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

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Basic information

Entry
Database: PDB / ID: 4opi
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 / : / : / Geranylgeranyl reductase catalytic domain / FAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich ...: / Geranylgeranyl reductase family / : / : / Geranylgeranyl reductase catalytic domain / 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 / GERANYLGERANYL DIPHOSPHATE / Digeranylgeranylglycerophospholipid reductase
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)52,4824
Polymers50,7941
Non-polymers1,6883
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.792, 82.983, 106.376
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: 50793.996 Da / Num. of mol.: 1 / Mutation: F219L
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: Chemical ChemComp-GRG / GERANYLGERANYL DIPHOSPHATE


Mass: 450.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H36O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.77 Å3/Da / Density % sol: 55.62 %
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: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2013
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. all: 28092 / Num. obs: 27895 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rsym value: 0.068
Reflection shellResolution: 2.24→2.28 Å / Redundancy: 5.4 % / Rsym value: 0.547 / % possible all: 93.5

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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: 2.24→38.655 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 30.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 1116 5 %RANDOM
Rwork0.1898 ---
obs0.1918 22317 80.24 %-
all-27812 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.24→38.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3566 0 107 47 3720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023755
X-RAY DIFFRACTIONf_angle_d0.7165074
X-RAY DIFFRACTIONf_dihedral_angle_d14.0251442
X-RAY DIFFRACTIONf_chiral_restr0.024533
X-RAY DIFFRACTIONf_plane_restr0.003648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.34250.4338490.3442949X-RAY DIFFRACTION29
2.3425-2.4660.3313760.25581446X-RAY DIFFRACTION45
2.466-2.62040.23861250.23532368X-RAY DIFFRACTION73
2.6204-2.82270.27331630.24843096X-RAY DIFFRACTION94
2.8227-3.10660.30851700.22773231X-RAY DIFFRACTION99
3.1066-3.55590.25511750.2023310X-RAY DIFFRACTION100
3.5559-4.4790.21541750.16363317X-RAY DIFFRACTION100
4.479-38.6550.18251830.16153484X-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)
12.77250.2903-1.03191.937-0.47945.00630.0673-0.110.3745-0.13740.06040.1437-0.42050.1537-0.10650.2541-0.0274-0.01790.2537-0.00540.3268-15.230125.1117-8.2991
22.4588-0.0084-0.36631.23450.17682.2673-0.21690.08350.0668-0.2120.1245-0.09040.02460.25440.07270.2907-0.0107-0.01510.2727-0.00780.175-14.450616.2813-12.7711
36.61693.92980.06896.1663-2.78497.64850.18260.35890.7579-0.08150.05030.8455-0.9808-0.3769-0.17460.67230.0995-0.0380.6826-0.13550.364-20.363310.1187-32.7798
41.8136-1.4668-2.21741.76882.14676.29020.08040.546-0.6028-0.1093-0.12440.37450.7372-0.81810.18270.4694-0.064-0.00290.4623-0.1940.4116-21.4737-0.2828-25.9101
56.0090.8136-2.80632.6531.58976.4634-0.46340.1276-1.5999-0.2748-0.1456-0.40461.79430.99550.58480.76730.21750.09270.3538-0.00690.5476-15.5143-3.9545-11.5091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 224 )
2X-RAY DIFFRACTION2chain 'A' and (resid 225 through 356 )
3X-RAY DIFFRACTION3chain 'A' and (resid 357 through 386 )
4X-RAY DIFFRACTION4chain 'A' and (resid 387 through 429 )
5X-RAY DIFFRACTION5chain 'A' and (resid 430 through 452 )

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