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- PDB-1ejd: Crystal structure of unliganded mura (type1) -

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Basic information

Entry
Database: PDB / ID: 1ejd
TitleCrystal structure of unliganded mura (type1)
ComponentsUDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYLTRANSFERASE
KeywordsTRANSFERASE / inside-out alpha/beta barrel
Function / homology
Function and homology information


UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / cytoplasm
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
CYCLOHEXYLAMMONIUM ION / PHOSPHATE ION / UDP-N-acetylglucosamine 1-carboxyvinyltransferase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
AuthorsEschenburg, S. / Schonbrunn, E.
Citation
Journal: Proteins / Year: 2000
Title: Comparative X-ray analysis of the un-liganded fosfomycin-target murA.
Authors: Eschenburg, S. / Schonbrunn, E.
#1: Journal: Biochemistry / Year: 2000
Title: Role of the Loop Containing Residue 115 in the Induced-fit Mechanism of the Bacterial Cell Wall Biosynthetic Enzyme MurA
Authors: Schonbrunn, E. / Eschenburg, S. / Krekel, F. / Luger, K. / Amrhein, N.
#2: Journal: Structure / Year: 1996
Title: Crystal structure of UDP-N-acetylglucosamine enolpyruvyltransferase, the target of the antibiotic fosfomycin
Authors: Schonbrunn, E. / Sack, S. / Eschenburg, S. / Perrakis, A. / Krekel, F. / Amrhein, N. / Mandelkow, E.
History
DepositionMar 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.4Aug 9, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_validate_polymer_linkage / 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 / _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_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 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)91,58422
Polymers89,6592
Non-polymers1,92520
Water16,628923
1
A: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,69510
Polymers44,8291
Non-polymers8659
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,89012
Polymers44,8291
Non-polymers1,06011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYLTRANSFERASE
hetero molecules

B: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYLTRANSFERASE
hetero molecules

A: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYLTRANSFERASE
hetero molecules

A: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,16944
Polymers179,3184
Non-polymers3,85140
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
crystal symmetry operation3_545x+1/2,y-1/2,z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
Buried area17890 Å2
ΔGint-208 kcal/mol
Surface area58080 Å2
MethodPISA
4
B: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYLTRANSFERASE
hetero molecules

A: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,58422
Polymers89,6592
Non-polymers1,92520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545x+1/2,y-1/2,z1
Buried area6280 Å2
ΔGint-86 kcal/mol
Surface area31710 Å2
MethodPISA
5
B: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYLTRANSFERASE
hetero molecules

B: UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,77924
Polymers89,6592
Non-polymers2,12122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area6790 Å2
ΔGint-105 kcal/mol
Surface area33040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.177, 156.297, 84.036
Angle α, β, γ (deg.)90.00, 91.63, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-424-

HOH

21B-925-

HOH

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Components

#1: Protein UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYLTRANSFERASE / MURA / EPT


Mass: 44829.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P33038, UDP-N-acetylglucosamine 1-carboxyvinyltransferase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-HAI / CYCLOHEXYLAMMONIUM ION


Mass: 100.182 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 923 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.19 Å3/Da / Density % sol: 61.45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1 M sodium/potassium phosphate including 30 mM cyclohexylammonium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
pH: 6.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.8 Msodium/potassium phosphate1drop
240 mMcyclohexylammmonium1drop
30.8 Msodium/potassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 6, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.55→17 Å / Num. all: 155426 / Num. obs: 155426 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.75 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 24.2
Reflection shellResolution: 1.55→1.57 Å / Rmerge(I) obs: 0.246 / % possible all: 87.1
Reflection
*PLUS
Num. measured all: 738470
Reflection shell
*PLUS
% possible obs: 87.1 % / Mean I/σ(I) obs: 3.9

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementStarting model: 1NAW without solvent molecules

1naw


Resolution: 1.55→17 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: the following HOH were modelled as alternatives to their respective PO4: HOH 9 PO4 2424 HOH 1 PO4 2432 HOH 7 PO4 2427 HOH 11 PO4 2432 There is either the HOH molecule or the PO4, so they do ...Details: the following HOH were modelled as alternatives to their respective PO4: HOH 9 PO4 2424 HOH 1 PO4 2432 HOH 7 PO4 2427 HOH 11 PO4 2432 There is either the HOH molecule or the PO4, so they do not see each other. The PO4 ions in these HOH-PO4 pairs are labelled alternate conformation A, and the HOH is labelled alternate conformation B. The same is valid for O HOH 8 and NH2 ARG252 in chain B. The water molecule occupies one of the alternative side chain positions. HOH 8 has alternate conformation A, since it occupies alternate conformation A NH2 ARG252.
RfactorNum. reflection% reflectionSelection details
Rfree0.207 4686 3 %RANDOM
Rwork0.185 ---
all-155426 --
obs-155426 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.2566 Å2 / ksol: 0.388307 e/Å3
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å20 Å20.57 Å2
2--1.55 Å20 Å2
3----3.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.55→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6286 0 110 923 7319
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d1.26
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.248 676 2.9 %
Rwork0.233 22991 -
obs--87.7 %
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.26

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