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- PDB-2r2d: Structure of a quorum-quenching lactonase (AiiB) from Agrobacteri... -

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Basic information

Entry
Database: PDB / ID: 2r2d
TitleStructure of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens
ComponentsZn-dependent hydrolases
KeywordsHYDROLASE / lactonase / N-acyl hompserine lactone / di-nuclear zinc center / quorum quenching / AiiB / phosphate / Agrobacterium tumefaciens
Function / homology
Function and homology information


acyl-L-homoserine-lactone lactonohydrolase activity / quorum-quenching N-acyl-homoserine lactonase / metal ion binding
Similarity search - Function
Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / N-acyl homoserine lactonase AiiB
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsLiu, D. / Thomas, P.W. / Momb, J. / Hoang, Q. / Petsko, G.A. / Ringe, D. / Fast, W.
CitationJournal: Biochemistry / Year: 2007
Title: Structure and specificity of a quorum-quenching lactonase (AiiB) from Agrobacterium tumefaciens.
Authors: Liu, D. / Thomas, P.W. / Momb, J. / Hoang, Q.Q. / Petsko, G.A. / Ringe, D. / Fast, W.
History
DepositionAug 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jun 17, 2015Group: Derived calculations
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 21, 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_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.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

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Assembly

Deposited unit
A: Zn-dependent hydrolases
B: Zn-dependent hydrolases
C: Zn-dependent hydrolases
D: Zn-dependent hydrolases
E: Zn-dependent hydrolases
F: Zn-dependent hydrolases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,13937
Polymers183,5786
Non-polymers2,56131
Water27,4011521
1
A: Zn-dependent hydrolases
hetero molecules

E: Zn-dependent hydrolases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,10813
Polymers61,1932
Non-polymers91511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area4100 Å2
ΔGint-196 kcal/mol
Surface area22300 Å2
MethodPISA
2
B: Zn-dependent hydrolases
C: Zn-dependent hydrolases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,20314
Polymers61,1932
Non-polymers1,01012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-202 kcal/mol
Surface area22430 Å2
MethodPISA
3
D: Zn-dependent hydrolases
hetero molecules

F: Zn-dependent hydrolases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,82810
Polymers61,1932
Non-polymers6368
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,y+1/2,-z-11
Buried area3660 Å2
ΔGint-191 kcal/mol
Surface area22440 Å2
MethodPISA
4
F: Zn-dependent hydrolases
hetero molecules

A: Zn-dependent hydrolases
hetero molecules

D: Zn-dependent hydrolases
hetero molecules

E: Zn-dependent hydrolases
hetero molecules

B: Zn-dependent hydrolases
C: Zn-dependent hydrolases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,13937
Polymers183,5786
Non-polymers2,56131
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
crystal symmetry operation2_544-x,y-1/2,-z-11
crystal symmetry operation2_645-x+1,y-1/2,-z1
identity operation1_555x,y,z1
Buried area16120 Å2
ΔGint-618 kcal/mol
Surface area63390 Å2
MethodPISA
5
E: Zn-dependent hydrolases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0096
Polymers30,5961
Non-polymers4135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Zn-dependent hydrolases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9145
Polymers30,5961
Non-polymers3184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: Zn-dependent hydrolases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0987
Polymers30,5961
Non-polymers5026
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
B: Zn-dependent hydrolases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1017
Polymers30,5961
Non-polymers5056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
C: Zn-dependent hydrolases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1017
Polymers30,5961
Non-polymers5056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
D: Zn-dependent hydrolases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9145
Polymers30,5961
Non-polymers3184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.146, 158.033, 80.439
Angle α, β, γ (deg.)90.00, 104.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Zn-dependent hydrolases / AGR_pTi_140p


Mass: 30596.324 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58/ATCC 33970 / Gene: aiiB / Plasmid: pMAL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CKY2
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1521 / 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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 35% glycerol anhydrous and 0.26 M ammonium dihydrogen phosphate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.75→79.06 Å / Num. obs: 185201 / % possible obs: 96.8 % / Redundancy: 2.9 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.6
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 1.1 / Num. unique all: 15044 / % possible all: 79.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Iceicedata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→18.1 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.921 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(I): 1 / ESU R: 0.179 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21267 9324 5 %RANDOM
Rwork0.15898 ---
obs0.16169 175810 96.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.798 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20.19 Å2
2--0.83 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.75→18.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12924 0 117 1521 14562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02114037
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.95919187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96751802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80722.909691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.795152259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.10715140
X-RAY DIFFRACTIONr_chiral_restr0.1260.22108
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210998
X-RAY DIFFRACTIONr_nbd_refined0.2080.26922
X-RAY DIFFRACTIONr_nbtor_refined0.3080.29480
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.21294
X-RAY DIFFRACTIONr_metal_ion_refined0.0980.225
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.2195
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.258
X-RAY DIFFRACTIONr_mcbond_it1.2791.58803
X-RAY DIFFRACTIONr_mcangle_it1.972213967
X-RAY DIFFRACTIONr_scbond_it3.20335845
X-RAY DIFFRACTIONr_scangle_it4.6044.55173
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 512 -
Rwork0.261 9807 -
obs-15044 73.14 %

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