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- PDB-6rlg: Crystal structure of LdtMt2 from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 6rlg
TitleCrystal structure of LdtMt2 from Mycobacterium tuberculosis
ComponentsL,D-transpeptidase 2
KeywordsANTIMICROBIAL PROTEIN / beta lactmase / antibiotic resistance / tuberculosis
Function / homology
Function and homology information


peptidoglycan-based cell wall biogenesis / peptidoglycan-protein cross-linking / peptidoglycan metabolic process / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan-based cell wall / cell wall organization / regulation of cell shape / extracellular region ...peptidoglycan-based cell wall biogenesis / peptidoglycan-protein cross-linking / peptidoglycan metabolic process / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan-based cell wall / cell wall organization / regulation of cell shape / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Immunoglobulin-like - #3710 / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Immunoglobulin-like - #3710 / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
NITRATE ION / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51000183032 Å
AuthorsBrem, J. / Lohans, C. / Schofield, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: Chem.Commun.(Camb.) / Year: 2019
Title: Targeting the Mycobacterium tuberculosis transpeptidase LdtMt2with cysteine-reactive inhibitors including ebselen.
Authors: de Munnik, M. / Lohans, C.T. / Lang, P.A. / Langley, G.W. / Malla, T.R. / Tumber, A. / Schofield, C.J. / Brem, J.
History
DepositionMay 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: L,D-transpeptidase 2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,24621
Polymers76,0242
Non-polymers1,22119
Water14,916828
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,92516
Polymers38,0121
Non-polymers91315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3205
Polymers38,0121
Non-polymers3084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.950, 93.920, 75.570
Angle α, β, γ (deg.)90.000, 93.030, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUVALVAL(chain 'A' and ((resid 57 and (name N or name...AA57 - 664 - 13
12ASPASPALAALA(chain 'A' and ((resid 57 and (name N or name...AA68 - 7715 - 24
13VALVALTHRTHR(chain 'A' and ((resid 57 and (name N or name...AA79 - 9226 - 39
14VALVALASNASN(chain 'A' and ((resid 57 and (name N or name...AA94 - 9541 - 42
15ASNASNPROPRO(chain 'A' and ((resid 57 and (name N or name...AA97 - 10044 - 47
16ALAALATRPTRP(chain 'A' and ((resid 57 and (name N or name...AA102 - 11249 - 59
17THRTHRTYRTYR(chain 'A' and ((resid 57 and (name N or name...AA114 - 12061 - 67
18ARGARGTHRTHR(chain 'A' and ((resid 57 and (name N or name...AA123 - 12570 - 72
19ASNASNSERSER(chain 'A' and ((resid 57 and (name N or name...AA127 - 14674 - 93
110PROPROLYSLYS(chain 'A' and ((resid 57 and (name N or name...AA148 - 18995 - 136
111THRTHRPROPRO(chain 'A' and ((resid 57 and (name N or name...AA191 - 194138 - 141
112VALVALGLUGLU(chain 'A' and ((resid 57 and (name N or name...AA196 - 235143 - 182
113PHEPHEVALVAL(chain 'A' and ((resid 57 and (name N or name...AA238 - 294185 - 241
114ARGARGLYSLYS(chain 'A' and ((resid 57 and (name N or name...AA297 - 299244 - 246
115ILEILELYSLYS(chain 'A' and ((resid 57 and (name N or name...AA301 - 370248 - 317
116GLYGLYLYSLYS(chain 'A' and ((resid 57 and (name N or name...AA372 - 407319 - 354
217LEULEUVALVAL(chain 'B' and (resid 57 through 66 or resid 68...BB57 - 664 - 13
218ASPASPALAALA(chain 'B' and (resid 57 through 66 or resid 68...BB68 - 7715 - 24
219VALVALTHRTHR(chain 'B' and (resid 57 through 66 or resid 68...BB79 - 9226 - 39
220VALVALASNASN(chain 'B' and (resid 57 through 66 or resid 68...BB94 - 9541 - 42
221ASNASNPROPRO(chain 'B' and (resid 57 through 66 or resid 68...BB97 - 10044 - 47
222ALAALATRPTRP(chain 'B' and (resid 57 through 66 or resid 68...BB102 - 11249 - 59
223THRTHRTYRTYR(chain 'B' and (resid 57 through 66 or resid 68...BB114 - 12061 - 67
224ARGARGTHRTHR(chain 'B' and (resid 57 through 66 or resid 68...BB123 - 12570 - 72
225ASNASNSERSER(chain 'B' and (resid 57 through 66 or resid 68...BB127 - 14674 - 93
226PROPROLYSLYS(chain 'B' and (resid 57 through 66 or resid 68...BB148 - 18995 - 136
227THRTHRPROPRO(chain 'B' and (resid 57 through 66 or resid 68...BB191 - 194138 - 141
228VALVALGLUGLU(chain 'B' and (resid 57 through 66 or resid 68...BB196 - 235143 - 182
229PHEPHEVALVAL(chain 'B' and (resid 57 through 66 or resid 68...BB238 - 294185 - 241
230ARGARGLYSLYS(chain 'B' and (resid 57 through 66 or resid 68...BB297 - 299244 - 246
231ILEILELYSLYS(chain 'B' and (resid 57 through 66 or resid 68...BB301 - 370248 - 317
232GLYGLYLYSLYS(chain 'B' and (resid 57 through 66 or resid 68...BB372 - 407319 - 354

