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- PDB-4h18: Three dimensional structure of corynomycoloyl tranferase C -

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Basic information

Entry
Database: PDB / ID: 4h18
TitleThree dimensional structure of corynomycoloyl tranferase C
ComponentsCmt1
KeywordsTRANSFERASE / alpha / beta hydrolase / mycoloyltransferase / trehalose O-mycolyltransferase / external membrane
Function / homologyEsterase-like / Putative esterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Cmt1
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.755 Å
AuthorsHuc, E. / de Sousa D'Auria, C. / Li de la Sierra-Gallay, I. / Salmeron, C.H. / van Tilbeurgh, H. / Bayan, N. / Houssin, C.H. / Daffe, M. / Tropis, M.
CitationJournal: J.Bacteriol. / Year: 2013
Title: Identification of a mycoloyl transferase selectively involved in o-acylation of polypeptides in corynebacteriales.
Authors: Huc, E. / de Sousa-D'Auria, C. / de la Sierra-Gallay, I.L. / Salmeron, C. / van Tilbeurgh, H. / Bayan, N. / Houssin, C. / Daffe, M. / Tropis, M.
History
DepositionSep 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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: Cmt1
B: Cmt1
C: Cmt1
D: Cmt1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,4885
Polymers161,4644
Non-polymers241
Water17,619978
1
A: Cmt1


Theoretical massNumber of molelcules
Total (without water)40,3661
Polymers40,3661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cmt1


Theoretical massNumber of molelcules
Total (without water)40,3661
Polymers40,3661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cmt1


Theoretical massNumber of molelcules
Total (without water)40,3661
Polymers40,3661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cmt1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3902
Polymers40,3661
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Cmt1

C: Cmt1


Theoretical massNumber of molelcules
Total (without water)80,7322
Polymers80,7322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Buried area1310 Å2
ΔGint-16 kcal/mol
Surface area23780 Å2
MethodPISA
6
D: Cmt1
hetero molecules

B: Cmt1


Theoretical massNumber of molelcules
Total (without water)80,7563
Polymers80,7322
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area1410 Å2
ΔGint-22 kcal/mol
Surface area23710 Å2
MethodPISA
7
C: Cmt1

B: Cmt1

A: Cmt1
D: Cmt1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,4885
Polymers161,4644
Non-polymers241
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-47 kcal/mol
Surface area44680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.804, 190.688, 78.497
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-434-

HOH

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Components

#1: Protein
Cmt1 / Hypothetical esterase / Putative uncharacterized protein Cgl0343 / Trehalose corynomycolyl transferase


Mass: 40365.941 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: ATCC 13032 / Gene: cmt1, Cmt1, cg0413, Cgl0343, WA5_0336 / Plasmid: pCGl482 / Production host: Corynebacterium glutamicum (bacteria) / References: UniProt: Q8NTG4, trehalose O-mycolyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 978 / 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: 1.99 Å3/Da / Density % sol: 38.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 4000, 0.2M magnesium chloride, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2011 / Details: mirrors
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.755→42.811 Å / Num. all: 128497 / Num. obs: 128495 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.89 % / Biso Wilson estimate: 22.82 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 9.46
Reflection shellResolution: 1.755→1.86 Å / Redundancy: 3.91 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.6 / Num. unique all: 20505 / % possible all: 99.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VA5

1va5


Resolution: 1.755→37.646 Å / SU ML: 0.18 / σ(F): 1.99 / Phase error: 18.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2031 6424 5 %RANDOM
Rwork0.163 ---
obs0.165 128479 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.755→37.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9495 0 1 978 10474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129832
X-RAY DIFFRACTIONf_angle_d1.38613435
X-RAY DIFFRACTIONf_dihedral_angle_d14.0033483
X-RAY DIFFRACTIONf_chiral_restr0.0961439
X-RAY DIFFRACTIONf_plane_restr0.0081761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.755-1.77480.28342050.23913902X-RAY DIFFRACTION97
1.7748-1.79570.26372130.22564049X-RAY DIFFRACTION100
1.7957-1.81760.27452140.20854058X-RAY DIFFRACTION100
1.8176-1.84060.25892110.19684020X-RAY DIFFRACTION100
1.8406-1.86480.2432140.19044059X-RAY DIFFRACTION100
1.8648-1.89030.25092110.18964012X-RAY DIFFRACTION100
1.8903-1.91730.2442150.18494076X-RAY DIFFRACTION100
1.9173-1.9460.24442130.17294056X-RAY DIFFRACTION100
1.946-1.97640.21632120.17274027X-RAY DIFFRACTION100
1.9764-2.00880.21262150.16784075X-RAY DIFFRACTION100
2.0088-2.04340.2212120.15914034X-RAY DIFFRACTION100
2.0434-2.08060.21492120.16064022X-RAY DIFFRACTION100
2.0806-2.12060.22122140.16254068X-RAY DIFFRACTION100
2.1206-2.16390.21122130.15964044X-RAY DIFFRACTION100
2.1639-2.21090.21162130.1594052X-RAY DIFFRACTION100
2.2109-2.26230.22192140.16124062X-RAY DIFFRACTION100
2.2623-2.31890.20132140.16224067X-RAY DIFFRACTION100
2.3189-2.38160.22140.15934078X-RAY DIFFRACTION100
2.3816-2.45160.21792140.16014064X-RAY DIFFRACTION100
2.4516-2.53080.21252150.16154074X-RAY DIFFRACTION100
2.5308-2.62120.20652140.16454064X-RAY DIFFRACTION100
2.6212-2.72610.2182140.16634075X-RAY DIFFRACTION100
2.7261-2.85010.21232150.16754082X-RAY DIFFRACTION100
2.8501-3.00030.19252150.16444091X-RAY DIFFRACTION99
3.0003-3.18820.19062150.16114090X-RAY DIFFRACTION99
3.1882-3.43420.18582180.15644129X-RAY DIFFRACTION99
3.4342-3.77960.19342150.154084X-RAY DIFFRACTION99
3.7796-4.32580.16512170.13444119X-RAY DIFFRACTION99
4.3258-5.44740.16692190.14084164X-RAY DIFFRACTION99
5.4474-37.65490.15912240.17014258X-RAY DIFFRACTION97

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