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- PDB-3se7: ancient VanA -

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Basic information

Entry
Database: PDB / ID: 3se7
Titleancient VanA
ComponentsVanA
KeywordsLIGASE / alpha-beta structure / D-alanine-D-lactate ligase
Function / homology
Function and homology information


Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsWright, G.D. / Morar, M.
CitationJournal: Nature / Year: 2011
Title: Antibiotic resistance is ancient.
Authors: D'Costa, V.M. / King, C.E. / Kalan, L. / Morar, M. / Sung, W.W. / Schwarz, C. / Froese, D. / Zazula, G. / Calmels, F. / Debruyne, R. / Golding, G.B. / Poinar, H.N. / Wright, G.D.
History
DepositionJun 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: VanA
B: VanA
C: VanA
D: VanA
E: VanA
F: VanA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,53824
Polymers222,2036
Non-polymers3,33518
Water4,234235
1
A: VanA
B: VanA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1798
Polymers74,0682
Non-polymers1,1126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-25 kcal/mol
Surface area24570 Å2
MethodPISA
2
C: VanA
D: VanA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1798
Polymers74,0682
Non-polymers1,1126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-25 kcal/mol
Surface area24710 Å2
MethodPISA
3
E: VanA
F: VanA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1798
Polymers74,0682
Non-polymers1,1126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-25 kcal/mol
Surface area24730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.133, 136.032, 178.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A2 - 342
2116B2 - 342
3116C2 - 342
4116D2 - 342
5116E2 - 342
6116F2 - 342

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Components

#1: Protein
VanA


Mass: 37033.844 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Gene: VanA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate, 25% PEG3000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.07→108.1 Å / Num. all: 38900 / Num. obs: 38823 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.07→3.12 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.07→108.1 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.889 / SU B: 48.182 / SU ML: 0.392 / Cross valid method: THROUGHOUT / ESU R Free: 0.521 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26268 1963 5.1 %RANDOM
Rwork0.19348 ---
all0.19705 36990 --
obs0.19705 36901 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.808 Å2
Baniso -1Baniso -2Baniso -3
1-4.66 Å20 Å20 Å2
2---4.98 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 3.07→108.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14492 0 198 235 14925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.02214921
X-RAY DIFFRACTIONr_angle_refined_deg1.1771.9920339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.72151958
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13223.924553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.565152317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4191591
X-RAY DIFFRACTIONr_chiral_restr0.0750.22418
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111075
X-RAY DIFFRACTIONr_mcbond_it0.9031.59726
X-RAY DIFFRACTIONr_mcangle_it1.677215545
X-RAY DIFFRACTIONr_scbond_it2.55335195
X-RAY DIFFRACTIONr_scangle_it4.2334.54794
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2341 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.275
Bloose positional0.255
Cloose positional0.295
Dloose positional0.295
Eloose positional0.35
Floose positional0.285
Aloose thermal3.4310
Bloose thermal2.8410
Cloose thermal2.7610
Dloose thermal2.8910
Eloose thermal2.9210
Floose thermal2.910
LS refinement shellResolution: 3.07→3.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 137 -
Rwork0.226 2698 -
obs--99.44 %
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)
10.5651-0.53650.54874.5554-0.26652.24140.0089-0.06090.1996-0.2406-0.0016-0.2787-0.08390.1282-0.00730.0203-0.00040.02970.0797-0.02380.14-37.125235.6036-6.056
21.5656-0.10270.662.99870.99772.22130.0399-0.1464-0.0950.0154-0.02820.11560.3146-0.1079-0.01170.0583-0.01150.01090.03660.01210.0742-37.53786.8999-5.8413
31.0717-0.11780.07112.2548-0.40152.59790.0405-0.05150.0941-0.0191-0.0005-0.1707-0.12940.1699-0.040.01230.0022-0.00620.0896-0.04330.1031-45.152935.9342-68.4327
41.51290.01810.42694.29121.30372.8786-0.0799-0.1697-0.15430.19890.03610.25660.2422-0.1560.04390.03140.0040.02080.07120.01990.1353-45.62077.0296-67.8284
50.9675-0.31080.19072.5563-1.39683.42040.071-0.0615-0.0679-0.0235-0.0167-0.00750.49280.0934-0.05430.12170.00290.03210.0782-0.01640.098-3.241430.0773-50.7712
61.02450.74640.47145.271.75512.89730.0365-0.15270.1650.566-0.09410.2564-0.1674-0.10710.05760.12120.020.04880.10610.01060.1114-3.065359.2326-51.3064
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 339
2X-RAY DIFFRACTION2B1 - 340
3X-RAY DIFFRACTION3C1 - 339
4X-RAY DIFFRACTION4D1 - 340
5X-RAY DIFFRACTION5E1 - 339
6X-RAY DIFFRACTION6F1 - 339

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