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- PDB-4g9g: Crystal structures of N-acyl homoserine lactonase AidH E219G mutant -

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Basic information

Entry
Database: PDB / ID: 4g9g
TitleCrystal structures of N-acyl homoserine lactonase AidH E219G mutant
ComponentsAlpha/beta hydrolase fold proteinAlpha/beta hydrolase superfamily
KeywordsHYDROLASE / alpha/beta-hydrolase fold / AHL-lactonase / AHL-binding
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds
Similarity search - Function
Alpha/beta hydrolase family / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Alpha/beta hydrolase fold protein
Similarity search - Component
Biological speciesOchrobactrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsLiang, D.C. / Yan, X.X. / Gao, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: High-resolution structures of AidH complexes provide insights into a novel catalytic mechanism for N-acyl homoserine lactonase
Authors: Gao, A. / Mei, G.Y. / Liu, S. / Wang, P. / Tang, Q. / Liu, Y.P. / Wen, H. / An, X.M. / Zhang, L.Q. / Yan, X.X. / Liang, D.C.
History
DepositionJul 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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.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_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: Alpha/beta hydrolase fold protein
B: Alpha/beta hydrolase fold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2804
Polymers61,1632
Non-polymers1172
Water19,0061055
1
A: Alpha/beta hydrolase fold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6402
Polymers30,5811
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha/beta hydrolase fold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6402
Polymers30,5811
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.378, 129.567, 44.728
Angle α, β, γ (deg.)90.00, 111.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha/beta hydrolase fold protein / Alpha/beta hydrolase superfamily / AHL-lactonase


Mass: 30581.303 Da / Num. of mol.: 2 / Mutation: E219G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochrobactrum (bacteria) / Strain: T63 / Gene: aidH / Production host: Escherichia coli (E. coli) / References: UniProt: D2J2T6
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1055 / 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: 1.87 Å3/Da / Density % sol: 34.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 35% PEG8000, 0.2M LiAc, 0.1M NaAc, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 22, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→20 Å / Num. obs: 96822 / % possible obs: 51.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 9.81 Å2
Reflection shellResolution: 1.35→1.4 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G5X

