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- PDB-1qrr: CRYSTAL STRUCTURE OF SQD1 PROTEIN COMPLEX WITH NAD AND UDP-GLUCOSE -

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Basic information

Entry
Database: PDB / ID: 1qrr
TitleCRYSTAL STRUCTURE OF SQD1 PROTEIN COMPLEX WITH NAD AND UDP-GLUCOSE
Componentssulfolipid biosynthesis (SQD1) PROTEIN
KeywordsISOMERASE / ROSSMANN FOLD / SHORT HYDROGEN BONDS / SDR HOMOLOG
Function / homology
Function and homology information


UDP-sulfoquinovose synthase / UDPsulfoquinovose synthase activity / glycolipid biosynthetic process / sulfotransferase activity / cellular response to phosphate starvation / chloroplast / zinc ion binding / plasma membrane
Similarity search - Function
UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-sulfoquinovose synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsMulichak, A.M. / Theisen, M.J. / Essigmann, B. / Benning, C. / Garavito, R.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Crystal structure of SQD1, an enzyme involved in the biosynthesis of the plant sulfolipid headgroup donor UDP-sulfoquinovose.
Authors: Mulichak, A.M. / Theisen, M.J. / Essigmann, B. / Benning, C. / Garavito, R.M.
History
DepositionJun 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: sulfolipid biosynthesis (SQD1) PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7865
Polymers44,3641
Non-polymers1,4224
Water6,323351
1
A: sulfolipid biosynthesis (SQD1) PROTEIN
hetero molecules

A: sulfolipid biosynthesis (SQD1) PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,57210
Polymers88,7292
Non-polymers2,8448
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)159.610, 159.610, 98.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-600-

HOH

21A-601-

HOH

DetailsThe biological assembly is a dimer comprised of chain A and a second chain generated by the crystallographic two-fold rotation axis along z.

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Components

#1: Protein sulfolipid biosynthesis (SQD1) PROTEIN


Mass: 44364.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / References: UniProt: O48917
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

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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: 3.55 Å3/Da / Density % sol: 65.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ammonium sulfate, MES buffer, NAD+, UDP-glucose, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13-4 mg/mlprotein1drop
21.0 Mammonium sulfate1drop
30.1 MMES1drop
45 mMNAD+1drop
55 mMUDP-glucose1drop
61.0-2.0 Mammonium sulfate1reservoir
70.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Dec 8, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. all: 75606 / Num. obs: 75606 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.35 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 9.59
Reflection shellResolution: 1.6→1.656 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.384 / Num. unique all: 4965 / % possible all: 60.3
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 60.3 %

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Processing

Software
NameVersionClassification
SOLVEphasing
X-PLOR3.851refinement
FRAMBOdata collection
SAINTV. 5.0data scaling
RefinementResolution: 1.6→30 Å / σ(F): 1 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.191 3228 -RANDOM
Rwork0.17 ---
obs0.179 63023 75.4 %-
all-68263 --
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 90 351 3481
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.37
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 30 Å / σ(F): 1 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.5

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