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- PDB-6fqb: MurT/GatD peptidoglycan amidotransferase complex from Streptococc... -

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Basic information

Entry
Database: PDB / ID: 6fqb
TitleMurT/GatD peptidoglycan amidotransferase complex from Streptococcus pneumoniae R6
Components
  • Cobyric acid synthase
  • Mur ligase family protein
KeywordsLIGASE / Mur family / amidotransferase / cytosolic
Function / homology
Function and homology information


lipid II isoglutaminyl synthase (glutamine-hydrolysing) / carbon-nitrogen ligase activity on lipid II / acid-amino acid ligase activity / glutaminase / cobalamin biosynthetic process / glutaminase activity / glutamine metabolic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape ...lipid II isoglutaminyl synthase (glutamine-hydrolysing) / carbon-nitrogen ligase activity on lipid II / acid-amino acid ligase activity / glutaminase / cobalamin biosynthetic process / glutaminase activity / glutamine metabolic process / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / transferase activity / zinc ion binding / ATP binding
Similarity search - Function
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT, C-terminal / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT / MurT ligase C-terminal / CobB/CobQ-like glutamine amidotransferase / Cobyric acid synthase, glutamine amidotransferase type 1 / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD / CobB/CobQ-like glutamine amidotransferase domain / CobBQ-type GATase domain profile. / Mur ligase, central / Mur-like, catalytic domain superfamily ...Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT, C-terminal / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT / MurT ligase C-terminal / CobB/CobQ-like glutamine amidotransferase / Cobyric acid synthase, glutamine amidotransferase type 1 / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD / CobB/CobQ-like glutamine amidotransferase domain / CobBQ-type GATase domain profile. / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
GLUTAMINE / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3 Å
AuthorsMorlot, C. / Contreras-Martel, C. / Leisico, F. / Straume, D. / Peters, K. / Hegnar, O.A. / Simon, N. / Villard, A.M. / Breukink, E. / Gravier-Pelletier, C. ...Morlot, C. / Contreras-Martel, C. / Leisico, F. / Straume, D. / Peters, K. / Hegnar, O.A. / Simon, N. / Villard, A.M. / Breukink, E. / Gravier-Pelletier, C. / Le Corre, L. / Vollmer, W. / Pietrancosta, N. / Havarstein, L.S. / Zapun, A.
Funding support France, 1items
OrganizationGrant numberCountry
INSERM-Astra Zeneca France
CitationJournal: Nat Commun / Year: 2018
Title: Structure of the essential peptidoglycan amidotransferase MurT/GatD complex from Streptococcus pneumoniae.
Authors: Morlot, C. / Straume, D. / Peters, K. / Hegnar, O.A. / Simon, N. / Villard, A.M. / Contreras-Martel, C. / Leisico, F. / Breukink, E. / Gravier-Pelletier, C. / Le Corre, L. / Vollmer, W. / ...Authors: Morlot, C. / Straume, D. / Peters, K. / Hegnar, O.A. / Simon, N. / Villard, A.M. / Contreras-Martel, C. / Leisico, F. / Breukink, E. / Gravier-Pelletier, C. / Le Corre, L. / Vollmer, W. / Pietrancosta, N. / Havarstein, L.S. / Zapun, A.
History
DepositionFeb 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
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.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mur ligase family protein
E: Cobyric acid synthase
B: Mur ligase family protein
F: Cobyric acid synthase
C: Mur ligase family protein
G: Cobyric acid synthase
D: Mur ligase family protein
H: Cobyric acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,23412
Polymers324,6508
Non-polymers5854
Water00
1
A: Mur ligase family protein
E: Cobyric acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3093
Polymers81,1622
Non-polymers1461
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-12 kcal/mol
Surface area26350 Å2
MethodPISA
2
B: Mur ligase family protein
F: Cobyric acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3093
Polymers81,1622
Non-polymers1461
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-10 kcal/mol
Surface area26280 Å2
MethodPISA
3
C: Mur ligase family protein
G: Cobyric acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3093
Polymers81,1622
Non-polymers1461
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-10 kcal/mol
Surface area25990 Å2
MethodPISA
4
D: Mur ligase family protein
H: Cobyric acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3093
Polymers81,1622
Non-polymers1461
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-11 kcal/mol
Surface area26340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)288.430, 288.430, 115.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14E
24F
15E
25G
16E
26H
17B
27C
18B
28D
19F
29G
110F
210H
111C
211D
112G
212H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERSERSERAA43 - 43861 - 456
21SERSERSERSERBC43 - 43861 - 456
12SERSERSERSERAA43 - 43861 - 456
22SERSERSERSERCE43 - 43861 - 456
13SERSERARGARGAA43 - 43961 - 457
23SERSERARGARGDG43 - 43961 - 457
14METMETALAALAEB1 - 2471 - 247
24METMETALAALAFD1 - 2471 - 247
15METMETALAALAEB1 - 2471 - 247
25METMETALAALAGF1 - 2471 - 247
16METMETALAALAEB1 - 2471 - 247
26METMETALAALAHH1 - 2471 - 247
17SERSERSERSERBC43 - 43861 - 456
27SERSERSERSERCE43 - 43861 - 456
18SERSERSERSERBC43 - 43861 - 456
28SERSERSERSERDG43 - 43861 - 456
19METMETALAALAFD1 - 2471 - 247
29METMETALAALAGF1 - 2471 - 247
110METMETALAALAFD1 - 2471 - 247
210METMETALAALAHH1 - 2471 - 247
111SERSERALAALACE43 - 43761 - 455
211SERSERALAALADG43 - 43761 - 455
112METMETALAALAGF1 - 2471 - 247
212METMETALAALAHH1 - 2471 - 247

