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- PDB-2z2c: MURA inhibited by unag-cnicin adduct -

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Basic information

Entry
Database: PDB / ID: 2z2c
TitleMURA inhibited by unag-cnicin adduct
ComponentsUDP-N-acetylglucosamine 1-carboxyvinyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PEPTIDOGLYCAN / TRANSFERASE / UDP-N-ACETYLGLUCOSAMINE / CNICIN / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


UDP-N-acetylglucosamine 1-carboxyvinyltransferase / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / cytosol
Similarity search - Function
UDP-N-acetylglucosamine 1-carboxyvinyltransferase / Enolpyruvate transferase domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Alpha Beta
Similarity search - Domain/homology
Chem-UDC / URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSteinbach, A. / Skarzynski, T. / Scheidig, A.J. / Klein, C.D.
CitationJournal: To be Published
Title: The Antibacterial Target Enzyme Mura Synthesizes its Own Non-Covalent Suicide Inhibitor from the Natural Product Cnicin
Authors: Steinbach, A. / Skarzynski, T. / Scheidig, A.J. / Klein, C.D.
History
DepositionMay 17, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Non-polymer description
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_validate_polymer_linkage / software
Item: _pdbx_validate_polymer_linkage.auth_atom_id_1 / _pdbx_validate_polymer_linkage.dist
Revision 1.4Jun 24, 2020Group: Advisory / Data collection / Derived calculations / Category: database_PDB_caveat / diffrn_source / struct_conn
Item: _database_PDB_caveat.text / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Nov 1, 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: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
B: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
C: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
D: UDP-N-acetylglucosamine 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,38612
Polymers181,3564
Non-polymers3,0308
Water16,790932
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14730 Å2
ΔGint-26 kcal/mol
Surface area50650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.127, 80.369, 84.871
Angle α, β, γ (deg.)108.69, 111.07, 101.17
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
UDP-N-acetylglucosamine 1-carboxyvinyltransferase / Enoylpyruvate transferase / UDP-N-acetylglucosamine enolpyruvyl transferase / EPT


Mass: 45339.117 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: MURA / Plasmid: PET 30A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: P0A749, UDP-N-acetylglucosamine 1-carboxyvinyltransferase
#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Sugar
ChemComp-UDC / 2-acetamido-3-O-[(2S,3S)-2-carboxy-3,4-dihydroxybutan-2-yl]-2-deoxy-alpha-D-glucopyranose / 2-(acetylamino)-3-O-[(2S,3S)-2-carboxy-3,4-dihydroxybutan-2-yl]-2-deoxy-alpha-D-glucopyranose / N-acetyl-3-O-[(2S,3S)-2-carboxy-3,4-dihydroxybutan-2-yl]-alpha-D-glucosamine / 2-acetamido-3-O-[(2S,3S)-2-carboxy-3,4-dihydroxybutan-2-yl]-2-deoxy-alpha-D-glucose / 2-acetamido-3-O-[(2S,3S)-2-carboxy-3,4-dihydroxybutan-2-yl]-2-deoxy-D-glucose / 2-acetamido-3-O-[(2S,3S)-2-carboxy-3,4-dihydroxybutan-2-yl]-2-deoxy-glucose


Type: D-saccharide, alpha linking / Mass: 353.322 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H23NO10
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 932 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE LAST FOUR RESIDUES LEU VAL PRO ARG ARE LEFT-OVERS FROM A THROMBIN CLEAVAGE SITE.

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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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15% PEG 4000, 100mM TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.03317 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 22, 2006 / Details: MIRRORS
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.05→19.14 Å / Num. all: 89740 / Num. obs: 84171 / % possible obs: 93.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 7.5
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 2.7 / Num. unique all: 5854 / Rsym value: 0.295 / % possible all: 93.2

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
MAR345dtbdata collection
MAR345data collection
XDSdata scaling
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UAE

1uae


Resolution: 2.05→19.14 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.895 / SU B: 12.7 / SU ML: 0.184 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27068 4202 5 %RANDOM
Rwork0.19102 ---
obs0.19487 79991 93.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.419 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å2-0.05 Å2
3----0.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.238 Å0.298 Å
Luzzati d res low-5 Å
Luzzati sigma a0 Å0 Å
Refinement stepCycle: LAST / Resolution: 2.05→19.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12532 0 192 932 13656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02212904
X-RAY DIFFRACTIONr_angle_refined_deg1.711.99617500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82751660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42623.889504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.229152212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.73215100
X-RAY DIFFRACTIONr_chiral_restr0.110.22104
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029448
X-RAY DIFFRACTIONr_nbd_refined0.2390.27411
X-RAY DIFFRACTIONr_nbtor_refined0.3140.28819
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.21175
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.213
X-RAY DIFFRACTIONr_mcbond_it0.8141.58436
X-RAY DIFFRACTIONr_mcangle_it1.269213264
X-RAY DIFFRACTIONr_scbond_it2.19634851
X-RAY DIFFRACTIONr_scangle_it3.3194.54236
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 298 -
Rwork0.239 5856 -
obs--93.61 %
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)
11.813-0.25240.13732.6708-0.250.80820.0080.0602-0.05290.14490.0230.2433-0.00460.0264-0.0311-0.2003-0.0166-0.0062-0.04560.0236-0.17740.5630.294-0.034
21.11250.2109-0.31731.9567-0.42270.8251-0.0723-0.0547-0.0537-0.00050.04130.13050.09660.02670.031-0.1898-0.02140.0087-0.02520.0438-0.168612.892-34.247-1.121
31.5015-0.3771-0.11961.38820.06010.6689-0.06220.0362-0.0451-0.1361-0.04850.0406-0.0559-0.02760.1107-0.1094-0.0276-0.0285-0.04470.0195-0.1843-1.76-0.736-36.743
43.2447-1.2876-0.32982.15470.16180.7705-0.0365-0.0979-0.43580.006-0.01090.00870.1353-0.0610.0474-0.0919-0.0740.0225-0.00830.028-0.0817-0.829-37.453-35.788
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 4181 - 418
2X-RAY DIFFRACTION2BB1 - 4181 - 418
3X-RAY DIFFRACTION3CC1 - 4181 - 418
4X-RAY DIFFRACTION4DD1 - 4181 - 418

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