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- PDB-4xvo: L,D-transpeptidase from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 4xvo
TitleL,D-transpeptidase from Mycobacterium smegmatis
ComponentsL,D-transpeptidase
KeywordsTRANSFERASE / L / D-transpeptidase / Mycobacterium / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


acyltransferase activity / peptidoglycan biosynthetic process
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 catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / Immunoglobulin-like / Beta Barrel ...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 catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / ErfK/YbiS/YcfS/YnhG family protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsOsipiuk, J. / Wu, R. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: to be published
Title: L,D-transpeptidase from Mycobacterium smegmatis
Authors: Osipiuk, J. / Wu, R. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionJan 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L,D-transpeptidase
B: L,D-transpeptidase
C: L,D-transpeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1797
Polymers71,7993
Non-polymers3804
Water3,135174
1
A: L,D-transpeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1233
Polymers23,9331
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: L,D-transpeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0282
Polymers23,9331
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: L,D-transpeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0282
Polymers23,9331
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.390, 160.047, 209.912
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Detailsbiological unit is the same as asymmetric unit

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Components

#1: Protein L,D-transpeptidase / ErfK/YbiS/YcfS/YnhG family protein


Mass: 23933.105 Da / Num. of mol.: 3 / Fragment: UNP residues 71-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEI_3449 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I7G323
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 5.4 Å3/Da / Density % sol: 77.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 1M sodium/potassium phosphate buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 47865 / Num. obs: 47865 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 52.68 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.043 / Rrim(I) all: 0.11 / Χ2: 1.958 / Net I/av σ(I): 25.413 / Net I/σ(I): 9 / Num. measured all: 307944
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.6-2.645.70.9691.9423280.7580.4240.94995.8
2.64-2.696.20.78722720.8370.330.975960.856
2.69-2.746.40.58623310.8790.2381.03196.70.634
2.74-2.86.50.52223380.9220.2131.04996.70.565
2.8-2.866.50.48323100.9380.1961.07496.90.522
2.86-2.936.40.39123430.9540.161.17497.50.423
2.93-36.40.35523610.950.1451.15497.60.384
3-3.086.50.25823620.9730.1051.29197.70.279
3.08-3.176.50.20323600.980.0831.44198.70.22
3.17-3.286.40.16423950.9910.0671.58990.178
3.28-3.396.50.14823940.990.0611.77198.90.16
3.39-3.536.50.12523920.9920.0511.93398.90.135
3.53-3.696.50.10524090.9920.0432.199.30.114
3.69-3.886.60.09124300.9950.0372.31499.20.098
3.88-4.136.50.07924000.9970.0332.39299.60.086
4.13-4.456.50.07124410.9960.0292.75499.60.077
4.45-4.896.60.06824630.9970.0283.11699.60.074
4.89-5.66.60.07324400.9970.033.5011000.079
5.6-7.056.60.0724960.9970.0293.3961000.076
7.05-506.30.05226000.9940.0223.42899.70.056

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Processing

Software
NameVersionClassification
HKL-3000data reduction
PHENIX(phenix.refine: 1.8.2_1309)refinement
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→42.281 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 2410 5.04 %
Rwork0.198 45365 -
obs0.1999 47775 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.81 Å2 / Biso mean: 53.9023 Å2 / Biso min: 14.25 Å2
Refinement stepCycle: final / Resolution: 2.6→42.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4899 0 20 174 5093
Biso mean--82.2 46.37 -
Num. residues----651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035184
X-RAY DIFFRACTIONf_angle_d0.7257136
X-RAY DIFFRACTIONf_chiral_restr0.047803
X-RAY DIFFRACTIONf_plane_restr0.003923
X-RAY DIFFRACTIONf_dihedral_angle_d12.2561842
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.583-2.63580.29661220.2652126224879
2.6358-2.69310.31221560.25632570272696
2.6931-2.75570.22331050.23082644274996
2.7557-2.82460.27351120.24112658277097
2.8246-2.90090.35071590.25692650280997
2.9009-2.98630.38791470.28242620276797
2.9863-3.08260.29961460.27272666281298
3.0826-3.19280.31841190.2282722284199
3.1928-3.32060.28671400.23022674281499
3.3206-3.47160.281270.21592728285599
3.4716-3.65460.2792090.20952640284999
3.6546-3.88340.21611600.1882722288299
3.8834-4.1830.22511140.166627512865100
4.183-4.60350.18131580.14732725288399
4.6035-5.26850.18711510.146427612912100
5.2685-6.63370.20151570.185328012958100
6.6337-42.28650.18991280.19972907303599
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)
10.05950.0348-0.00670.0333-0.02370.04540.1165-0.0440.29490.06130.06220.0937-0.16240.08360.16480.5152-0.54530.09010.1420.05680.448560.343532.491428.3855
20.0569-0.00940.12970.1261-0.02730.3178-0.06590.06330.1022-0.2257-0.1857-0.06080.10620.0688-0.21060.4219-0.09970.01480.13050.04610.17452.026212.454410.3624
30.03970.0320.01310.0585-0.05470.17060.1013-0.10970.20270.01780.0387-0.2913-0.02440.15950.1238-0.11640.04110.06580.7213-0.03720.462281.41394.00163.387
40.15770.0760.01720.1426-0.1540.3143-0.22590.1522-0.0062-0.18050.0001-0.11180.1288-0.0569-0.19380.109-0.05990.05070.46030.00580.168459.92551.208945.3731
50.0470.0058-0.04870.0093-0.02090.07150.0414-0.0396-0.07380.0390.1088-0.26710.12180.07870.16620.50030.43820.05280.0866-0.06390.48968.9565-30.186396.5497
60.1782-0.0745-0.09740.11990.05570.0769-0.07930.2815-0.10860.0485-0.0527-0.03290.0453-0.1096-0.18540.36530.21760.06080.2001-0.05010.175655.1873-12.987483.6571
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 43 through 128 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 259 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 43 through 128 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 129 through 259 )B0
5X-RAY DIFFRACTION5chain 'C' and (resid 43 through 106 )C0
6X-RAY DIFFRACTION6chain 'C' and (resid 107 through 259 )C0

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