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- PDB-4opl: Constructing tailored isoprenoid products by structure-guided mod... -

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Basic information

Entry
Database: PDB / ID: 4opl
TitleConstructing tailored isoprenoid products by structure-guided modification of geranylgeranyl reductase.
ComponentsConserved Archaeal protein
KeywordsOXIDOREDUCTASE / Rossmann Fold / Archaeal Protein
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors / glycerophospholipid metabolic process / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / phospholipid biosynthetic process
Similarity search - Function
Geranylgeranyl reductase family / FAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Digeranylgeranylglycerophospholipid reductase
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsMcAndrew, R.P. / Kung, Y. / Xie, X. / Liu, C. / Pereira, J.H. / Keasling, J.D. / Adams, P.D.
CitationJournal: Structure / Year: 2014
Title: Constructing tailored isoprenoid products by structure-guided modification of geranylgeranyl reductase.
Authors: Kung, Y. / McAndrew, R.P. / Xie, X. / Liu, C.C. / Pereira, J.H. / Adams, P.D. / Keasling, J.D.
History
DepositionFeb 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conserved Archaeal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6502
Polymers50,8621
Non-polymers7881
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.331, 78.840, 105.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Conserved Archaeal protein


Mass: 50862.027 Da / Num. of mol.: 1 / Mutation: I206F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
Gene: Saci_0986 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4JA33, EC: 1.3.1.83
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Tris pH 7.5, 10% PEG 3350 and 0.2 M L-proline, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2012
RadiationMonochromator: Double crystal Si(111)and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. all: 20447 / Num. obs: 19915 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.1 %
Reflection shellResolution: 2.48→2.52 Å / Redundancy: 5.7 % / % possible all: 77.1

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Processing

Software
NameVersionClassification
BOSdata collection
PHENIX(phenix.phaser: dev_1525)model building
PHENIX(phenix.refine: dev_1525)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXdev_1525phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→43.984 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 32.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2917 713 4.9 %
Rwork0.2592 --
obs0.2608 14260 61.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→43.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3572 0 53 8 3633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023711
X-RAY DIFFRACTIONf_angle_d0.5445017
X-RAY DIFFRACTIONf_dihedral_angle_d10.8241402
X-RAY DIFFRACTIONf_chiral_restr0.021531
X-RAY DIFFRACTIONf_plane_restr0.003642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.62380.4303340.3632677X-RAY DIFFRACTION16
2.6238-2.76210.4593480.3653990X-RAY DIFFRACTION23
2.7621-2.93510.3616810.36331534X-RAY DIFFRACTION35
2.9351-3.16170.35831320.37372484X-RAY DIFFRACTION59
3.1617-3.47980.32851500.33673025X-RAY DIFFRACTION70
3.4798-3.9830.34521980.28483789X-RAY DIFFRACTION88
3.983-5.0170.24622240.21984289X-RAY DIFFRACTION100
5.017-43.99090.2362190.18784277X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.49530.34710.16590.04680.062.22-0.6275-0.32880.85320.13480.2522-0.0017-0.6045-0.07540.41841.17830.4175-0.52920.6101-0.23010.7421-21.359427.7956-5.1434
23.528-0.3721.17470.7464-0.10591.7657-0.83860.02160.90360.00610.2725-0.0815-1.05380.1390.27530.79650.0034-0.36540.64430.07260.155-14.155821.066-10.0118
33.246-0.1627-1.06960.95730.6487.78160.01110.8603-0.6202-0.1621-0.06970.2542-0.0781-0.29860.10080.34440.0709-0.0280.7276-0.2120.2702-19.6972.562-23.346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 79 )
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 340 )
3X-RAY DIFFRACTION3chain 'A' and (resid 341 through 452 )

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