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- PDB-4ecl: Crystal structure of the cytoplasmic domain of vancomycin resista... -

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Basic information

Entry
Database: PDB / ID: 4ecl
TitleCrystal structure of the cytoplasmic domain of vancomycin resistance serine racemase VanTg
ComponentsSerine racemase
KeywordsISOMERASE / antibiotic resistance / vancomycin resistance / Center for Structural Genomics of Infectious Diseases (CSGID) / alpha/beta barrel / TIM barrel / Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme / Acyltransferase family / L-serine racemase / D-serine racemase / L-serine / D-serine / PLP / pyridoxal 5-phosphate / cytoplasmic
Function / homology
Function and homology information


alanine racemase / D-alanine biosynthetic process / alanine racemase activity / acyltransferase activity, transferring groups other than amino-acyl groups / pyridoxal phosphate binding / response to antibiotic / membrane / cytosol
Similarity search - Function
Serine/alanine racemase / Acyltransferase 3 domain / Acyltransferase family / Alanine racemase, pyridoxal-phosphate attachment site / Alanine racemase pyridoxal-phosphate attachment site. / Alanine racemase / Alanine racemase, C-terminal / Alanine racemase, C-terminal domain / Alanine racemase, C-terminal domain / Alanine racemase, N-terminal ...Serine/alanine racemase / Acyltransferase 3 domain / Acyltransferase family / Alanine racemase, pyridoxal-phosphate attachment site / Alanine racemase pyridoxal-phosphate attachment site. / Alanine racemase / Alanine racemase, C-terminal / Alanine racemase, C-terminal domain / Alanine racemase, C-terminal domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / Alanine racemase / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.017 Å
AuthorsStogios, P.J. / Wawrzak, Z. / Minasov, G. / Evdokimova, E. / Egorova, O. / Cosme, J. / Di Leo, R. / Krishnamoorthy, M. / Meziane-Cherif, D. / Courvalin, P. ...Stogios, P.J. / Wawrzak, Z. / Minasov, G. / Evdokimova, E. / Egorova, O. / Cosme, J. / Di Leo, R. / Krishnamoorthy, M. / Meziane-Cherif, D. / Courvalin, P. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: MBio / Year: 2015
Title: Structural and Functional Adaptation of Vancomycin Resistance VanT Serine Racemases.
Authors: Meziane-Cherif, D. / Stogios, P.J. / Evdokimova, E. / Egorova, O. / Savchenko, A. / Courvalin, P.
History
DepositionMar 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
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_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_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: Serine racemase
B: Serine racemase
C: Serine racemase
D: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,41116
Polymers166,7444
Non-polymers66812
Water12,484693
1
A: Serine racemase
B: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7068
Polymers83,3722
Non-polymers3346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-100 kcal/mol
Surface area28870 Å2
MethodPISA
2
C: Serine racemase
D: Serine racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7068
Polymers83,3722
Non-polymers3346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-86 kcal/mol
Surface area28840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.682, 82.341, 117.468
Angle α, β, γ (deg.)90.00, 90.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Serine racemase / VanTG


Mass: 41685.879 Da / Num. of mol.: 4 / Fragment: cytoplasmic domain (UNP residues 339-712)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: BM4518 / Gene: vanTG / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6WRY3
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M MES pH 6.5, 30% PEG 5K MME, cryoprotectant: paratone oil, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 31, 2010 / Details: mirrors
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.017→20 Å / Num. all: 98585 / Num. obs: 97205 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Rsym value: 0.112 / Net I/σ(I): 16.83
Reflection shellResolution: 2.017→2.05 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.86 / Rsym value: 0.547 / % possible all: 95.4

