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- PDB-1hm0: CRYSTAL STRUCTURE OF S.PNEUMONIAE N-ACETYLGLUCOSAMINE 1-PHOSPHATE... -

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Basic information

Entry
Database: PDB / ID: 1hm0
TitleCRYSTAL STRUCTURE OF S.PNEUMONIAE N-ACETYLGLUCOSAMINE 1-PHOSPHATE URIDYLTRANSFERASE, GLMU
ComponentsN-ACETYLGLUCOSAMINE 1-PHOSPHATE URIDYLTRANSFERASE
KeywordsTRANSFERASE / Rossmann-like fold / left-handed-beta-helix / trimer / domain-interchange
Function / homology
Function and homology information


glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell morphogenesis / cell wall organization / regulation of cell shape ...glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell morphogenesis / cell wall organization / regulation of cell shape / magnesium ion binding / cytoplasm
Similarity search - Function
Bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase / GlmU, C-terminal LbH domain / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat ...Bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase / GlmU, C-terminal LbH domain / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Bifunctional protein GlmU
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSulzenbacher, G. / Gal, L. / Peneff, C. / Fassy, F. / Bourne, Y.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of Streptococcus pneumoniae N-acetylglucosamine-1-phosphate uridyltransferase bound to acetyl-coenzyme A reveals a novel active site architecture.
Authors: Sulzenbacher, G. / Gal, L. / Peneff, C. / Fassy, F. / Bourne, Y.
History
DepositionDec 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _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: N-ACETYLGLUCOSAMINE 1-PHOSPHATE URIDYLTRANSFERASE
B: N-ACETYLGLUCOSAMINE 1-PHOSPHATE URIDYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3208
Polymers101,0792
Non-polymers2406
Water3,333185
1
A: N-ACETYLGLUCOSAMINE 1-PHOSPHATE URIDYLTRANSFERASE
hetero molecules

A: N-ACETYLGLUCOSAMINE 1-PHOSPHATE URIDYLTRANSFERASE
hetero molecules

A: N-ACETYLGLUCOSAMINE 1-PHOSPHATE URIDYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,98012
Polymers151,6193
Non-polymers3619
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area10900 Å2
ΔGint-69 kcal/mol
Surface area51250 Å2
MethodPISA
2
B: N-ACETYLGLUCOSAMINE 1-PHOSPHATE URIDYLTRANSFERASE
hetero molecules

B: N-ACETYLGLUCOSAMINE 1-PHOSPHATE URIDYLTRANSFERASE
hetero molecules

B: N-ACETYLGLUCOSAMINE 1-PHOSPHATE URIDYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,98012
Polymers151,6193
Non-polymers3619
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area11000 Å2
ΔGint-66 kcal/mol
Surface area50960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.715, 92.715, 280.387
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Cell settingtrigonal
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-901-

CA

21A-903-

CA

31B-901-

CA

41B-903-

CA

51A-943-

HOH

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Components

#1: Protein N-ACETYLGLUCOSAMINE 1-PHOSPHATE URIDYLTRANSFERASE / E.C.2.7.7.23 / GLMU


Mass: 50539.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: APO-FORM / Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: GLMU / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q97R46, UDP-N-acetylglucosamine diphosphorylase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 26 % PEG 400 (w/w), 300 mM CaCl2, 50 mM NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
113 mg/mlprotein1drop
226 %(v/v)PEG4001reservoir
350 mM1reservoirNaCl
4300 mM1reservoirCaCl2pH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9324 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9324 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 39944 / Num. obs: 37758 / % possible obs: 95.1 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 48.66 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.2
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1291 / % possible all: 97.6
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 79968 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 97.6 %

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMACrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Details: used maximum likelihood refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.244 3766 10 %RANDOM
Rwork0.2071 ---
all0.2108 37758 --
obs0.2108 33992 94.5 %-
Displacement parametersBiso mean: 50.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20.45 Å20 Å2
2--0.9 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6624 0 6 185 6815
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.021
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.6541.946
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord0.1790.5
X-RAY DIFFRACTIONp_mcbond_it1.7371.5
X-RAY DIFFRACTIONp_mcangle_it3.0152
X-RAY DIFFRACTIONp_scbond_it3.5652.5
X-RAY DIFFRACTIONp_scangle_it5.3563
X-RAY DIFFRACTIONp_plane_restr0.0070.02
X-RAY DIFFRACTIONp_chiral_restr0.1160.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.207 / Rfactor Rfree: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS

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