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
Mur ligase family protein / UDP-N-acetylmuramyl peptide synthase / UDP-N-acetylmuramyl tripeptide synthetase / Mur ligase


Mass: 51940.234 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria)
Gene: A4260_05845, ERS019420_00606, ERS020535_00125, ERS021368_00525, ERS022199_00743, ERS043879_01366
Plasmid: pET30-HAT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star
References: UniProt: A0A0B7LND9, UniProt: Q8DNZ9*PLUS, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein
Cobyric acid synthase / Glutamine amidotransferase


Mass: 29222.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria)
Gene: A4260_05840, AWW74_09320, CHL72_09035, CIT24_04835, CS877_04020, CSH34_00860, ERS003549_02292, ERS019166_00428, ERS019416_00232, ERS019420_00605, ERS019499_01955, ERS019595_01427, ERS020136_ ...Gene: A4260_05840, AWW74_09320, CHL72_09035, CIT24_04835, CS877_04020, CSH34_00860, ERS003549_02292, ERS019166_00428, ERS019416_00232, ERS019420_00605, ERS019499_01955, ERS019595_01427, ERS020136_01107, ERS020137_00292, ERS020140_00887, ERS020142_00808, ERS020143_01959, ERS020147_00746, ERS020148_00821, ERS020178_04008, ERS020408_00223, ERS020474_01302, ERS020521_00204, ERS020522_00778, ERS020523_00656, ERS020524_01042, ERS020526_00540, ERS020526_04035, ERS020527_01973, ERS020528_00148, ERS020541_00600, ERS020692_00332, ERS020827_01405, ERS020831_02169, ERS021300_01369, ERS021447_05442, ERS021629_07046, ERS021762_02260, ERS021858_02776, ERS022045_06260, ERS022071_00358, ERS022199_00742, ERS022232_05365, ERS022363_01901, ERS022390_00924, ERS044004_01668, ERS068943_01580, ERS232497_02277, ERS232498_04930, ERS232508_01880, ERS409064_00176, ERS558328_00424, SAMEA1026345_00620, SAMEA2626854_01213, SAMEA2626872_01126
Plasmid: pET30-HAT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star
References: UniProt: A0A062WUX3, UniProt: Q8DNZ8*PLUS, EC: 6.3.5.10
#3: Chemical
ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H10N2O3
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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.2 M tri-sodium citrate pH 6.1 14% PEG 3350 4 mM NiSO4
PH range: 6.0-6.2

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Data collection

DiffractionMean temperature: 193.15 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 68725 / % possible obs: 96.2 % / Redundancy: 3 % / Rsym value: 0.058 / Net I/σ(I): 15.4
Reflection shellResolution: 3→3.18 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 11055 / Rsym value: 0.447 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 22.948 / SU ML: 0.362 / Cross valid method: THROUGHOUT / ESU R Free: 0.405 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22809 6854 10 %RANDOM
Rwork0.18923 ---
obs0.19315 61871 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 86.337 Å2
Baniso -1Baniso -2Baniso -3
1--2.67 Å2-1.33 Å20 Å2
2---2.67 Å20 Å2
3---8.66 Å2
Refinement stepCycle: 1 / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19687 0 40 0 19727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01920115
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218262
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.95927279
X-RAY DIFFRACTIONr_angle_other_deg0.994342415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.83352483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53425.152986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33153307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3811581
X-RAY DIFFRACTIONr_chiral_restr0.0830.23043
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0222558
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023991
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.7198.60410004
X-RAY DIFFRACTIONr_mcbond_other5.7188.60410003
X-RAY DIFFRACTIONr_mcangle_it8.67612.89412463
X-RAY DIFFRACTIONr_mcangle_other8.67612.89412464
X-RAY DIFFRACTIONr_scbond_it5.7849.04810111
X-RAY DIFFRACTIONr_scbond_other5.7799.04710108
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.91613.40914817
X-RAY DIFFRACTIONr_long_range_B_refined11.63421684
X-RAY DIFFRACTIONr_long_range_B_other11.63421685
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A230460.08
12B230460.08
21A231180.06
22C231180.06
31A232080.07
32D232080.07
41E161160.06
42F161160.06
51E161020.07
52G161020.07
61E160220.07
62H160220.07
71B229260.07
72C229260.07
81B228500.08
82D228500.08
91F160620.06
92G160620.06
101F160020.07
102H160020.07
111C229680.08
112D229680.08
121G160080.08
122H160080.08
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.575 497 -
Rwork0.511 4588 -
obs--96.73 %

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