). HYDROGENS HAVE BEEN ADDED IN 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). RESIDUES 85-88 IN A SUBUNIT ARE DISORDERED. THE GEOMETRY IS POOR IN THIS REGION. (5). 10-KETO PALMITIC ACIDS (10-OXO-HEXADECANOIC ACID; OHA) WERE MODELLED IN THE ACTIVE SITE POCKETS. THE CARBOXYL GROUPS OF THE HEAD GROUPS OF THE FATTY ACIDS INTERACT WITH THE SIDE CHAINS OF SER 8, TYR 66, ARG 102 AND TYR 64. THE OHA ASSOCIATED WITH CHAIN C HAS THE BEST DENSITY. THE ASSIGNMENT OF THE FATTY ACIDS WAS BASED ON ELECTRON DENSITY AND THE STRUCTURAL SIMILARITY WITH OTHER MONOOXYGENASES. THEY COULD BE OTHER SIMILAR LIPIDS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.231
2164
5 %
RANDOM
Rwork
0.197
-
-
-
obs
0.198
42910
99.68 %
-
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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