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- PDB-1i2c: CRYSTAL STRUCTURE OF MUTANT T145A SQD1 PROTEIN COMPLEX WITH NAD A... -

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Basic information

Entry
Database: PDB / ID: 1i2c
TitleCRYSTAL STRUCTURE OF MUTANT T145A SQD1 PROTEIN COMPLEX WITH NAD AND UDP-GLUCOSE
ComponentsSULFOLIPID BIOSYNTHESIS PROTEIN SQD1
KeywordsBIOSYNTHETIC PROTEIN / SDR / short-chain dehydrogenase/reductase / Rossmann fold
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 / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTheisen, M.J. / Sanda, S.L. / Ginell, S.L. / Benning, C. / Garavito, R.M.
CitationJournal: To be Published
Title: Characterization of the Active Site of UDP-sulfoquinovose Synthase: Formation of the Sulfonic Acid Product in the Crystalline State.
Authors: Theisen, M.J. / Sanda, S.L. / Ginell, S.L. / Benning, C. / Garavito, R.M.
History
DepositionFeb 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1.6Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SULFOLIPID BIOSYNTHESIS PROTEIN SQD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9015
Polymers45,4801
Non-polymers1,4224
Water7,170398
1
A: SULFOLIPID BIOSYNTHESIS PROTEIN SQD1
hetero molecules

A: SULFOLIPID BIOSYNTHESIS PROTEIN SQD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,80310
Polymers90,9592
Non-polymers2,8448
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area9920 Å2
ΔGint-107 kcal/mol
Surface area25290 Å2
MethodPISA, PQS
2
A: SULFOLIPID BIOSYNTHESIS PROTEIN SQD1
hetero molecules

A: SULFOLIPID BIOSYNTHESIS PROTEIN SQD1
hetero molecules

A: SULFOLIPID BIOSYNTHESIS PROTEIN SQD1
hetero molecules

A: SULFOLIPID BIOSYNTHESIS PROTEIN SQD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,60520
Polymers181,9184
Non-polymers5,68716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_556y,x,-z+11
Buried area23380 Å2
ΔGint-235 kcal/mol
Surface area47030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.682, 159.682, 99.038
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 solution form is likely a dimer generated by 2-fold rotation of the crystallographic asymmetric unit about the c-axis: -x -y z

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Components

#1: Protein SULFOLIPID BIOSYNTHESIS PROTEIN SQD1


Mass: 45479.508 Da / Num. of mol.: 1 / Mutation: T145A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: COLUMBIA (COL-2) / Gene: SQD1 / Plasmid: PSQD1 / Production host: Escherichia coli (E. coli) / References: UniProt: O48917
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / 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


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


Mass: 18.015 Da / Num. of mol.: 398 / 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: 3.5 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ammonium sulfate, sodium chloride, MES buffer, NAD+, UDP-glucose, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 31, 2000 / Details: Osmic Max-Flux confocal, multilayer mirrors
RadiationMonochromator: Osmic Max-Flux confocal, multilayer mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 82759 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 4.42 % / Biso Wilson estimate: 15.24 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 13.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 1.5 / % possible all: 97.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
CCP4data reduction
CNS0.9Arefinement
CrystalClear(MSC/RIGAKU)data reduction
CCP4data scaling
CNS0.9Aphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QRR

1qrr


Resolution: 1.6→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.185 4125 5 %R-free flags were assigned using the CCP4 suite, based on a standard set of flags used for all SQD1 structural refinements.
Rwork0.177 ---
all-82704 --
obs-82704 98.8 %-
Solvent computationBsol: 57.55 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso mean: 17.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 90 398 3521
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0053
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_dihedral_angle_d22.09
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.409
X-RAY DIFFRACTIONc_mcangle_it0.69
X-RAY DIFFRACTIONc_scbond_it0.661
X-RAY DIFFRACTIONc_scangle_it1.012
LS refinement shellResolution: 1.6→1.66 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3043 421 5 %
Rwork0.2914 7619 -
obs-8040 97.6 %

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