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- PDB-2yqc: Crystal Structure of uridine-diphospho-N-acetylglucosamine pyroph... -

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Basic information

Entry
Database: PDB / ID: 2yqc
TitleCrystal Structure of uridine-diphospho-N-acetylglucosamine pyrophosphorylase from Candida albicans, in the apo-like form
ComponentsUDP-N-acetylglucosamine pyrophosphorylase
KeywordsTRANSFERASE / Pyrophosphorylase / N-acetylglucosamine / Uridine-diphospho-N-acetylglucosamine / N-acetylglucosamine-1-phosphate / Candida albicans
Function / homology
Function and homology information


UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / cytoplasm
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 pyrophosphorylase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMiki, K. / Maruyama, D. / Nishitani, Y. / Nonaka, T. / Kita, A.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal Structure of Uridine-diphospho-N-acetylglucosamine Pyrophosphorylase from Candida albicans and Catalytic Reaction Mechanism
Authors: Maruyama, D. / Nishitani, Y. / Nonaka, T. / Kita, A. / Fukami, T.A. / Mio, T. / Yamada-Okabe, H. / Yamada-Okabe, T. / Miki, K.
History
DepositionMar 30, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 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: UDP-N-acetylglucosamine pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8443
Polymers54,7281
Non-polymers1162
Water7,855436
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.774, 62.891, 90.602
Angle α, β, γ (deg.)90.00, 97.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UDP-N-acetylglucosamine pyrophosphorylase


Mass: 54727.832 Da / Num. of mol.: 1 / Mutation: S216L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: O74933, UDP-N-acetylglucosamine diphosphorylase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 30% PEG 6000, 0.1M ammonium sulfate, 5% glycerol, 0.001M N-acetylglucosamine-1-phosphate, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 28, 2003
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 40383 / % possible obs: 90.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.8 Å2 / Rsym value: 0.111 / Net I/σ(I): 11.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 3729 / Rsym value: 0.337 / % possible all: 68.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JVD

1jvd


Resolution: 1.9→39.7 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1219636.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The intensity of the reflection used for the refinement is more than 0 sigma, but that of the unique reflections in the table of the statistics of the X-ray crystallography at the article is ...Details: The intensity of the reflection used for the refinement is more than 0 sigma, but that of the unique reflections in the table of the statistics of the X-ray crystallography at the article is more than 1 sigma. Therefore, the number of reflections in the refinement section is larger than that in the data collection.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 2055 4.9 %RANDOM
Rwork0.174 ---
obs0.174 41523 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.1034 Å2 / ksol: 0.353506 e/Å3
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.98 Å20 Å2-0.4 Å2
2---0.86 Å20 Å2
3----2.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.9→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3720 0 7 436 4163
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONc_scbond_it2.472
X-RAY DIFFRACTIONc_scangle_it3.512.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.263 290 4.5 %
Rwork0.22 6113 -
obs-6403 92.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4ligand.paramligand.top

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