- PDB-3oz2: Crystal structure of a geranylgeranyl bacteriochlorophyll reducta... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3oz2
Title
Crystal structure of a geranylgeranyl bacteriochlorophyll reductase-like (Ta0516) from Thermoplasma acidophilum at 1.60 A resolution
Components
Digeranylgeranylglycerophospholipid reductase
Keywords
Flavoprotein / oxidoreductase / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information
2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase [NAD(P)H] / membrane lipid biosynthetic process / glycerophospholipid metabolic process / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / geranylgeranyl reductase activity / phospholipid biosynthetic process / FAD binding / NAD binding / NADP binding / plasma membrane Similarity search - Function
Mass: 44029.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: Ta0516 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 References: UniProt: Q9HKS9, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor
Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
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Details
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 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: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 15.00% Glycerol, 8.50% iso-Propanol, 17.00% PEG-4000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.6→45.257 Å / Num. obs: 55071 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.479 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.16
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.6-1.64
0.466
2.4
14404
4009
1
99.6
1.64-1.69
0.372
3
14078
3912
1
99.5
1.69-1.74
0.305
3.7
13773
3820
1
99.6
1.74-1.79
0.252
4.5
13485
3726
1
99.7
1.79-1.85
0.205
5.5
13195
3623
1
99.8
1.85-1.91
0.155
7.1
12708
3500
1
99.9
1.91-1.98
0.116
9.2
12328
3382
1
99.9
1.98-2.07
0.096
11.2
11996
3281
1
99.9
2.07-2.16
0.079
13.4
11420
3126
1
99.9
2.16-2.26
0.07
15.2
10887
2980
1
99.8
2.26-2.39
0.061
17.4
10483
2862
1
99.8
2.39-2.53
0.054
19.1
9911
2709
1
99.6
2.53-2.7
0.051
20.6
9339
2554
1
99.5
2.7-2.92
0.046
23.1
8633
2368
1
99.1
2.92-3.2
0.04
25.6
8021
2200
1
99.4
3.2-3.58
0.035
28.1
7215
1984
1
98.6
3.58-4.13
0.033
30.1
6360
1765
1
98.5
4.13-5.06
0.032
30.7
5337
1500
1
98
5.06-7.16
0.039
29.5
4104
1180
1
96.4
7.16-45.257
0.038
29.4
2120
648
1
89.4
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
SHELX
phasing
REFMAC
5.5.0110
refinement
XSCALE
datascaling
PDB_EXTRACT
3.1
dataextraction
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.6→45.257 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 2.679 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.074 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. 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. FAD IS MODELED BASED ON DENSITY AND FUNCTION. 6. A BACTERIAL LIPID FOUND IN THE ACTIVE SITE WAS TENTATIVELY ASSIGNED AS A PHOSPHATIDYLGYLCEROL (OZ2) BASED ON DENSITY AND FUNCTION. THE DENSITY FOR THE HEAD GROUP AND LIPID TAILS ARE POORLY DEFINED. 7. ETHYLENE GLYCOL (EDO) AND GLYCEROL (GOL) WERE MODELED BASED ON CRYSTALLIZATION/CYRO CONDITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1706
2794
5.1 %
RANDOM
Rwork
0.153
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obs
0.1539
55071
99.35 %
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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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