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.017→19.915 Å / SU ML: 0.24 / σ(F): 1.38 / Phase error: 28.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 1871 2.06 %
Rwork0.1813 --
obs0.1824 97095 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.456 Å2 / ksol: 0.374 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--12.1641 Å20 Å24.9458 Å2
2--29.2864 Å20 Å2
3----17.1223 Å2
Refinement stepCycle: LAST / Resolution: 2.017→19.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11506 0 28 693 12227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711798
X-RAY DIFFRACTIONf_angle_d1.03715958
X-RAY DIFFRACTIONf_dihedral_angle_d13.2954436
X-RAY DIFFRACTIONf_chiral_restr0.0691871
X-RAY DIFFRACTIONf_plane_restr0.0042010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.017-2.04170.37321300.33125853X-RAY DIFFRACTION87
2.0417-2.06750.45551170.29396527X-RAY DIFFRACTION95
2.0675-2.09470.30681490.27866509X-RAY DIFFRACTION97
2.0947-2.12340.33851470.26336684X-RAY DIFFRACTION98
2.1234-2.15370.39781360.27156673X-RAY DIFFRACTION98
2.1537-2.18580.30791100.23666674X-RAY DIFFRACTION98
2.1858-2.21990.2671720.23256611X-RAY DIFFRACTION98
2.2199-2.25620.29671210.22296688X-RAY DIFFRACTION98
2.2562-2.29510.26371370.226632X-RAY DIFFRACTION98
2.2951-2.33680.28441410.21286773X-RAY DIFFRACTION98
2.3368-2.38160.34821280.21376673X-RAY DIFFRACTION98
2.3816-2.43020.29781500.21096644X-RAY DIFFRACTION98
2.4302-2.48290.28891500.20696690X-RAY DIFFRACTION99
2.4829-2.54060.26751220.19466720X-RAY DIFFRACTION99
2.5406-2.6040.27141520.18326696X-RAY DIFFRACTION99
2.604-2.67420.23031400.18416623X-RAY DIFFRACTION98
2.6742-2.75270.24671460.17456748X-RAY DIFFRACTION99
2.7527-2.84130.24171480.19116729X-RAY DIFFRACTION99
2.8413-2.94260.24511440.18886726X-RAY DIFFRACTION99
2.9426-3.060.25041130.19016764X-RAY DIFFRACTION99
3.06-3.19870.20331400.18236713X-RAY DIFFRACTION99
3.1987-3.36660.24851520.15896674X-RAY DIFFRACTION99
3.3666-3.57640.17061420.15276834X-RAY DIFFRACTION99
3.5764-3.85070.16661420.13126650X-RAY DIFFRACTION99
3.8507-4.23480.22351500.13196752X-RAY DIFFRACTION100
4.2348-4.83990.14091480.1256793X-RAY DIFFRACTION100
4.8399-6.0690.16251480.1516766X-RAY DIFFRACTION100
6.069-19.91590.18841400.1646742X-RAY DIFFRACTION99
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)
11.55940.1342-0.14440.7013-0.03521.5309-0.01250.2204-0.0427-0.0537-0.0075-0.0110.035-0.03160.0140.1514-0.0062-0.01420.1525-0.0230.175827.0179-1.194326.4044
21.1514-0.2281-0.18820.90950.07772.06390.0232-0.27630.0660.0361-0.0920.0334-0.2677-0.09730.04980.2013-0.0113-0.01940.3092-0.02290.193425.47911.387558.5949
30.9168-0.06650.21460.40580.04211.2586-0.0344-0.09080.03580.0470.0331-0.0045-0.0552-0.0173-0.00220.1671-0.004-0.01250.3933-0.00340.168744.81061.735168.3945
40.93540.238-0.26050.40730.24621.68180.0387-0.13650.12820.0328-0.0619-0.0075-0.16040.19330.03050.2069-0.04250.00640.34030.00190.215146.61629.36434.625
51.6376-0.3498-0.28150.36680.01181.7306-0.0316-0.36510.0593-0.0020.0473-0.0220.1501-0.146-0.01490.17540.00820.01850.17050.00020.165290.607-36.494-9.494
61.17950.08520.32810.2579-0.26862.00210.00410.0174-0.1190.05150.0095-0.07920.1196-0.11020.01380.1817-0.011-0.00320.11740.01060.185292.105-43.44524.133
70.93860.1854-0.00650.40010.05191.23220.01-0.1149-0.08010.0352-0.0105-0.0295-0.0578-0.1346-0.01070.1983-0.01690.02560.01630.00550.209172.2184-33.401832.3778
81.06210.1052-0.09210.9710.03581.6308-0.14530.322-0.1646-0.02380.06880.0040.2323-0.26680.08460.2124-0.07420.02450.212-0.05390.225571.3335-46.4090.8317
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 2:244
2X-RAY DIFFRACTION2chain A and resi 245:373
3X-RAY DIFFRACTION3chain B and resi 2:244
4X-RAY DIFFRACTION4chain B and resi 245:373
5X-RAY DIFFRACTION5chain C and resi 2:244
6X-RAY DIFFRACTION6chain C and resi 245:373
7X-RAY DIFFRACTION7chain D and resi 2:244
8X-RAY DIFFRACTION8chain D and resi 245:373

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