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- PDB-4fce: Crystal structure of Yersinia pestis GlmU in complex with alpha-D... -

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Basic information

Entry
Database: PDB / ID: 4fce
TitleCrystal structure of Yersinia pestis GlmU in complex with alpha-D-glucosamine 1-phosphate (GP1)
ComponentsBifunctional protein GlmU
KeywordsTRANSFERASE / glmU. CSGID / NIAID / Structural Genomics / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / glmU / GP1 / alpha-D-glucosamine 1-phosphate
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 / lipopolysaccharide biosynthetic process / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell morphogenesis / cell wall organization ...glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / lipopolysaccharide biosynthetic process / 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 / MobA-like NTP transferase / MobA-like NTP transferase domain / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) ...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 transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / 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
Chem-GP1 / Bifunctional protein GlmU / Bifunctional protein GlmU
Similarity search - Component
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.955 Å
AuthorsNocek, B. / Kuhn, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of Yersinia pestis GlmU in complex with alpha-D-glucosamine 1-phosphate (GP1)
Authors: Nocek, B. / Kuhn, M. / Anderson, W.F. / Joachimiak, A.
History
DepositionMay 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Source and taxonomy
Revision 1.2Sep 28, 2016Group: Structure summary
Revision 1.3Dec 14, 2016Group: Structure summary
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software
Revision 1.5Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional protein GlmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6687
Polymers49,1741
Non-polymers4946
Water6,269348
1
A: Bifunctional protein GlmU
hetero molecules

A: Bifunctional protein GlmU
hetero molecules

A: Bifunctional protein GlmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,00421
Polymers147,5223
Non-polymers1,48218
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 area15640 Å2
ΔGint-25 kcal/mol
Surface area49360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.571, 87.571, 251.368
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-501-

MG

21A-502-

MG

31A-883-

HOH

41A-921-

HOH

51A-923-

HOH

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Components

#1: Protein Bifunctional protein GlmU / UDP-N-acetylglucosamine pyrophosphorylase / N-acetylglucosamine-1-phosphate uridyltransferase / ...UDP-N-acetylglucosamine pyrophosphorylase / N-acetylglucosamine-1-phosphate uridyltransferase / Glucosamine-1-phosphate N-acetyltransferase


Mass: 49173.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Strain: CO92 / Gene: glmU, YPTB3965 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3
References: UniProt: Q663R0, UniProt: Q8Z9S7*PLUS, UDP-N-acetylglucosamine diphosphorylase, glucosamine-1-phosphate N-acetyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Sugar ChemComp-GP1 / 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose / GLUCOSAMINE 1-PHOSPHATE / 1-O-phosphono-alpha-D-glucosamine / 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucose / 2-amino-2-deoxy-1-O-phosphono-D-glucose / 2-amino-2-deoxy-1-O-phosphono-glucose


Type: D-saccharide / Mass: 259.151 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14NO8P
IdentifierTypeProgram
a-D-Glcp1PO3NIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Mg acetate 10% Peg 8000, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2012 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. all: 42090 / Num. obs: 42078 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Redundancy: 14.4 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 28

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
MOLREPphasing
REFMAC(phenix.refine: 1.7.3_928)refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3FWW

