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- PDB-1p3d: Crystal Structure of UDP-N-acetylmuramic acid:L-alanine ligase (M... -

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Basic information

Entry
Database: PDB / ID: 1p3d
TitleCrystal Structure of UDP-N-acetylmuramic acid:L-alanine ligase (MurC) in Complex with UMA and ANP.
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE / UDP-N-acetylmuramate--L-alanine ligase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 17, 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: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...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_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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 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-acetylmuramate--alanine ligase
B: UDP-N-acetylmuramate--alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,25410
Polymers105,5212
Non-polymers2,7338
Water14,250791
1
A: UDP-N-acetylmuramate--alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1275
Polymers52,7611
Non-polymers1,3674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-N-acetylmuramate--alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1275
Polymers52,7611
Non-polymers1,3674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.920, 87.328, 86.113
Angle α, β, γ (deg.)90.00, 104.86, 90.00
Int Tables number4
Space group name H-MP1211

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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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-UMA / URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE


Type: L-peptide linking / Mass: 750.494 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H36N4O20P2
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 791 / 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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, isopropanol, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 mg/mlprotein1drop
25 mMUNAM1drop
35 mMAla1drop
45 mMMn2+1drop
55 mMAMP-PNP1drop
620 %PEG40001reservoir
710 %isopropanol1reservoir
8100 mMHEPES1reservoirpH7.5

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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: Sep 30, 2002
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. all: 117454 / Num. obs: 113461 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.31 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 13.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.47 / Num. unique all: 10574 / % possible all: 90.5
Reflection
*PLUS
Num. measured all: 488589
Reflection shell
*PLUS
% possible obs: 90.5 % / Rmerge(I) obs: 0.54

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P31

1p31


Resolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.899 / SU ML: 0.062 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.096 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19436 5691 5 %RANDOM
Rwork0.16822 ---
all0.16953 107740 --
obs0.16953 107740 96.53 %-
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: 14.505 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å20 Å2-0.44 Å2
2--1.4 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7099 0 164 791 8054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0217390
X-RAY DIFFRACTIONr_angle_refined_deg1.1291.97710034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.465921
X-RAY DIFFRACTIONr_chiral_restr0.0840.21148
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025515
X-RAY DIFFRACTIONr_nbd_refined0.1890.23777
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0940.2796
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.236
X-RAY DIFFRACTIONr_mcbond_it0.3331.54578
X-RAY DIFFRACTIONr_mcangle_it0.64227360
X-RAY DIFFRACTIONr_scbond_it1.37732812
X-RAY DIFFRACTIONr_scangle_it2.1074.52674
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.262 378
Rwork0.244 7178
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)
13.2953-0.64770.08781.8397-0.40812.4143-0.0043-0.35350.0190.1329-0.0302-0.26610.03360.51050.03440.08570.0098-0.00160.3012-0.00420.139623.656-1.44461.374
21.41920.18270.08151.12480.04142.5431-0.02490.09150.044-0.25090.03360.1047-0.17280.0185-0.00880.16010.0023-0.00420.0842-0.01170.08939.5253.84437.948
32.6549-0.18880.02422.69220.37553.16980.12980.5243-0.056-0.26450.1374-0.3661-0.20850.9315-0.26730.213-0.00810.080.5276-0.13470.166933.676-4.99728.776
45.18810.4720.3412.187-0.32332.16580.01790.5250.1779-0.22250.09760.3875-0.0236-0.3295-0.11540.09860.028-0.01070.19220.04090.1826-18.54389.29454.839
51.4338-0.0022-0.53760.8487-0.01661.77140.0039-0.1185-0.08710.1368-0.0224-0.0120.06410.27650.01860.09750.01620.02080.03790.010.111-4.41883.4877.884
62.03680.637-0.73082.4521-0.08071.68640.0722-0.02190.18840.137-0.03650.3507-0.0155-0.1446-0.03570.14760.01930.08080.00260.0130.2094-29.43974.33983.528
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11 - 11811 - 118
2X-RAY DIFFRACTION2AA119 - 324119 - 324
3X-RAY DIFFRACTION3AA325 - 473325 - 473
4X-RAY DIFFRACTION4BB14 - 11814 - 118
5X-RAY DIFFRACTION5BB119 - 324119 - 324
6X-RAY DIFFRACTION6BB325 - 473325 - 473
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rfree: 0.194 / Rfactor Rwork: 0.168
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_deg1.13
LS refinement shell
*PLUS
Highest resolution: 1.7 Å

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