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

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Basic information

Entry
Database: PDB / ID: 4opt
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: 2.6 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 6, 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

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Assembly

Deposited unit
A: Conserved Archaeal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2214
Polymers50,8871
Non-polymers1,3343
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.652, 82.198, 106.363
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 / Geranylgeranyl Reductase


Mass: 50887.016 Da / Num. of mol.: 1 / Mutation: I206F, L377H
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.: 1 / Source method: obtained synthetically / Formula: C20H36O7P2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.73 Å3/Da / Density % sol: 55.01 %
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: 2.6→50 Å / Num. all: 18265 / Num. obs: 17900 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 %
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 5.5 % / % possible all: 81.4

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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: 2.6→45.491 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 25.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2206 729 5.01 %RANDOM
Rwork0.192 ---
obs0.1935 14560 81.71 %-
all-17819 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→45.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3574 0 87 17 3678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023746
X-RAY DIFFRACTIONf_angle_d0.5755064
X-RAY DIFFRACTIONf_dihedral_angle_d12.4931425
X-RAY DIFFRACTIONf_chiral_restr0.023530
X-RAY DIFFRACTIONf_plane_restr0.002647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.79740.3133750.26371431X-RAY DIFFRACTION43
2.7974-3.07890.26711250.25192362X-RAY DIFFRACTION71
3.0789-3.52420.29471640.22563124X-RAY DIFFRACTION93
3.5242-4.43960.1971780.18493371X-RAY DIFFRACTION100
4.4396-45.49840.18711870.16213543X-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)
13.14440.3965-1.1721.7171-0.5724.40780.1729-0.180.5576-0.09520.07840.2068-0.44060.1165-0.20530.2778-0.0252-0.01760.2988-0.00160.4103-15.261524.9481-8.3373
22.9251-0.0476-0.53471.0841-0.01032.9082-0.15580.11710.0474-0.14250.0548-0.07230.09270.14410.06950.2719-0.0035-0.04470.25980.00650.1952-14.447616.1305-12.8021
32.46360.6901-1.78960.3863-0.83217.58940.02810.6102-0.4518-0.1094-0.03220.33290.1958-0.45630.02660.50440.08690.030.3311-0.15380.4664-19.75882.0863-24.6668
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 452 )

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