4g5x


Resolution: 1.35→19.869 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.898 / SU ML: 0.15 / σ(F): 1.35 / Phase error: 17.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1775 4770 5 %
Rwork0.1412 --
obs0.143 95339 96.97 %
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 111.478 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso max: 71.98 Å2 / Biso mean: 18.6257 Å2 / Biso min: 2.81 Å2
Baniso -1Baniso -2Baniso -3
1-1.8825 Å20 Å2-2.8861 Å2
2---3.8798 Å2-0 Å2
3---1.9973 Å2
Refinement stepCycle: LAST / Resolution: 1.35→19.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4223 0 2 1055 5280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064471
X-RAY DIFFRACTIONf_angle_d1.0466073
X-RAY DIFFRACTIONf_chiral_restr0.07637
X-RAY DIFFRACTIONf_plane_restr0.005829
X-RAY DIFFRACTIONf_dihedral_angle_d12.0971658
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.39820.22464420.18888915935795
1.3982-1.45420.1964570.16128924938195
1.4542-1.52040.17844400.14048975941596
1.5204-1.60050.16885080.13519011951997
1.6005-1.70070.16764780.13099059953797
1.7007-1.8320.17345050.13749087959298
1.832-2.01610.17374710.13859197966898
2.0161-2.30750.17584920.13889193968599
2.3075-2.90580.18344960.14449254975099
2.9058-19.87140.17334810.13718954943595
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)
10.2163-0.1235-0.31651.27570.42541.09570.015-0.04770.0323-0.25540.0337-0.2655-0.00250.1759-0.0560.1575-0.01450.05430.0966-0.01810.12029.70192.579319.0919
20.0912-0.29870.05161.49760.20210.6577-0.04140.02390.0083-0.23920.0543-0.1217-0.04440.0405-0.01370.0536-0.01510.00730.0421-0.00060.0342.37244.72923.7116
30.2199-0.0442-0.21171.503-0.12780.1386-0.0409-0.0009-0.01210.01150.02970.05610.01570.0121-0.02150.05960.0013-0.00890.06460.00070.0662-5.4232.413632.0609
40.24570.18830.10163.16720.15570.0681-0.01470.0445-0.0166-1.09890.06370.63740.0167-0.1373-0.03740.40880.0081-0.24780.0992-0.02010.2407-15.73050.83111.0468
50.59920.46680.65642.0087-0.52361.88570.13390.09640.0644-0.6836-0.00520.38980.28860.1803-0.1220.2472-0.0012-0.10260.09920.00130.1496-12.608212.355613.5838
60.2205-0.2468-0.04452.29920.27420.01790.03180.075-0.0044-0.76680.0250.06810.0621-0.0069-0.05350.2899-0.0057-0.03390.09410.00640.0701-6.03822.214311.6409
76.3389-0.39944.83181.45370.13163.8756-0.0191-0.5302-0.0717-0.28830.05390.434-0.0115-0.5946-0.06230.1177-0.0248-0.0540.12910.01930.1214-12.8188-8.447422.9031
80.4578-0.472-0.27040.9433-0.12160.5097-0.0014-0.0168-0.06420.1037-0.01030.22770.0043-0.0498-0.00470.07970.00780.02730.05190.00270.0732-10.4476-2.971739.4967
90.12620.226-0.13191.199-0.16110.8635-0.01250.01810.03750.05880.04980.2231-0.1295-0.031-0.0290.07120.01380.00280.06320.00880.0952-13.034413.430833.3316
100.43190.29710.38591.28870.31770.501-0.0814-0.00740.07440.1385-0.0017-0.088-0.11850.00560.08930.1073-0.0026-0.0290.0723-0.0020.0927-0.374218.592536.7922
113.21223.17891.25683.28791.17971.1117-0.21630.3988-0.2503-0.36580.2225-0.4291-0.20610.2837-0.02980.096-0.04920.00060.1267-0.01350.111214.3391-22.023728.0448
120.70780.34130.13110.36490.2370.3943-0.04550.0075-0.14930.0090.0588-0.12060.01940.0454-0.02160.04260.0018-0.00370.0614-0.02380.09886.4183-33.738330.9745
131.05561.01640.9791.71661.8652.175-0.16020.03810.1899-0.2562-0.00320.1075-0.27070.05010.16260.0643-0.0086-0.02650.0679-0.00090.12419.5032-20.612133.3821
140.23050.3267-0.12860.67030.02730.1124-0.01940.00460.031-0.02710.01780.0269-0.0263-0.00010.00140.05630.0038-0.01160.0652-0.0010.0738-1.8246-21.554431.489
152.1186-1.0669-0.55461.5211-0.03470.2835-0.1598-0.36860.05730.34970.1541-0.0364-0.13970.1995-0.02120.13820.02950.00350.1802-0.0260.1038-8.377-22.474851.7044
160.79250.05060.31480.1083-0.0650.32870.0224-0.1154-0.04090.0741-0.0650.03730.0627-0.03880.00610.15930.015-0.03850.1137-0.01310.11338.4687-22.91153.5885
171.3482-0.95521.02870.6891-0.67181.6137-0.0208-0.17230.07810.31220.1428-0.41850.30580.1452-0.11990.11030.0353-0.04350.0742-0.0290.09835.7549-34.43448.8939
180.8133-0.18050.4790.2336-0.16880.484-0.0174-0.0568-0.02560.07230.0456-0.0926-0.00120.0164-0.02690.09020.0238-0.03720.0924-0.02660.115610.4984-21.315645.8761
194.7212-1.48474.05972.2515-1.55863.5297-0.3662-0.69660.14750.42150.20660.0278-0.3025-0.78360.10960.12610.03720.01430.189-0.00020.092-3.8314-10.169843.1819
200.5915-0.00270.22370.66280.12290.21330.0333-0.0446-0.07340.00890.00280.12010.0338-0.0562-0.02560.0551-0.0031-0.00090.07340.00690.0907-9.5498-32.656837.236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:19)A2 - 19
2X-RAY DIFFRACTION2(chain A and resid 20:86)A20 - 86
3X-RAY DIFFRACTION3(chain A and resid 87:142)A87 - 142
4X-RAY DIFFRACTION4(chain A and resid 143:156)A143 - 156
5X-RAY DIFFRACTION5(chain A and resid 157:170)A157 - 170
6X-RAY DIFFRACTION6(chain A and resid 171:185)A171 - 185
7X-RAY DIFFRACTION7(chain A and resid 186:195)A186 - 195
8X-RAY DIFFRACTION8(chain A and resid 196:207)A196 - 207
9X-RAY DIFFRACTION9(chain A and resid 208:256)A208 - 256
10X-RAY DIFFRACTION10(chain A and resid 257:273)A257 - 273
11X-RAY DIFFRACTION11(chain B and resid 3:17)B3 - 17
12X-RAY DIFFRACTION12(chain B and resid 18:51)B18 - 51
13X-RAY DIFFRACTION13(chain B and resid 52:73)B52 - 73
14X-RAY DIFFRACTION14(chain B and resid 74:131)B74 - 131
15X-RAY DIFFRACTION15(chain B and resid 132:143)B132 - 143
16X-RAY DIFFRACTION16(chain B and resid 144:162)B144 - 162
17X-RAY DIFFRACTION17(chain B and resid 163:169)B163 - 169
18X-RAY DIFFRACTION18(chain B and resid 170:189)B170 - 189
19X-RAY DIFFRACTION19(chain B and resid 190:197)B190 - 197
20X-RAY DIFFRACTION20(chain B and resid 198:273)B198 - 273

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