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- PDB-1i24: HIGH RESOLUTION CRYSTAL STRUCTURE OF THE WILD-TYPE PROTEIN SQD1, ... -

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Basic information

Entry
Database: PDB / ID: 1i24
TitleHIGH RESOLUTION CRYSTAL STRUCTURE OF THE WILD-TYPE PROTEIN SQD1, 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 5, 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 1.4Aug 9, 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

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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)46,9315
Polymers45,5101
Non-polymers1,4224
Water6,954386
1
A: SULFOLIPID BIOSYNTHESIS PROTEIN SQD1
hetero molecules

A: SULFOLIPID BIOSYNTHESIS PROTEIN SQD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,86310
Polymers91,0192
Non-polymers2,8448
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area9990 Å2
ΔGint-99 kcal/mol
Surface area25600 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)187,72620
Polymers182,0384
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 area23530 Å2
ΔGint-220 kcal/mol
Surface area47660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.243, 160.243, 99.273
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

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Components

#1: Protein SULFOLIPID BIOSYNTHESIS PROTEIN SQD1


Mass: 45509.531 Da / Num. of mol.: 1
Fragment: RECOMBINANT SQD1, LACKING N-TERMINAL PUTATIVE CHLOROPLAST TARGETTING SEQUENCE, AND WITH N-TERMINAL 6X HISTIDINE TAG
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 / 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.: 386 / 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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.03321
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 23, 1999
RadiationMonochromator: SAGITALLY FOCUSING SI (111) DOUBLE CRYSTAL MONOCHROMATOR AND VERTICALLY FOCUSING MIRROR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.14→99 Å / Num. obs: 196326 / % possible obs: 86.4 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 11.59 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 21.4
Reflection shellResolution: 1.14→1.19 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 1.7 / % possible all: 38

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Processing

Software
NameVersionClassification
d*TREKdata scaling
HKL-2000data collection
SCALEPACKdata scaling
TRUNCATEdata reduction
CNS0.9Arefinement
d*TREKdata reduction
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
CNS0.9Aphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QRR

1qrr


Resolution: 1.2→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.198 9260 5 %REFLECTIONS FOR CROSS-VALIDATION WERE SELECTED FROM A STANDARD SET OF DUMMY DATA GENERATED USING THE CCP4 SUITE, WHERE 5% OF THE RELECTIONS ARE FLAGGED. THE SELECTED REFLECTIONS MATCH THOSE IN PDB ENTRY 1QRR.
Rwork0.192 ---
obs0.192 184009 92.3 %-
Solvent computationBsol: 68.07 Å2 / ksol: 0.439 e/Å3
Displacement parametersBiso mean: 13.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.15 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 90 386 3508
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.58
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.74
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.798
X-RAY DIFFRACTIONc_mcangle_it1.117
X-RAY DIFFRACTIONc_scbond_it1.361
X-RAY DIFFRACTIONc_scangle_it1.983
LS refinement shellResolution: 1.2→1.24 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2984 806 5 %
Rwork0.2813 14360 -
obs--82.1 %

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