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- PDB-3oc9: Crystal structure of putative UDP-N-acetylglucosamine pyrophospho... -

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Basic information

Entry
Database: PDB / ID: 3oc9
TitleCrystal structure of putative UDP-N-acetylglucosamine pyrophosphorylase from Entamoeba histolytica
ComponentsUDP-N-acetylglucosamine pyrophosphorylase
KeywordsTRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / anaerobic parasitic protozoan / amoebic dysentery / amoebic liver abscess / cysts / UDP-N-acetylglucosamine diphosphorylase / nucleotidyl transferase
Function / homology
Function and homology information


UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process
Similarity search - Function
UDP-sugar pyrophosphorylase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
UDP-N-acetylglucosamine diphosphorylase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Structure of uridine diphosphate N-acetylglucosamine pyrophosphorylase from Entamoeba histolytica.
Authors: Edwards, T.E. / Gardberg, A.S. / Phan, I.Q. / Zhang, Y. / Staker, B.L. / Myler, P.J. / Lorimer, D.D.
History
DepositionAug 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 13, 2015Group: Database references
Revision 1.3May 20, 2015Group: Database references
Revision 1.4Sep 6, 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

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7593
Polymers46,6001
Non-polymers1582
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.520, 77.540, 86.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UDP-N-acetylglucosamine pyrophosphorylase


Mass: 46600.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: EHI_021200
References: UniProt: C4M036, UDP-N-acetylglucosamine diphosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PLASMID USED TO EXPRESS THE SEQUENCE WAS GENERATED FROM GENOMIC DNA. THE SEQUENCE WAS VERIFIED ...THE PLASMID USED TO EXPRESS THE SEQUENCE WAS GENERATED FROM GENOMIC DNA. THE SEQUENCE WAS VERIFIED IN BOTH THE FORWARD AND REVERSE DIRECTION, YET DIFFERS AT THESE TWO AMINO ACIDS FROM THE PREVIOUSLY PUBLISHED GENOMIC SEQUENCE IN UNP

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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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 96.3 mg/mL of EnhiA.01126.b.A1 PS00631 3C cleaved against JCSG+ condition H9, 0.2 M lithium sulfate, 0.1 M BisTris pH 5.5, 25% PEG 3350 with 15% ethylene glycol as cryo-protectant, crystal ...Details: 96.3 mg/mL of EnhiA.01126.b.A1 PS00631 3C cleaved against JCSG+ condition H9, 0.2 M lithium sulfate, 0.1 M BisTris pH 5.5, 25% PEG 3350 with 15% ethylene glycol as cryo-protectant, crystal tracking ID 216241h9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 48592 / Num. obs: 48589 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 32.461 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 30.45
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.850.5294.4324713573100
1.85-1.90.4155.8338763437100
1.9-1.950.3057.9329253350100
1.95-2.010.23610.2322073277100
2.01-2.080.17213.6312903176100
2.08-2.150.13816.8301513064100
2.15-2.230.10821.2291982971100
2.23-2.320.08825282142872100
2.32-2.430.07329.1270402743100
2.43-2.550.0633.5258912630100
2.55-2.680.05337.8244382498100
2.68-2.850.04643.4232392386100
2.85-3.040.0448.9215582226100
3.04-3.290.03555200942088100
3.29-3.60.03261.7184941950100
3.6-4.020.02967.6164761765100
4.02-4.650.02770.4142221565100
4.65-5.690.02471.8124501334100
5.69-8.050.02469.998451059100
8.050.0272.7532662599.5

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Phasing

Phasing MRRfactor: 59.43 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å46.15 Å
Translation3 Å46.15 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1jv1 molecule A residues 68-407

1jv1


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.224 / WRfactor Rwork: 0.1865 / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.8605 / SU B: 5.172 / SU ML: 0.074 / SU R Cruickshank DPI: 0.119 / SU Rfree: 0.1176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 2450 5.1 %RANDOM
Rwork0.189 ---
obs0.1909 48468 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 89.86 Å2 / Biso mean: 31.9097 Å2 / Biso min: 10.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3199 0 9 380 3588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223405
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9654634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7865439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6825.063160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15815614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1891510
X-RAY DIFFRACTIONr_chiral_restr0.0980.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212589
X-RAY DIFFRACTIONr_mcbond_it0.7011.52051
X-RAY DIFFRACTIONr_mcangle_it1.29423347
X-RAY DIFFRACTIONr_scbond_it1.94931354
X-RAY DIFFRACTIONr_scangle_it3.3364.51267
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 202 -
Rwork0.283 3358 -
all-3560 -
obs--99.69 %
Refinement TLS params.Method: refined / Origin x: 67.9234 Å / Origin y: 70.8686 Å / Origin z: 18.2509 Å
111213212223313233
T0.0354 Å20.0039 Å2-0.0253 Å2-0.0456 Å2-0.0047 Å2--0.0549 Å2
L0.2404 °2-0.2223 °20.1475 °2-0.3857 °2-0.0246 °2--0.1795 °2
S0.0055 Å °0.0011 Å °0.014 Å °-0.0004 Å °0.0258 Å °-0.0601 Å °0.0091 Å °-0.01 Å °-0.0313 Å °

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