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

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Basic information

Entry
Database: PDB / ID: 4opg
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: 2.07 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 27, 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)52,7346
Polymers50,8531
Non-polymers1,8815
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.232, 81.700, 105.857
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: 50853.000 Da / Num. of mol.: 1 / Mutation: 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.: 2 / Source method: obtained synthetically / Formula: C20H36O7P2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.69 Å3/Da / Density % sol: 54.25 %
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: Dec 19, 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: 2.07→50 Å / Num. all: 34257 / Num. obs: 34256 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.07→2.11 Å / Redundancy: 8 % / % possible all: 99.9

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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: 2.07→45.214 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 23.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 1460 5 %RANDOM
Rwork0.1855 ---
obs0.1855 29195 85.25 %-
all-34246 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→45.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3571 0 117 131 3819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023770
X-RAY DIFFRACTIONf_angle_d0.6125095
X-RAY DIFFRACTIONf_dihedral_angle_d13.1981442
X-RAY DIFFRACTIONf_chiral_restr0.024531
X-RAY DIFFRACTIONf_plane_restr0.003650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.14170.234710.20671335X-RAY DIFFRACTION42
2.1417-2.22740.2724970.20761864X-RAY DIFFRACTION58
2.2274-2.32880.25851210.20342297X-RAY DIFFRACTION71
2.3288-2.45160.23441420.21412686X-RAY DIFFRACTION84
2.4516-2.60510.25271600.21253058X-RAY DIFFRACTION95
2.6051-2.80630.29091710.22463242X-RAY DIFFRACTION100
2.8063-3.08860.27361710.21663241X-RAY DIFFRACTION100
3.0886-3.53540.20281720.19543275X-RAY DIFFRACTION100
3.5354-4.45360.15321730.15463299X-RAY DIFFRACTION100
4.4536-45.2140.1611820.15793438X-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)
12.45170.7314-1.13441.3011-0.64123.31250.1124-0.08730.4384-0.05240.07530.2494-0.26910.195-0.08740.1563-0.0022-0.02640.1510.03670.2744-14.983624.946-7.9976
21.84170.1065-0.1890.52170.2951.5414-0.1430.11770.1595-0.15030.1150.01110.06140.09190.00820.16630.0203-0.01890.13380.04770.1642-14.001317.6219-11.4219
31.11121.1555-1.84072.0932-1.03128.0513-0.01530.4193-0.1879-0.2716-0.0720.1169-0.4176-0.01840.01270.32140.0351-0.05540.3252-0.08730.1805-16.16218.419-29.4109
43.6580.3017-0.43421.3427-0.68912.62770.44790.40480.37640.0514-0.28710.4141-0.6127-0.9005-0.1250.44170.1141-0.00270.4757-0.21960.4813-22.8594.7648-32.2
51.57230.1227-1.17310.8248-0.34472.5365-0.19080.251-0.8388-0.00930.04790.16721.19620.07680.21270.43930.07350.03220.2374-0.07330.3839-18.9671-2.2147-15.2078
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 340 )
3X-RAY DIFFRACTION3chain 'A' and (resid 341 through 374 )
4X-RAY DIFFRACTION4chain 'A' and (resid 375 through 404 )
5X-RAY DIFFRACTION5chain 'A' and (resid 405 through 452 )

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