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- PDB-6lqb: A third intermediate state of L,D-transpeptidase LdtMt2-ertapenem... -

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Basic information

Entry
Database: PDB / ID: 6lqb
TitleA third intermediate state of L,D-transpeptidase LdtMt2-ertapenem adduct
ComponentsL,D-transpeptidase 2
KeywordsTRANSFERASE / YKUD DOMAIN / L / D-TRANSPEPTIDASE / BETA-LACTAM BINDING
Function / homology
Function and homology information


peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / cell wall organization / regulation of cell shape / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
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.
Similarity search - Domain/homology
Chem-2RG / ACETIC ACID / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLi, D.F. / Qin, Y.L.
CitationJournal: Prog.Biochem.Biophys. / Year: 2020
Title: A New State I-plus Observed for the L,D-transpeptidase LdtMt2-ertapenem Adduct
Authors: Wang, X.Y. / Qin, Y.L. / Han, Q. / Gu, X.E. / Yan, Z. / Fu, K. / Li, D.F. / Deng, K.
History
DepositionJan 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: 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)59,9449
Polymers58,5612
Non-polymers1,3837
Water7,242402
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0345
Polymers29,2801
Non-polymers7544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-1 kcal/mol
Surface area12620 Å2
MethodPISA
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9104
Polymers29,2801
Non-polymers6303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.181, 73.207, 103.803
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 142 through 155 or resid 157 through 405))
21(chain B and (resid 142 through 155 or resid 157 through 405))

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
11THRTHRTYRTYR(chain A and (resid 142 through 155 or resid 157 through 405))AA142 - 1553 - 16
12METMETASNASN(chain A and (resid 142 through 155 or resid 157 through 405))AA157 - 40518 - 266
21THRTHRTYRTYR(chain B and (resid 142 through 155 or resid 157 through 405))BB142 - 1553 - 16
22METMETASNASN(chain B and (resid 142 through 155 or resid 157 through 405))BB157 - 40518 - 266

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Components

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


Mass: 29280.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: ldtB, lppS, Rv2518c, RVBD_2518c, P425_02624 / Plasmid: PMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: I6Y9J2, Transferases; Acyltransferases; Aminoacyltransferases
#2: Chemical ChemComp-2RG / (2S,3R,4S)-4-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid / ERTAPENEM, bound form POST-ISOMERIZED


Mass: 477.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H27N3O7S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20 mM Tris-HCl pH 8.0, 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9777 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 1.7→44.97 Å / Num. obs: 57876 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.025 / Rrim(I) all: 0.091 / Net I/σ(I): 20.3 / Num. measured all: 760265
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.7313.30.983989129900.9160.2771.0193.199.9
9-44.9711.60.0353944650.9980.010.03254.299.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VYP

3vyp


Resolution: 1.7→44.969 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2095 2003 3.47 %
Rwork0.1806 55791 -
obs0.1816 57794 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.75 Å2 / Biso mean: 27.1735 Å2 / Biso min: 12.42 Å2
Refinement stepCycle: final / Resolution: 1.7→44.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4080 0 129 402 4611
Biso mean--42.54 36.14 -
Num. residues----531
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1586X-RAY DIFFRACTION4.802TORSIONAL
12B1586X-RAY DIFFRACTION4.802TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.7-1.74250.32521430.26133907
1.7425-1.78960.25031440.24043946
1.7896-1.84230.27311440.2143923
1.8423-1.90180.23381420.19113923
1.9018-1.96970.2411290.183951
1.9697-2.04860.21031560.17683943
2.0486-2.14180.2081390.17313964
2.1418-2.25470.20121360.17423964
2.2547-2.3960.2081480.18073959
2.396-2.5810.21311430.17843988
2.581-2.84070.23051460.18094000
2.8407-3.25160.19281410.17034026
3.2516-4.09630.18991440.16434068
4.0963-44.9690.18941480.18234229
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)
10.6417-0.21410.07671.8004-0.11280.5020.0346-0.0647-0.08380.1049-0.05320.02750.06030.00950.01940.1578-0.01680.00650.18940.0030.1434-39.8971-13.1262-13.886
20.0596-0.4871-0.34271.7090.90861.4864-0.0195-0.26310.28480.59430.4622-0.61610.30370.4632-0.26030.29660.0507-0.06750.3352-0.14660.3309-37.77166.3708-0.2607
30.6601-0.4527-0.06681.30120.30660.73610.015-0.0320.02780.0656-0.0158-0.064-0.0271-0.01530.00090.1508-0.01710.00360.1619-0.01020.1635-40.12133.4362-13.8118
41.1540.01530.19791.9096-0.66431.27480.3156-0.1671-0.73690.369-0.15060.17360.56680.2112-0.14560.5406-0.0357-0.0940.38140.10630.4046-9.2039-24.457-6.0681
50.6666-0.0373-0.49831.1774-0.48361.28890.26190.131-0.2401-0.3151-0.22020.07640.72770.3778-0.01690.33620.1015-0.030.21280.00150.1938-4.6804-17.7228-15.942
62.2234-0.95110.61852.5641-0.96061.44150.32110.1872-0.2665-0.2545-0.02120.3480.4301-0.0499-0.28550.3402-0.016-0.04330.1902-0.01050.1959-14.0354-12.4907-22.5317
70.4856-0.77170.39152.2933-1.40981.05380.2835-0.4329-0.5770.11210.2580.26271.3191-0.3501-0.2640.89290.0571-0.2180.22910.06230.4271-8.176-26.049-9.9059
80.735-0.3833-0.19021.1998-0.04560.9853-0.04280.09060.0487-0.04990.03030.0783-0.11190.0507-0.01120.1553-0.011-0.00420.17190.00880.1612-9.34210.893-19.0528
90.5510.0966-0.04510.78230.68251.94690.0245-0.15030.07030.23180.0046-0.08260.12610.012-0.00320.21220.00320.01470.18220.00440.1774-6.80474.0533-3.7117
102.6533-1.00041.49810.72180.06282.15030.0269-0.04980.21320.22380.0237-0.5373-0.16780.2249-0.01150.3646-0.0096-0.03160.3064-0.06190.4174-0.179612.97554.2091
110.86280.2408-0.07721.17080.18521.5018-0.0482-0.029-0.0330.05080.0349-0.0150.04450.09590.01360.14960.0223-0.00020.16450.00850.1331-6.54865.1258-13.4666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 141 through 289 )A141 - 289
2X-RAY DIFFRACTION2chain 'A' and (resid 290 through 323 )A290 - 323
3X-RAY DIFFRACTION3chain 'A' and (resid 324 through 407 )A324 - 407
4X-RAY DIFFRACTION4chain 'B' and (resid 142 through 164 )B142 - 164
5X-RAY DIFFRACTION5chain 'B' and (resid 165 through 212 )B165 - 212
6X-RAY DIFFRACTION6chain 'B' and (resid 213 through 226 )B213 - 226
7X-RAY DIFFRACTION7chain 'B' and (resid 227 through 249 )B227 - 249
8X-RAY DIFFRACTION8chain 'B' and (resid 250 through 289 )B250 - 289
9X-RAY DIFFRACTION9chain 'B' and (resid 290 through 308 )B290 - 308
10X-RAY DIFFRACTION10chain 'B' and (resid 309 through 323 )B309 - 323
11X-RAY DIFFRACTION11chain 'B' and (resid 324 through 405 )B324 - 405

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