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- PDB-3atr: Geranylgeranyl Reductase (GGR) from Sulfolobus acidocaldarius co-... -

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Basic information

Entry
Database: PDB / ID: 3atr
TitleGeranylgeranyl Reductase (GGR) from Sulfolobus acidocaldarius co-crystallized with its ligand
ComponentsConserved Archaeal protein
KeywordsOXIDOREDUCTASE / Saturating double bonds / archaeal membrane precursor / like 2 / 3-di-O-geranylgeranylglyceryl phosphate
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 / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
nonane / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / PYROPHOSPHATE / Digeranylgeranylglycerophospholipid reductase
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsFujihashi, M. / Sasaki, D. / Iwata, Y. / Yoshimura, T. / Hemmi, H. / Miki, K.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structure and mutation analysis of archaeal geranylgeranyl reductase
Authors: Sasaki, D. / Fujihashi, M. / Iwata, Y. / Murakami, M. / Yoshimura, T. / Hemmi, H. / Miki, K.
History
DepositionJan 12, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 25, 2013Group: Database references
Revision 1.3Oct 30, 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)51,9224
Polymers50,8281
Non-polymers1,0943
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.984, 82.054, 105.837
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: 50828.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Gene: Saci_0986 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / References: UniProt: Q4JA33
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical ChemComp-DD9 / nonane


Mass: 128.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20
#4: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 54.28 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 4.6
Details: 3.5-4.5M Sodium Formate, 0.1M Sodium Acetate Buffer, pH 4.6, temperature 293K, LIQUID DIFFUSION

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 49575 / % possible obs: 96.6 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 37.7
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.334 / % possible all: 74.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→30.18 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.861 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20957 2514 5.1 %RANDOM
Rwork0.17668 ---
obs0.17836 46938 96.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.386 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20 Å2
2--2.31 Å20 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3569 0 71 162 3802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223819
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6582.0095186
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8615475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84924.294163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84915674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4841520
X-RAY DIFFRACTIONr_chiral_restr0.1150.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212876
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9151.52298
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63223706
X-RAY DIFFRACTIONr_scbond_it2.80431521
X-RAY DIFFRACTIONr_scangle_it4.5414.51476
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.803→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 150 -
Rwork0.235 2671 -
obs--75.31 %
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)
10.9621-0.313-0.45790.56880.32941.62770.04030.0150.12080.01530.0024-0.0775-0.124-0.0389-0.04270.0160.0056-0.00740.0183-0.01510.049214.117724.39758.9932
20.5837-0.0335-0.12190.11950.12520.8584-0.0343-0.0726-0.01690.04440.0209-0.0230.02710.0250.01340.07050.0012-0.00140.0613-0.01140.049715.233915.048114.7658
33.69571.1051-3.02961.8225-1.3579.120.4108-0.0620.2005-0.0243-0.2696-0.2165-0.72080.7811-0.14120.1669-0.04890.04730.21590.13450.154721.83765.367333.2907
42.2076-0.053-3.25460.51580.558912.2509-0.3663-0.1045-0.50920.06750.03320.0481.23860.16690.33310.22060.03950.06030.0130.03420.159919.3988-2.230314.2248
51.25150.3259-1.28030.55231.06835.51640.0386-0.01950.11970.044-0.07440.08440.0787-0.20560.03590.07960.00920.00910.0995-0.01940.087711.644623.34618.5715
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 240
2X-RAY DIFFRACTION2A241 - 370
3X-RAY DIFFRACTION3A371 - 407
4X-RAY DIFFRACTION4A408 - 452
5X-RAY DIFFRACTION5A501

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