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- PDB-9sqj: Crystal Structure of the MurT/GatD Enzyme Complex from Streptococ... -

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Basic information

Entry
Database: PDB / ID: 9sqj
TitleCrystal Structure of the MurT/GatD Enzyme Complex from Streptococcus pyogenes with bound AMPPNP
Components(Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit ...) x 2
KeywordsLIGASE / Peptidoglycan / Amidotransferase / Complex
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 / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / transferase activity ...lipid II isoglutaminyl synthase (glutamine-hydrolysing) / carbon-nitrogen ligase activity on lipid II / acid-amino acid ligase activity / glutaminase / cobalamin biosynthetic process / glutaminase activity / 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. ...: / : / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD / Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
Similarity search - Component
Biological speciesStreptococcus pyogenes MGAS10270 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.981 Å
AuthorsVoelpel, S.V. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: Crystal Structure of the MurT/GatD peptidoglycan amidotransferase complex from Streptococcus pyogenes
Authors: Voelpel, S.V. / Stehle, T.
History
DepositionSep 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
CCC: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD
BBB: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
DDD: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,67112
Polymers157,2954
Non-polymers1,3768
Water12,953719
1
AAA: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
CCC: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3366
Polymers78,6482
Non-polymers6884
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-23 kcal/mol
Surface area25860 Å2
MethodPISA
2
BBB: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT
DDD: Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3366
Polymers78,6482
Non-polymers6884
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-22 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.289, 101.210, 177.296
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit ... , 2 types, 4 molecules AAABBBCCCDDD

#1: Protein Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT


Mass: 49037.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes MGAS10270 (bacteria)
Gene: murT, SAMEA1711581_01631 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A8B6J667, lipid II isoglutaminyl synthase (glutamine-hydrolysing)
#2: Protein Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD / Lipid II isoglutaminyl synthase glutaminase subunit


Mass: 29610.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes MGAS10270 (bacteria)
Gene: gatD, E0F67_01185 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A5S4TG60, lipid II isoglutaminyl synthase (glutamine-hydrolysing), glutaminase

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Non-polymers , 5 types, 727 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 719 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 17% (w/v) PEG 3350 0.2 M HEPES pH 7.0 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03321 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.981→49.112 Å / Num. obs: 110500 / % possible obs: 99.55 % / Redundancy: 10.3 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1669 / Rpim(I) all: 0.05389 / Rrim(I) all: 0.1756 / Net I/σ(I): 11.12
Reflection shellResolution: 1.981→2.051 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 1.05 / Num. unique obs: 10870 / CC1/2: 0.474 / CC star: 0.802 / Rpim(I) all: 0.703 / % possible all: 99.14

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.981→49.112 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: FREE R-VALUE / ESU R: 0.148 / ESU R Free: 0.138
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2173 1547 1.4 %
Rwork0.1803 108950 -
all0.181 --
obs-110497 99.559 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 49.396 Å2
Baniso -1Baniso -2Baniso -3
1--1.497 Å2-0 Å20 Å2
2--1.3 Å2-0 Å2
3---0.196 Å2
Refinement stepCycle: LAST / Resolution: 1.981→49.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10153 0 78 719 10950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01310524
X-RAY DIFFRACTIONr_bond_other_d0.0360.0179503
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.64414311
X-RAY DIFFRACTIONr_angle_other_deg2.3861.57322045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.11851322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99524.128516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.829151724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8961535
X-RAY DIFFRACTIONr_chiral_restr0.0730.21441
X-RAY DIFFRACTIONr_chiral_restr_other0.4520.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211870
X-RAY DIFFRACTIONr_gen_planes_other0.010.022129
X-RAY DIFFRACTIONr_nbd_refined0.1980.21931
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.28630
X-RAY DIFFRACTIONr_nbtor_refined0.1670.25181
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.24340
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2708
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0690.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2720.225
X-RAY DIFFRACTIONr_nbd_other0.3550.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2110.224
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1330.21
X-RAY DIFFRACTIONr_mcbond_it3.6725.1475276
X-RAY DIFFRACTIONr_mcbond_other3.675.1475275
X-RAY DIFFRACTIONr_mcangle_it4.8477.7036602
X-RAY DIFFRACTIONr_mcangle_other4.8487.7046603
X-RAY DIFFRACTIONr_scbond_it4.9425.5465248
X-RAY DIFFRACTIONr_scbond_other4.9415.5465249
X-RAY DIFFRACTIONr_scangle_it6.8088.1517709
X-RAY DIFFRACTIONr_scangle_other6.8088.1517710
X-RAY DIFFRACTIONr_lrange_it8.15760.8311739
X-RAY DIFFRACTIONr_lrange_other8.15660.82911739
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.981-2.0320.3841120.33178870.33180870.5420.59598.91180.325
2.032-2.0880.3121100.2977900.2979160.7080.71199.79790.274
2.088-2.1480.3141070.26775390.26777080.7620.7799.19560.243
2.148-2.2140.2951040.23773300.23874730.7740.83899.47810.211
2.214-2.2860.2821010.21271290.21372430.8490.88299.82050.186
2.286-2.3660.244990.20269080.20270230.8890.89999.77220.174
2.366-2.4560.243940.19466710.19567850.8730.89199.70520.166
2.456-2.5560.234910.19364020.19365160.8660.88299.6470.164
2.556-2.6690.241880.18461800.18562960.8650.86299.55530.158
2.669-2.7990.25840.17959080.1860130.8330.86299.65080.155
2.799-2.950.236800.17856260.17957130.8370.86299.87750.156
2.95-3.1280.209750.1852870.18154240.8930.88198.85690.161
3.128-3.3430.217710.17550410.17551130.880.89599.98040.161
3.343-3.6090.205670.17247100.17247780.8790.88799.97910.162
3.609-3.9520.204620.16843390.16844020.8390.85399.97730.161
3.952-4.4140.148560.1439730.1440300.8240.81699.97520.136
4.414-5.090.135500.11734910.11735540.7610.77199.63420.116
5.09-6.2180.136410.14329270.14330340.5710.60497.82470.137
6.218-8.7240.236340.16123790.16224130.5190.6231000.159
8.724-49.1120.244210.20814330.20814550.6790.65599.93130.217

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