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- PDB-1p31: Crystal Structure of UDP-N-acetylmuramic acid:L-alanine Ligase (M... -

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Basic information

Entry
Database: PDB / ID: 1p31
TitleCrystal Structure of UDP-N-acetylmuramic acid:L-alanine Ligase (MurC) from Haemophilus influenzae
ComponentsUDP-N-acetylmuramate--alanine ligase
KeywordsLIGASE / alpha/beta protein
Function / homology
Function and homology information


UDP-N-acetylmuramate-L-alanine ligase / UDP-N-acetylmuramate-L-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / ATP binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramate--L-alanine ligase / : / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central ...UDP-N-acetylmuramate--L-alanine ligase / : / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Protein-Tyrosine Phosphatase; Chain A / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EPU / UDP-N-acetylmuramate--L-alanine ligase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsMol, C.D. / Brooun, A. / Dougan, D.R. / Hilgers, M.T. / Tari, L.W. / Wijnands, R.A. / Knuth, M.W. / McRee, D.E. / Swanson, R.V.
CitationJournal: J.Bacteriol. / Year: 2003
Title: Crystal Structures of Active Fully Assembled Substrate- and Product-Bound Complexes of UDP-N-Acetylmuramic Acid:L-Alanine Ligase (MurC) from Haemophilus influenzae.
Authors: Mol, C.D. / Brooun, A. / Dougan, D.R. / Hilgers, M.T. / Tari, L.W. / Wijnands, R.A. / Knuth, M.W. / McRee, D.E. / Swanson, R.V.
History
DepositionApr 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / 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 / _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.conn_type_id / _struct_conn.id / _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 / _struct_ref_seq_dif.details / _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-acetylmuramate--alanine ligase
B: UDP-N-acetylmuramate--alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,9738
Polymers105,5212
Non-polymers1,4526
Water12,611700
1
A: UDP-N-acetylmuramate--alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4874
Polymers52,7611
Non-polymers7263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-N-acetylmuramate--alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4874
Polymers52,7611
Non-polymers7263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.523, 92.274, 118.174
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UDP-N-acetylmuramate--alanine ligase / UDP-N-acetylmuramoyl-L-alanine synthetase


Mass: 52760.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: MURC / Plasmid: pSX29 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41
References: UniProt: P45066, UDP-N-acetylmuramate-L-alanine ligase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EPU / URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID / ENOLPYRUVYL-URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 677.400 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N3O19P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 700 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 277 K / Method: nanovolume / pH: 8.1
Details: PEG 4000, glycerol, magnesium chloride, Tris, pH 8.1, nanovolume, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.9 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
114 mg/mlprotein1drop
225 mMTris1droppH7.9
3150 mM1dropNaCl
45 mMdithiothreitol1drop
55 mMUNAM substrate1drop
624 %PEG40001reservoir
720 %glycerol1reservoir
8160 mM1reservoirMgCl2
9100 mMTris1reservoirpH8.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 31, 2002
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→25 Å / Num. all: 86600 / Num. obs: 77944 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.45 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 10.8
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3 / Num. unique all: 5314 / % possible all: 93
Reflection
*PLUS
% possible obs: 90 % / Num. measured all: 347154
Reflection shell
*PLUS
% possible obs: 93 %

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→25 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.59 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.144 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20836 3868 5 %RANDOM
Rwork0.16938 ---
all0.17135 73241 --
obs0.17135 73241 89.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.859 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å20 Å2
2---1.65 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.85→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7115 0 92 700 7907
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0217357
X-RAY DIFFRACTIONr_angle_refined_deg1.1121.9649973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5235927
X-RAY DIFFRACTIONr_chiral_restr0.0750.21137
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025530
X-RAY DIFFRACTIONr_nbd_refined0.1940.23669
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2657
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.247
X-RAY DIFFRACTIONr_mcbond_it0.4431.54593
X-RAY DIFFRACTIONr_mcangle_it0.88527384
X-RAY DIFFRACTIONr_scbond_it1.87932764
X-RAY DIFFRACTIONr_scangle_it2.964.52587
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.249 269
Rwork0.198 5507
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)
12.00530.0342-0.11494.8587-0.56482.1914-0.10410.30780.1276-0.49660.02080.04980.0947-0.08170.08330.1005-0.0348-0.00270.14410.0110.076859.19552.987-12.931
20.71070.0138-0.14012.08150.50632.3653-0.06340.0024-0.06150.1591-0.0450.21660.1826-0.18140.10850.012-0.00540.02450.0749-0.0040.071452.88349.20113.92
31.3473-0.18750.43762.1784-0.08021.2051-0.02690.0186-0.05050.05760.03440.1621-0.0642-0.0363-0.00750.00890.00290.01180.07820.01480.104845.56876.0939.604
41.3951-0.79640.41963.6552-1.10181.87380.08060.0890.0574-0.3875-0.0340.00960.1686-0.0157-0.04650.11270.0133-0.02390.08170.00870.0729.29829.207-9.285
50.80370.00040.45051.4113-0.36421.5481-0.0082-0.0320.01210.0668-0.0052-0.01070.0702-0.01960.01350.02070.0213-0.02810.0632-0.00040.058114.57925.1617.667
61.342-0.09470.3062.7388-0.06951.5094-0.0598-0.04880.06260.23330.0775-0.1448-0.1012-0.0858-0.01770.05930.0289-0.0160.1013-0.00750.07865.84450.9416.85
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 11812 - 118
2X-RAY DIFFRACTION2AA119 - 324119 - 324
3X-RAY DIFFRACTION3AA325 - 473325 - 473
4X-RAY DIFFRACTION4BB12 - 11812 - 118
5X-RAY DIFFRACTION5BB119 - 324119 - 324
6X-RAY DIFFRACTION6BB325 - 473325 - 473
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rfree: 0.208 / Rfactor Rwork: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.008
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.11
LS refinement shell
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 1.9 Å

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