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

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Basic information

Entry
Database: PDB / ID: 4opd
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: 1.81 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
B: Conserved Archaeal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,93410
Polymers101,6562
Non-polymers4,2788
Water14,250791
1
A: Conserved Archaeal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9675
Polymers50,8281
Non-polymers2,1394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Conserved Archaeal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9675
Polymers50,8281
Non-polymers2,1394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.079, 63.234, 65.102
Angle α, β, γ (deg.)120.98, 89.97, 88.55
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Conserved Archaeal protein


Mass: 50828.012 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical
ChemComp-GRG / GERANYLGERANYL DIPHOSPHATE


Mass: 450.443 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H36O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 791 / 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: 2.19 Å3/Da / Density % sol: 43.81 %
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: Aug 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. all: 78094 / Num. obs: 75985 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.81→1.87 Å / Redundancy: 2.6 % / Rsym value: 0.547 / % possible all: 93.4

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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: 1.81→42.101 Å / SU ML: 0.18 / σ(F): 0.09 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1911 1925 2.68 %RANDOM
Rwork0.146 ---
obs0.146 71762 90.65 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→42.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7136 0 256 791 8183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077740
X-RAY DIFFRACTIONf_angle_d1.06410493
X-RAY DIFFRACTIONf_dihedral_angle_d16.293029
X-RAY DIFFRACTIONf_chiral_restr0.0431098
X-RAY DIFFRACTIONf_plane_restr0.0051350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.86980.31751500.22225262X-RAY DIFFRACTION69
1.8698-1.94460.23781800.1766441X-RAY DIFFRACTION84
1.9446-2.03310.21891870.15456893X-RAY DIFFRACTION89
2.0331-2.14030.19741850.14936952X-RAY DIFFRACTION91
2.1403-2.27440.22221990.14397165X-RAY DIFFRACTION92
2.2744-2.450.20491940.14847257X-RAY DIFFRACTION94
2.45-2.69650.20982030.15417269X-RAY DIFFRACTION95
2.6965-3.08660.18832010.15257446X-RAY DIFFRACTION96
3.0866-3.88830.1792090.13677548X-RAY DIFFRACTION98
3.8883-42.1010.14942170.12797604X-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)
11.4891-0.01780.91880.22510.16671.0477-0.13-0.02650.3046-0.0767-0.03690.1465-0.1515-0.1120.16350.13780.0327-0.03320.1278-0.020.1903-29.4693-29.451816.747
21.13550.21030.14181.20960.62650.90230.0022-0.0905-0.03640.0004-0.10070.17580.0547-0.1730.0820.0938-0.00310.00140.1278-0.0030.1061-32.8052-47.276419.4683
31.4536-0.32160.25183.2340.21332.0256-0.0643-0.24150.22590.2946-0.10760.1432-0.1474-0.04940.13750.1246-0.0088-0.01260.1784-0.05320.1436-14.9408-26.740634.3742
41.10130.40250.2260.95950.02530.3344-0.03860.01820.1053-0.12030.00920.082-0.0468-0.01430.03240.08640.0145-0.00480.09160.00050.0859-21.6097-39.258413.6977
52.07590.8233-0.2341.84641.16462.33990.04840.21550.3208-0.20130.1381-0.1516-0.25290.1481-0.16970.1520.00930.02190.22340.02370.233.1632-31.097921.3371
64.11311.94052.08122.98651.73242.906-0.04480.3446-0.5156-0.1740.1883-0.44860.13570.4411-0.11060.15360.02310.04170.2182-0.02880.2184-5.1952-47.958210.8908
71.68040.9429-0.3281.1446-0.14360.355-0.12220.2602-0.1913-0.19520.1318-0.2247-0.0090.0588-0.02060.1439-0.0090.04290.153-0.03640.169-35.7237-60.635136.111
82.3822-2.1919-0.72972.1750.91661.0803-0.081-0.25220.14880.17760.2664-0.5969-0.02120.2271-0.17110.1085-0.0092-0.01450.1554-0.02860.2601-23.8379-52.165754.5377
91.09780.71340.1681.34280.15130.6208-0.00310.0499-0.2507-0.02360.055-0.18390.09430.0244-0.04990.09020.00910.01050.09120.00260.1451-44.9728-65.8645.6302
102.86772.02960.16222.4550.34950.5451-0.10180.13690.0715-0.1540.06580.131-0.0983-0.05040.0410.1270.0313-0.01720.12060.01910.1043-53.2204-53.350141.8824
113.57922.070.08983.2189-0.31871.3534-0.20770.61490.1457-0.31870.02170.166-0.042-0.08440.20370.14750.0185-0.00160.29730.02050.3004-70.3178-59.998939.0544
125.01633.20810.6015.39481.07481.73470.0004-0.36940.52030.0471-0.09710.494-0.2045-0.24560.07890.14530.05370.00310.173-0.03090.1966-58.6856-45.503150.2109
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:116 )A2 - 116
2X-RAY DIFFRACTION2( CHAIN A AND RESID 117:192 )A117 - 192
3X-RAY DIFFRACTION3( CHAIN A AND RESID 193:254 )A193 - 254
4X-RAY DIFFRACTION4( CHAIN A AND RESID 255:351 )A255 - 351
5X-RAY DIFFRACTION5( CHAIN A AND RESID 352:408 )A352 - 408
6X-RAY DIFFRACTION6( CHAIN A AND RESID 409:452 )A409 - 452
7X-RAY DIFFRACTION7( CHAIN B AND RESID 2:118 )B2 - 118
8X-RAY DIFFRACTION8( CHAIN B AND RESID 119:146 )B119 - 146
9X-RAY DIFFRACTION9( CHAIN B AND RESID 147:313 )B147 - 313
10X-RAY DIFFRACTION10( CHAIN B AND RESID 314:374 )B314 - 374
11X-RAY DIFFRACTION11( CHAIN B AND RESID 375:415 )B375 - 415
12X-RAY DIFFRACTION12( CHAIN B AND RESID 416:452 )B416 - 452

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