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- PDB-4a1k: Ykud L,D-transpeptidase -

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Basic information

Entry
Database: PDB / ID: 4a1k
TitleYkud L,D-transpeptidase
ComponentsPUTATIVE L, D-TRANSPEPTIDASE YKUD
KeywordsTRANSFERASE / PEPTIDOGLYCAN SYNTHESIS
Function / homology
Function and homology information


spore wall / Transferases / peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / sporulation resulting in formation of a cellular spore / glycosyltransferase activity / cell wall organization / regulation of cell shape
Similarity search - Function
Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / : / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain / LysM domain superfamily ...Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / : / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain / LysM domain superfamily / Lysin motif / LysM domain / LysM domain profile. / LysM domain / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Putative L,D-transpeptidase YkuD
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBlaise, M. / Fuglsang Midtgaard, S. / Roi Midtgaard, S. / Boesen, T. / Thirup, S.
CitationJournal: To be Published
Title: Structures of Three New Crystal Forms of the Ykud L,D-Transpeptidase from B. Subtilis.
Authors: Blaise, M. / Fuglsang Midtgaard, S. / Roi Midtgaard, S. / Boesen, T. / Thirup, S.
History
DepositionSep 15, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE L, D-TRANSPEPTIDASE YKUD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7762
Polymers17,6801
Non-polymers961
Water3,801211
1
A: PUTATIVE L, D-TRANSPEPTIDASE YKUD
hetero molecules

A: PUTATIVE L, D-TRANSPEPTIDASE YKUD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5534
Polymers35,3612
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1940 Å2
ΔGint-46.6 kcal/mol
Surface area14940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.900, 59.900, 117.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2027-

HOH

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Components

#1: Protein PUTATIVE L, D-TRANSPEPTIDASE YKUD / YKUD L\ / D TRANSPEPTIDASE / SPORE PROTEIN YKUD


Mass: 17680.348 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O34816, Transferases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 117 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLN 118 TO ALA
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: 2.99 Å3/Da / Density % sol: 58.82 % / Description: NONE
Crystal growDetails: 100 MM BIS-TRIS PH 6.5, 3 M NACL AND 2MM MURNAC MONOSACCHARIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Mar 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.75→53 Å / Num. obs: 22287 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 15.96 % / Biso Wilson estimate: 27.65 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 29.6
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 15.01 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.9 / % possible all: 99.9

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y7M

1y7m


Resolution: 1.75→28.789 Å / SU ML: 0.52 / σ(F): 1.99 / Phase error: 19.75 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2122 1999 9 %
Rwork0.1858 --
obs0.1883 22270 99.57 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.382 Å2 / ksol: 0.375 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.5735 Å20 Å20 Å2
2--8.5735 Å20 Å2
3---5.1249 Å2
Refinement stepCycle: LAST / Resolution: 1.75→28.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1243 0 5 211 1459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071299
X-RAY DIFFRACTIONf_angle_d1.0521775
X-RAY DIFFRACTIONf_dihedral_angle_d11.517476
X-RAY DIFFRACTIONf_chiral_restr0.074208
X-RAY DIFFRACTIONf_plane_restr0.005228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79380.3031380.28911397X-RAY DIFFRACTION100
1.7938-1.84230.34411410.30021432X-RAY DIFFRACTION100
1.8423-1.89650.2751400.25691415X-RAY DIFFRACTION100
1.8965-1.95770.28821400.21491420X-RAY DIFFRACTION100
1.9577-2.02760.24631410.20011441X-RAY DIFFRACTION100
2.0276-2.10880.22621400.19011414X-RAY DIFFRACTION100
2.1088-2.20480.24941430.1771453X-RAY DIFFRACTION100
2.2048-2.32090.22831420.18031438X-RAY DIFFRACTION100
2.3209-2.46630.23791410.1911431X-RAY DIFFRACTION100
2.4663-2.65660.25541440.20281458X-RAY DIFFRACTION100
2.6566-2.92370.22771440.19771461X-RAY DIFFRACTION100
2.9237-3.34620.23311460.19451480X-RAY DIFFRACTION100
3.3462-4.21380.18871470.15531501X-RAY DIFFRACTION100
4.2138-28.79320.14241520.16641530X-RAY DIFFRACTION95
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)
13.2862-1.254-2.28151.43950.28142.85830.05220.31810.0929-0.11660.0162-0.0026-0.1404-0.31990.00960.10520.05080.05790.30770.0490.113217.300420.0887-17.5526
20.65420.52640.06715.6994-1.64822.22050.3116-0.05870.48940.3982-0.0862-0.0263-0.4480.0972-0.00330.2669-0.03630.13360.12140.00170.21717.06323.9562-8.3766
33.80872.65784.50241.96242.98845.5399-0.3357-0.27390.8306-0.4308-0.07840.5912-1.0654-0.70260.450.39450.160.11640.29760.120.560717.623229.8352-18.1509
42.0832-2.52860.01124.9163-0.77380.31230.23090.26950.2001-0.07-0.2029-0.0715-0.132-0.0697-0.02850.1315-0.01360.05060.17080.02330.114926.567816.0329-15.3478
54.49242.65941.17663.34830.50251.9587-0.34120.45110.1138-0.59260.13060.19040.042-0.03390.17410.2605-0.0303-0.0260.1729-0.03540.103216.6524-1.0578-15.3025
64.82820.8187-0.51792.87410.21711.8229-0.04520.3969-0.0946-0.53090.106-0.4048-0.06710.1987-0.07910.2025-0.03230.07530.1031-0.07270.151824.0585-4.9702-15.5959
75.0231-0.64451.28570.30820.12120.6927-0.0188-0.09310.039-0.11990.05640.19660.0439-0.0933-0.02220.1631-0.0777-0.07850.14190.04770.17364.70062.6929-9.8141
82.18980.77940.50472.4828-1.38765.29840.02780.0654-0.057-0.0904-0.0897-0.13390.12790.26420.04870.0773-0.01560.0240.09830.02190.069220.93628.8189-7.3758
90.3842-0.1007-0.62730.6525-0.23481.28010.0434-0.155-0.256-0.07090.03830.20040.1765-0.0784-0.04010.1168-0.0343-0.03330.11590.05570.135312.98051.6082-2.0196
104.97130.4146-0.89894.2672-2.70686.0651-0.01030.0206-0.8067-0.0933-0.1548-0.25120.58850.01210.13350.17620.0083-0.00770.08790.0060.150624.0273-3.8413-3.6817
117.36330.88570.70814.7292-0.67335.68380.00820.32460.1385-0.3548-0.1470.23180.0994-0.07340.14350.1494-0.01180.02520.0673-0.01260.059319.22855.2137-14.6441
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:12)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 13:29)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 30:42)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 43:56)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 57:66)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 67:81)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 82:93)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 94:103)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 104:144)
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 145:154)
11X-RAY DIFFRACTION11CHAIN A AND (RESSEQ 155:165)

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