3fww


Resolution: 1.955→32.467 Å / SU ML: 0.18 / σ(F): 2 / Phase error: 19.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 1990 5.03 %RANDOM
Rwork0.1847 ---
all0.19 41534 --
obs0.1862 39544 93.56 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.368 Å2 / ksol: 0.339 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.649 Å20 Å2-0 Å2
2--1.649 Å20 Å2
3----3.298 Å2
Refinement stepCycle: LAST / Resolution: 1.955→32.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3249 0 30 348 3627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013371
X-RAY DIFFRACTIONf_angle_d1.134585
X-RAY DIFFRACTIONf_dihedral_angle_d12.3731209
X-RAY DIFFRACTIONf_chiral_restr0.063551
X-RAY DIFFRACTIONf_plane_restr0.005598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9555-2.00440.2183730.21781392X-RAY DIFFRACTION50
2.0044-2.05860.2524910.21552079X-RAY DIFFRACTION74
2.0586-2.11910.24521500.20542604X-RAY DIFFRACTION94
2.1191-2.18750.23551360.20142797X-RAY DIFFRACTION99
2.1875-2.26570.19891380.19122807X-RAY DIFFRACTION100
2.2657-2.35640.19981670.18232819X-RAY DIFFRACTION100
2.3564-2.46360.24371370.17912821X-RAY DIFFRACTION100
2.4636-2.59340.22641600.17452816X-RAY DIFFRACTION100
2.5934-2.75580.21311560.17812847X-RAY DIFFRACTION100
2.7558-2.96850.20671540.17392846X-RAY DIFFRACTION100
2.9685-3.26690.20791690.17782864X-RAY DIFFRACTION100
3.2669-3.73910.21641620.16722886X-RAY DIFFRACTION99
3.7391-4.70860.19381530.16172896X-RAY DIFFRACTION98
4.7086-32.47110.22951440.22023080X-RAY DIFFRACTION96
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)
10.369-0.44940.03081.2669-0.14340.423-0.0367-0.0604-0.06190.03920.0956-0.0990.0309-0.01580.02990.52380.2785-0.22580.09210.07790.627414.280718.835935.123
23.38760.67230.53692.4562-0.18411.78440.0552-0.1136-0.4552-0.1124-0.0349-0.23880.54980.2163-0.04330.32850.0415-0.00890.10930.02340.1775.363326.690926.6653
33.5783-1.91741.07994.3739-1.37223.66270.31920.4344-0.4595-1.0975-0.3285-0.01310.6520.39050.02060.69230.2172-0.0440.318-0.0490.541314.551317.734728.3728
41.6577-0.3072-1.47861.3155-2.23566.34780.21090.2354-0.2979-0.1256-0.04360.0470.7689-0.27510.02320.80010.2421-0.14990.3478-0.14060.6618.613213.209629.3661
51.3957-0.4482-0.1011.2602-0.57911.1996-0.0754-0.2943-0.49820.39230.1074-0.9380.70190.41730.08840.42550.2189-0.26360.03620.14840.50216.637521.591141.81
62.7512-0.4537-1.43734.5082-1.22554.3241-0.3461-0.7223-0.21341.20640.25690.29710.291-0.45060.00240.81690.04360.11450.69730.08230.31592.63826.187355.4274
72.012-0.5477-0.00553.37630.51761.9628-0.3135-0.6119-0.97230.8940.03080.25460.5318-0.00480.15930.59780.10780.03740.37610.17310.526410.53814.578647.7107
81.3376-0.3860.22171.3807-1.13951.4997-0.3771-0.5762-0.25150.81810.1888-0.47190.21610.04030.04420.7380.1061-0.14460.32130.19260.300912.351123.129149.0279
91.6020.8719-0.0551.8323-0.26481.6860.0586-0.0944-0.01070.1034-0.0334-0.04120.10390.3295-0.01120.10990.03610.00330.14-0.00340.10710.508945.111925.0835
102.90042.7876-0.47667.2218-1.31211.77490.1391-0.17550.21220.2091-0.3214-0.1408-0.09410.51570.0810.08720.03030.02770.3482-0.02320.088619.116248.332614.4401
111.5828-0.48120.13990.7112-0.40071.51870.01630.07960.0728-0.1863-0.0147-0.10160.14530.6299-0.00920.09480.01480.01020.1932-0.02090.118413.406248.76777.3233
124.02924.33830.03335.3668-0.3820.8541-0.0033-0.0824-0.31940.0496-0.1218-0.79480.13410.71940.07670.13180.04570.02250.3195-0.01010.115619.541249.04260.0258
133.1243-0.1456-0.24880.8029-0.51772.04440.0650.1592-0.1219-0.1464-0.0079-0.0980.22470.4233-0.04870.10810.03260.00950.1853-0.02260.118112.086947.2909-7.3706
142.68010.0852-0.30062.1656-0.58942.4190.09890.1061-0.1051-0.1312-0.0936-0.19210.18250.4161-0.01360.14460.03610.01950.2328-0.02980.099214.369547.3548-18.6103
153.8663-2.2164-0.05162.51990.0628-0.00020.22180.2007-0.2545-0.26370.20510.0737-0.05810.4805-0.01950.43130.1995-0.03270.6275-0.02370.1649-6.280759.3019-28.5311
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:16)
2X-RAY DIFFRACTION2(chain A and resid 17:43)
3X-RAY DIFFRACTION3(chain A and resid 44:62)
4X-RAY DIFFRACTION4(chain A and resid 63:83)
5X-RAY DIFFRACTION5(chain A and resid 84:133)
6X-RAY DIFFRACTION6(chain A and resid 134:165)
7X-RAY DIFFRACTION7(chain A and resid 166:195)
8X-RAY DIFFRACTION8(chain A and resid 196:224)
9X-RAY DIFFRACTION9(chain A and resid 225:280)
10X-RAY DIFFRACTION10(chain A and resid 281:291)
11X-RAY DIFFRACTION11(chain A and resid 292:333)
12X-RAY DIFFRACTION12(chain A and resid 334:343)
13X-RAY DIFFRACTION13(chain A and resid 344:388)
14X-RAY DIFFRACTION14(chain A and resid 389:437)
15X-RAY DIFFRACTION15(chain A and resid 438:449)

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