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- PDB-1hv9: STRUCTURE OF E. COLI GLMU: ANALYSIS OF PYROPHOSPHORYLASE AND ACET... -

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Basic information

Entry
Database: PDB / ID: 1hv9
TitleSTRUCTURE OF E. COLI GLMU: ANALYSIS OF PYROPHOSPHORYLASE AND ACETYLTRANSFERASE ACTIVE SITES
ComponentsUDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
KeywordsTRANSFERASE / left-handed parallel beta-helix
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 wall organization / cell morphogenesis / 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 wall organization / cell morphogenesis / regulation of cell shape / magnesium ion binding / identical protein binding / membrane / cytosol
Similarity search - Function
Bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase / GlmU, C-terminal LbH domain / : / MobA-like NTP transferase / MobA-like NTP transferase domain / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Hexapeptide repeat proteins ...Bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase / GlmU, C-terminal LbH domain / : / MobA-like NTP transferase / MobA-like NTP transferase domain / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 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
: / COENZYME A / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Bifunctional protein GlmU
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.1 Å
AuthorsOlsen, L.R. / Roderick, S.L.
Citation
Journal: Biochemistry / Year: 2001
Title: Structure of the Escherichia coli GlmU pyrophosphorylase and acetyltransferase active sites.
Authors: Olsen, L.R. / Roderick, S.L.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Purification, Crystallization and Preliminary X-ray Data for Escherichia coli GlmU: A Bifunctional Acetyltransferase/Uridyltransferase
Authors: Olsen, L.R. / Tian, Y. / Roderick, S.L.
History
DepositionJan 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 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_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.ptnr1_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
B: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,54611
Polymers98,5022
Non-polymers3,0449
Water4,630257
1
A: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
hetero molecules

A: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
hetero molecules

A: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,23115
Polymers147,7533
Non-polymers4,47812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area16350 Å2
ΔGint-52 kcal/mol
Surface area52850 Å2
MethodPISA
2
B: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
hetero molecules

B: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
hetero molecules

B: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,40818
Polymers147,7533
Non-polymers4,65515
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area17230 Å2
ΔGint-97 kcal/mol
Surface area52650 Å2
MethodPISA, PQS
3
A: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
hetero molecules

A: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
hetero molecules

A: UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,23115
Polymers147,7533
Non-polymers4,47812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
MethodPQS
Unit cell
Length a, b, c (Å)104.500, 104.500, 648.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-9030-

CO

21A-9031-

CO

31B-9028-

CO

41B-9029-

CO

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Components

#1: Protein UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE / N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE


Mass: 49250.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GLMU / Plasmid: PET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P0ACC7, UDP-N-acetylglucosamine diphosphorylase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 3.46 Å3/Da / Density % sol: 64.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: MES, ammonium sulfate, magnesium chloride, cobalt chloride, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
PH range low: 6.4 / PH range high: 5.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18.3 mg/mlprotein1drop
214 mMUDP-GlcNAc1drop
328 mM1dropMgCl2
419 mM1dropCoA
51.65 Mammonium sulfate1reservoir
650 mMMES1reservoir
72-10 mM1reservoirCoCl2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 6, 1999 / Details: confocal mirrors
RadiationMonochromator: confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30.25 Å / Num. all: 391782 / Num. obs: 391782 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 9.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 1.62 / % possible all: 82.2
Reflection
*PLUS
Num. obs: 91622 / % possible obs: 98 % / Num. measured all: 495967 / Rmerge(I) obs: 0.136

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.1→30.25 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 3799 5 %SHELLS
Rwork0.211 ---
all0.213 76727 --
obs0.211 76727 95.3 %-
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.1→30.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6758 0 179 257 7194
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d27.9
X-RAY DIFFRACTIONx_improper_angle_d0.61
X-RAY DIFFRACTIONx_mcbond_it1.061.5
X-RAY DIFFRACTIONx_mcangle_it1.672
X-RAY DIFFRACTIONx_scbond_it2.032
X-RAY DIFFRACTIONx_scangle_it3.212.5
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.329 310 4.9 %
Rwork0.28 6001 -
obs--79.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2COA_SLR.PARAMCOA_SLR.TOP
X-RAY DIFFRACTION3UD_XPLOR_PARAMUD_XPLOR_TOP
X-RAY DIFFRACTION4TIP3P.PARAMETERTIP3P.TOPOLOGY
X-RAY DIFFRACTION5COBALT.PARAMCOBALT.TOP
Software
*PLUS
Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.61
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.329 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.28 / Rfactor obs: 0.277

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