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

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Basic information

Entry
Database: PDB / ID: 4opc
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 / Chem-PGT / Digeranylgeranylglycerophospholipid reductase
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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

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Assembly

Deposited unit
A: Conserved Archaeal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3673
Polymers50,8281
Non-polymers1,5392
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.524, 65.253, 63.203
Angle α, β, γ (deg.)90.00, 91.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1012-

HOH

21A-1061-

HOH

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Components

#1: Protein Conserved Archaeal protein


Mass: 50828.012 Da / Num. of mol.: 1
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-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)


Mass: 751.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H79O10P / Comment: phospholipid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.2 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Tris pH 7.5, 10% PEG 3350, 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: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 6, 2010
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: 1.4→50 Å / Num. obs: 86371 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4.5 % / Rsym value: 0.506 / % possible all: 82.4

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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: 1.4→41.87 Å / SU ML: 0.12 / σ(F): 1.35 / Phase error: 18.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.178 1970 2.36 %
Rwork0.151 --
obs0.152 83421 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→41.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 104 461 4133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063865
X-RAY DIFFRACTIONf_angle_d1.0985239
X-RAY DIFFRACTIONf_dihedral_angle_d14.2621508
X-RAY DIFFRACTIONf_chiral_restr0.072554
X-RAY DIFFRACTIONf_plane_restr0.006667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.45140.25221800.22667209X-RAY DIFFRACTION86
1.4514-1.50950.21081900.18698028X-RAY DIFFRACTION95
1.5095-1.57820.22751870.16958108X-RAY DIFFRACTION96
1.5782-1.66140.19062000.15658167X-RAY DIFFRACTION97
1.6614-1.76550.18291980.15638172X-RAY DIFFRACTION97
1.7655-1.90180.20342050.1598204X-RAY DIFFRACTION98
1.9018-2.09320.16321980.14768304X-RAY DIFFRACTION98
2.0932-2.39610.1842080.14978328X-RAY DIFFRACTION99
2.3961-3.01870.19432050.15828432X-RAY DIFFRACTION99
3.0187-41.88740.14841990.13648499X-RAY DIFFRACTION99
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)
13.1923-0.05850.20073.30480.59412.29320.0041-0.28510.10020.20060.0330.2238-0.09880.0245-0.06340.12790.00890.00710.1248-0.04080.083221.627369.484537.5672
21.0944-0.5171-1.04010.71140.69331.91840.0885-0.19550.2483-0.03460.1094-0.1318-0.25510.3022-0.1880.13-0.0304-0.01320.1854-0.04040.156540.642667.85123.9641
31.7620.10940.14880.83250.29521.8475-0.0099-0.2111-0.06080.07760.0530.06720.0893-0.0315-0.04790.10460.01470.01110.09670.00890.089717.569158.861134.7038
42.273-0.2561-0.7181.23030.42341.746-0.0676-0.3055-0.1065-0.0430.0875-0.17460.15170.3823-0.05490.11430.0496-0.00270.18550.01270.108745.475954.026516.6296
51.2434-0.1652-1.1050.3246-0.01131.64540.07960.05890.1549-0.0333-0.01220.0438-0.1096-0.0757-0.07730.12210.018-0.00730.0964-0.00350.119821.096667.587218.2174
62.77760.1179-0.46051.76730.08373.65170.12650.19880.3523-0.0814-0.12320.0543-0.5669-0.0208-0.01640.2660.0326-0.00250.24490.0250.149337.747364.7795-4.7783
74.2585-1.2716-3.38110.74261.47464.57810.16790.59690.0053-0.2128-0.15480.1407-0.0618-0.6705-0.03870.20930.0434-0.0480.25510.01340.135417.784963.55472.9319
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:35 )A2 - 35
2X-RAY DIFFRACTION2( CHAIN A AND RESID 36:112 )A36 - 112
3X-RAY DIFFRACTION3( CHAIN A AND RESID 113:179 )A113 - 179
4X-RAY DIFFRACTION4( CHAIN A AND RESID 180:271 )A180 - 271
5X-RAY DIFFRACTION5( CHAIN A AND RESID 272:357 )A272 - 357
6X-RAY DIFFRACTION6( CHAIN A AND RESID 358:405 )A358 - 405
7X-RAY DIFFRACTION7( CHAIN A AND RESID 406:452 )A406 - 452

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