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein L,D-transpeptidase 2 / LDT 2 / Ldt(Mt2)


Mass: 38012.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: ldtB, MT2594, V735_02606 / Production host: Escherichia coli (E. coli)
References: UniProt: O53223, Transferases; Acyltransferases; Aminoacyltransferases

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Non-polymers , 5 types, 847 molecules

#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 828 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: 0.2 M Ammonium nitrate pH 6.3, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97952 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 30, 2018
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 1.51→33.79 Å / Num. obs: 132783 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 21.2079757645 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.0748 / Rpim(I) all: 0.032 / Rrim(I) all: 0.081 / Net I/σ(I): 12.03
Reflection shellResolution: 1.51→1.54 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6593 / CC1/2: 0.56 / Rpim(I) all: 0.685 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
SHELXDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DUJ

5duj


Resolution: 1.51000183032→33.7871482655 Å / SU ML: 0.173821797353 / Cross valid method: FREE R-VALUE / σ(F): 1.34349787152 / Phase error: 22.2968116321
RfactorNum. reflection% reflection
Rfree0.203826681086 6726 5.06842295635 %
Rwork0.180194769066 --
obs0.181402239935 132704 99.8082115539 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.1701442648 Å2
Refinement stepCycle: LAST / Resolution: 1.51000183032→33.7871482655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5237 0 78 828 6143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008599656405075649
X-RAY DIFFRACTIONf_angle_d0.992585718867736
X-RAY DIFFRACTIONf_chiral_restr0.0633409903721857
X-RAY DIFFRACTIONf_plane_restr0.007118805683721026
X-RAY DIFFRACTIONf_dihedral_angle_d12.66306250723262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.52720.3229261474311920.3379378775924210X-RAY DIFFRACTION99.7507364605
1.5272-1.54510.3359220944852180.3138478299244171X-RAY DIFFRACTION99.8862084661
1.5451-1.5640.2765205268882230.2880649015754221X-RAY DIFFRACTION99.9550157445
1.564-1.58380.2917605170562190.2784579531434145X-RAY DIFFRACTION99.931302954
1.5838-1.60460.2982371208362130.2728507170484279X-RAY DIFFRACTION99.8888147654
1.6046-1.62660.2810229103412380.2781687463944116X-RAY DIFFRACTION99.9540863177
1.6266-1.64980.2716107052832390.2626465601454251X-RAY DIFFRACTION100
1.6498-1.67440.2836407511342280.2494027795274131X-RAY DIFFRACTION99.954138959
1.6744-1.70060.257045154892230.2480031250864191X-RAY DIFFRACTION99.9773499434
1.7006-1.72850.2633267346472260.2370717763274206X-RAY DIFFRACTION99.932356257
1.7285-1.75830.2338578842992030.219666043594194X-RAY DIFFRACTION99.9318181818
1.7583-1.79030.2336825566832030.2079734106184235X-RAY DIFFRACTION99.954954955
1.7903-1.82470.2335951156892110.2060213012484183X-RAY DIFFRACTION99.9772468714
1.8247-1.86190.2146927669762000.1971922873194223X-RAY DIFFRACTION99.9548022599
1.8619-1.90240.2277501034822380.199643102714225X-RAY DIFFRACTION99.9328257949
1.9024-1.94670.2298999791561970.2066676613674181X-RAY DIFFRACTION99.8176014592
