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- PDB-4iiw: 2.6 Angstrom Crystal Structure of Putative yceG-like Protein lmo1... -

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Basic information

Entry
Database: PDB / ID: 4iiw
Title2.6 Angstrom Crystal Structure of Putative yceG-like Protein lmo1499 from Listeria monocytogenes
ComponentsLmo1499 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


peptidoglycan lytic transglycosylase / lytic endotransglycosylase activity / peptidoglycan biosynthetic process / cell wall organization / plasma membrane
Similarity search - Function
Endolytic murein transglycosylase / Endolytic murein transglycosylase / YceG-like family / Dna Ligase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Endolytic murein transglycosylase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.6 Angstrom Crystal Structure of Putative yceG-like Protein lmo1499 from Listeria monocytogenes
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lmo1499 protein
B: Lmo1499 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,82615
Polymers79,8872
Non-polymers93913
Water3,387188
1
B: Lmo1499 protein
hetero molecules

B: Lmo1499 protein
hetero molecules

B: Lmo1499 protein
hetero molecules

B: Lmo1499 protein
hetero molecules

A: Lmo1499 protein
hetero molecules

A: Lmo1499 protein
hetero molecules

A: Lmo1499 protein
hetero molecules

A: Lmo1499 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,30460
Polymers319,5478
Non-polymers3,75752
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_445x-1/2,y-1/2,z+1/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation7_545-y+1/2,x-1/2,z+1/21
crystal symmetry operation8_455y-1/2,-x+1/2,z+1/21
Buried area20340 Å2
ΔGint-325 kcal/mol
Surface area121740 Å2
MethodPISA
2
A: Lmo1499 protein
hetero molecules

A: Lmo1499 protein
hetero molecules

A: Lmo1499 protein
hetero molecules

A: Lmo1499 protein
hetero molecules

B: Lmo1499 protein
hetero molecules

B: Lmo1499 protein
hetero molecules

B: Lmo1499 protein
hetero molecules

B: Lmo1499 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,30460
Polymers319,5478
Non-polymers3,75752
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_554x+1/2,y+1/2,z-1/21
crystal symmetry operation6_554-x+1/2,-y+1/2,z-1/21
crystal symmetry operation7_554-y+1/2,x+1/2,z-1/21
crystal symmetry operation8_554y+1/2,-x+1/2,z-1/21
Buried area20820 Å2
ΔGint-356 kcal/mol
Surface area121500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.899, 126.899, 115.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-402-

CL

21A-403-

CL

31B-402-

CL

41B-403-

CL

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Components

#1: Protein Lmo1499 protein


Mass: 39943.387 Da / Num. of mol.: 2 / Fragment: UNP residues 32-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo1499 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: Q8Y725
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
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: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 7.1mg/mL, 0.25M Sodium cloride, 0.01M Tris-HCl pH 8.3, Screen: Trap96 (E8), 0.2M Ammonium sulfate, 0.1M Cacodyl. pH 6.5, 30% (w/v) PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2012 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 55066 / Num. obs: 55066 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 69.9 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 26.1
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2698 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→29.91 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 16.348 / SU ML: 0.162
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.408 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1414 5 %RANDOM
Rwork0.17096 ---
all0.17317 26680 --
obs0.17317 26680 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.203 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å2-0 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4836 0 46 188 5070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224988
X-RAY DIFFRACTIONr_bond_other_d0.0010.023378
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.996746
X-RAY DIFFRACTIONr_angle_other_deg0.79438369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.5755614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54926.019206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.10915942
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2791510
X-RAY DIFFRACTIONr_chiral_restr0.0780.2767
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215378
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02872
X-RAY DIFFRACTIONr_mcbond_it0.9741.53079
X-RAY DIFFRACTIONr_mcbond_other0.2321.51217
X-RAY DIFFRACTIONr_mcangle_it1.83325023
X-RAY DIFFRACTIONr_scbond_it2.96931909
X-RAY DIFFRACTIONr_scangle_it4.5664.51723
LS refinement shellResolution: 2.601→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 100 -
Rwork0.263 1894 -
obs-1894 98.62 %
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)
14.54890.9672-0.10933.825-0.09492.8273-0.0125-0.2786-0.03410.3604-0.01310.25960.0527-0.15060.02560.052-0.00840.02110.03770.02220.073748.502853.375858.9082
22.3727-0.1489-0.05732.35590.59092.9050.05390.10870.034-0.15480.0133-0.14690.09880.2268-0.06720.1101-0.03130.06980.09320.04140.157846.226322.766557.7665
35.23820.56940.06343.75011.69674.64640.16240.24970.14-0.5556-0.21030.48660.0407-0.41680.04790.27450.0169-0.02970.05640.00630.162432.882913.782242.8126
46.4111-0.78110.02183.57911.01925.00390.26010.70770.2109-0.806-0.10440.0431-0.21950.0691-0.15570.3418-0.00350.0270.10770.05470.110539.95314.930337.963
54.9913.1676-0.62562.0873-1.11978.7309-0.28982.37240.3033-0.17941.38920.2171-0.5216-1.2147-1.09941.73430.3662-0.0581.58830.16791.219330.483517.764523.8638
64.4187-0.17160.05635.32010.81494.80430.09070.60080.4406-0.6636-0.0385-0.2904-0.36940.3023-0.05220.1941-0.03590.10510.18260.08290.125713.269711.178492.4022
73.80030.11250.62991.9259-0.1474.82780.0113-0.3755-0.15490.12440.10760.01390.72-0.2004-0.1190.2038-0.07450.02280.13430.06420.149842.979319.203179.3378
83.84241.19352.91892.17621.04145.1143-0.4205-0.57820.42240.11840.1216-0.1071-0.3219-0.15260.29890.1230.0678-0.01620.273-0.06820.26252.643631.338990.3439
94.15270.36262.04065.79910.3976.56750.0255-1.05170.08450.53430.05690.04170.3838-0.5352-0.08240.09820.04440.03810.42040.01470.078952.473424.755298.1551
106.4915-5.6942-4.570615.9133-4.07329.2323-0.7325-0.5327-0.42691.68121.01621.2705-0.0804-0.1709-0.28380.9013-0.0087-0.03111.6177-0.1750.762249.12634.3443111.9696
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 116
2X-RAY DIFFRACTION2A117 - 213
3X-RAY DIFFRACTION3A214 - 271
4X-RAY DIFFRACTION4A272 - 325
5X-RAY DIFFRACTION5A326 - 349
6X-RAY DIFFRACTION6B42 - 112
7X-RAY DIFFRACTION7B113 - 198
8X-RAY DIFFRACTION8B199 - 270
9X-RAY DIFFRACTION9B271 - 325
10X-RAY DIFFRACTION10B326 - 348

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