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- PDB-8cid: Crystal structure of Oryza sativa UAM 2 -

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Basic information

Entry
Database: PDB / ID: 8cid
TitleCrystal structure of Oryza sativa UAM 2
ComponentsUDP-arabinopyranose mutase
KeywordsUNKNOWN FUNCTION / Inactive / UAM / RGP
Function / homology
Function and homology information


UDP-arabinopyranose mutase / UDP-L-arabinose metabolic process / plant-type cell wall biogenesis / intramolecular transferase activity / cell wall organization / Golgi apparatus / cytosol
Similarity search - Function
Reversibly glycosylated polypeptide / Reversibly glycosylated polypeptide family / Reversibly glycosylated polypeptide
Similarity search - Domain/homology
UDP-arabinopyranose mutase
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsFredslund, F. / Adams, P.D. / Welner, D.H.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF20CC0035580 Denmark
CitationJournal: To Be Published
Title: Crystal structure of Oryza sativa UAM 2
Authors: Fredslund, F. / Adams, P.D. / Welner, D.H.
History
DepositionFeb 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-arabinopyranose mutase
B: UDP-arabinopyranose mutase


Theoretical massNumber of molelcules
Total (without water)77,9062
Polymers77,9062
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-29 kcal/mol
Surface area25380 Å2
Unit cell
Length a, b, c (Å)115.390, 115.390, 157.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUALAA1 - 344
d_21ens_1GLUALAB1 - 344

NCS oper: (Code: givenMatrix: (-0.529637293869, 0.848170924305, -0.00950894878039), (0.848213207574, 0.529539993834, -0.01103401227), (-0.00432335970729, -0.0139096403449, -0.999893909606)Vector: -9. ...NCS oper: (Code: given
Matrix: (-0.529637293869, 0.848170924305, -0.00950894878039), (0.848213207574, 0.529539993834, -0.01103401227), (-0.00432335970729, -0.0139096403449, -0.999893909606)
Vector: -9.34248926631, 6.149610822, 121.717305841)

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Components

#1: Protein UDP-arabinopyranose mutase


Mass: 38952.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: amy, H0112G12.3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9ZR36, UDP-arabinopyranose mutase

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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: 3.29 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 25%(v/v) PEG 3350, 200 mM MgCl2
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 3.6→65.2 Å / Num. obs: 12771 / % possible obs: 98.9 % / Redundancy: 1.8 % / Biso Wilson estimate: 82.83 Å2 / Rrim(I) all: 0.197 / Net I/σ(I): 5.3
Reflection shellResolution: 3.6→3.8 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1256 / Rrim(I) all: 0.831 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→65.16 Å / SU ML: 0.1686 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.6858
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2725 1272 9.96 %
Rwork0.2437 11494 -
obs0.2469 12766 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.61 Å2
Refinement stepCycle: LAST / Resolution: 3.6→65.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5424 0 0 0 5424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00575556
X-RAY DIFFRACTIONf_angle_d0.96487534
X-RAY DIFFRACTIONf_chiral_restr0.0556834
X-RAY DIFFRACTIONf_plane_restr0.0111964
X-RAY DIFFRACTIONf_dihedral_angle_d13.50442030
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.13914283449 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.740.31281380.32391251X-RAY DIFFRACTION99.57
3.74-3.910.32941410.28741253X-RAY DIFFRACTION99.29
3.91-4.120.29661400.28211253X-RAY DIFFRACTION99.08
4.12-4.380.28251370.2531245X-RAY DIFFRACTION98.78
4.38-4.720.27141360.23291256X-RAY DIFFRACTION98.86
4.72-5.190.2551430.23091274X-RAY DIFFRACTION98.88
5.19-5.940.27641440.2361294X-RAY DIFFRACTION99.1
5.94-7.480.2931410.24431288X-RAY DIFFRACTION98.15
7.49-65.160.21671520.19781380X-RAY DIFFRACTION97.89
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)
10.9440550381730.1747969126450.1290457416121.0812957806-1.077360363161.1353906711-0.207388443779-0.636201139094-0.1845045509470.00808697319978-0.0307207809873-0.6851815599670.08745467856310.746094074212-0.0001235918566250.776873341637-0.000829636537823-0.04125962765361.021905702850.02272302224721.1564326501376.172324988190.006368095171.2198676001
22.28002332850.06695434737160.01149381982512.86161324918-0.2094410815782.77844946985-0.01836254701740.04192678052720.0503483918995-0.00762136689693-0.0564720645047-0.284497362586-0.00853639861210.2978507606751.83141785865E-50.714561467307-0.0226979706006-0.09039592526370.668041284031-0.03066622017780.70884527096658.847074857694.955114497764.1209115448
31.381630573030.4308934532080.2165176297180.459988671076-0.7079553329261.16098016787-0.0445150292997-0.379585689106-0.361997048362-0.03520555928940.136612658507-0.05475673922920.734061468788-0.142101905839-0.0004123201145471.05726154027-0.0854023862279-0.008463958687990.971117703638-0.07500719469341.1545152384659.391664136776.12252933960.6548471844
40.4112865728480.653156117548-0.09079784363220.999092299886-0.3106726138710.9260185931440.267148702260.5997100546470.109814415695-0.20547451751-0.1671808328160.418455416873-0.616273512745-1.212626057040.0008447161118931.253977746770.420725270752-0.1850592624431.857270536290.139893555221.2145710124125.9607045992117.56699921448.9785553383
51.68749218299-1.42189883636-0.7753330697781.97297435622-0.1640663451191.458115530950.09501371964340.432028469763-0.0157183282963-0.059327679561-0.1964163560180.340323534284-0.237290860087-0.8369301670880.0001031081702670.8925760236690.0804119367264-0.1519240441521.08415495257-0.04115385711210.8668898771439.4572395588105.64650531156.0255710016
60.873671357450.3518559049440.8281144935660.5898339515870.3676880104320.9885792749680.05255531310950.444766172759-0.372479467184-0.455975174893-0.2999401351980.484066417426-0.0602577732553-1.28670578767-0.002786345406261.154455860320.0626198200479-0.0139984575081.7749934704-0.1691180785491.3025334120722.980518932196.206767542559.7952157094
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 87 )AA4 - 871 - 84
22chain 'A' and (resid 88 through 269 )AA88 - 26985 - 266
33chain 'A' and (resid 270 through 346 )AA270 - 346267 - 343
44chain 'B' and (resid 4 through 87 )BB4 - 871 - 84
55chain 'B' and (resid 88 through 269 )BB88 - 26985 - 266
66chain 'B' and (resid 270 through 346 )BB270 - 346267 - 343

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