1.9467-1.99540.1940605473382440.1910024045554202X-RAY DIFFRACTION99.9550359712
1.9954-2.04930.1916623102082300.1801910312054199X-RAY DIFFRACTION99.9774266366
2.0493-2.10960.2155025245562260.186507743764180X-RAY DIFFRACTION99.5931283906
2.1096-2.17770.2002300816042500.1745449104844167X-RAY DIFFRACTION99.9321266968
2.1777-2.25550.1963197331432540.1726058094664149X-RAY DIFFRACTION99.5253164557
2.2555-2.34580.1718579398832220.1738320222394197X-RAY DIFFRACTION99.5494480739
2.3458-2.45250.187191525412530.1715125834584167X-RAY DIFFRACTION99.9321727334
2.4525-2.58180.205110179762270.1645413416134192X-RAY DIFFRACTION99.684186781
2.5818-2.74340.2060736615532190.1701355623754204X-RAY DIFFRACTION99.4826810616
2.7434-2.95520.2073033050752040.1739081268134253X-RAY DIFFRACTION99.9775684163
2.9552-3.25230.2098503300622430.1659199785994197X-RAY DIFFRACTION99.7752808989
3.2523-3.72240.1764985557282290.1570515828794199X-RAY DIFFRACTION99.3939393939
3.7224-4.68790.1541158718332090.1414868767584250X-RAY DIFFRACTION99.2432673047
4.6879-33.79560.2096713202132450.1749094604954260X-RAY DIFFRACTION99.49204947
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)
1-0.04426785295360.142405558512-0.1048467437510.405665937033-0.9754182528513.0621498638-0.01433150425210.01377799906-0.009847929117910.0136621151090.1137315640440.0118982271879-0.0852267954306-0.0573511134909-0.09260807025180.1783135295980.0467116288430.02988596690540.2188035246980.01410369045170.243247265952-11.0686894511-87.7203573834-12.4643478071
21.18150286195-0.08008826399860.06030644438831.485024799360.6067432084041.507462637770.159931086085-0.0195762515517-0.08955943088550.0911343913285-0.16857166064-0.0270962694870.0620133868672-0.0421837242230.01613668100630.17002066888-0.000168947752132-0.02667686283970.1485599523930.004516226942460.163592198761-17.4789319168-95.26312310417.9659274255
30.1903638723860.160746032901-0.3044284662030.2965729000880.5361637752432.15040082048-0.009912388098310.0465147580529-0.0358232039326-0.02064584400640.0802648058459-0.04841465780470.02899382217290.105825319804-0.07614815579910.1728518138440.0333655844564-0.02626881408640.171150285343-0.001902078615590.21699126306410.6544195459-101.89757774316.9655747961
41.687494172810.04152027528720.3686465783481.25658072597-0.4387643712631.483974566060.141504312307-0.2241022806650.07467201152130.128307694482-0.168019483714-0.0797959711395-0.1189464694860.04730189160110.02870442602860.186005949132-0.0399551638819-0.000121353848090.156239259158-0.003846450771160.15573884173813.5910153149-90.812980486554.3121103056
52.795277576361.840720404430.4392297885915.26262496828-1.329990346412.686089723960.0261337960434-0.156542651250.1551307236740.00117146718343-0.01695099463170.118713074408-0.0632052393147-0.145745116352-0.01094383808050.1248232180050.02222983924220.0108022107620.122790415081-0.007086681496770.147463652696-10.4744807036-77.4374788315-33.4356364539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 123 through 248 )
2X-RAY DIFFRACTION2chain 'B' and (resid 249 through 407 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 248 )
4X-RAY DIFFRACTION4chain 'A' and (resid 249 through 407 )
5X-RAY DIFFRACTION5chain 'B' and (resid 57 through 122 )

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