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- PDB-3atq: Geranylgeranyl Reductase (GGR) from Sulfolobus acidocaldarius -

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Basic information

Entry
Database: PDB / ID: 3atq
TitleGeranylgeranyl Reductase (GGR) from Sulfolobus acidocaldarius
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
TETRADECANE / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Digeranylgeranylglycerophospholipid reductase
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSasaki, D. / Fujihashi, M. / Murakami, M. / 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 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)51,8143
Polymers50,8281
Non-polymers9862
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.913, 80.935, 105.813
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-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.65 Å3/Da / Density % sol: 53.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: 3.5-4.5M Sodium formate, 0.1M Sodium acetate buffer, pH 4.6, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorDetector: 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: 1.85→50 Å / Num. obs: 46801 / % possible obs: 99.9 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 28.4
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.292 / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CGV

3cgv
PDB Unreleased entry


Resolution: 1.85→49.67 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.507 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20943 2353 5.1 %RANDOM
Rwork0.18838 ---
obs0.18945 44136 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.032 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å20 Å2
2--3.08 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 1.85→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3569 0 67 117 3753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223720
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.322.0115026
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6865451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44424.214159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97415658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5971520
X-RAY DIFFRACTIONr_chiral_restr0.0880.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212774
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_it0.6481.52238
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23123591
X-RAY DIFFRACTIONr_scbond_it2.15431482
X-RAY DIFFRACTIONr_scangle_it3.5364.51435
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 168 -
Rwork0.215 3155 -
obs--98.37 %
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)
10.9711-0.3576-0.36930.4280.22231.53530.04660.02840.16610.0214-0.004-0.1019-0.1211-0.059-0.04260.1026-0.0026-0.01070.0935-0.02250.141714.327224.38028.8254
20.7382-0.0399-0.08830.02840.02840.772-0.039-0.08560.00350.02210.0179-0.03670.01440.00630.02110.1572-0.0006-0.00390.1304-0.01670.134615.410615.204814.693
32.21272.1407-2.01572.2852-2.57914.9760.0325-0.1798-0.17620.1165-0.0941-0.1358-0.27270.22770.06160.1477-0.0346-0.02060.16530.08720.120321.85026.059233.6301
41.7767-0.2873-1.94110.62080.40489.9844-0.1852-0.0888-0.45560.0305-0.02880.00760.90570.11670.2140.2254-0.00120.03110.00920.03070.202519.5717-2.093514.8873
52.4128-0.34972.22580.67380.71188.76530.08660.05610.26440.0421-0.1382-0.04310.3128-0.33630.05160.15-0.00280.00640.1427-0.02530.16311.733123.3558.4211
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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