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- PDB-2ii1: Crystal structure of Acetamidase (10172637) from Bacillus Halodur... -

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Basic information

Entry
Database: PDB / ID: 2ii1
TitleCrystal structure of Acetamidase (10172637) from Bacillus Halodurans at 1.95 A resolution
ComponentsAcetamidase
KeywordsHYDROLASE / 10172637 / ACETAMIDASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / JCSG
Function / homologyAcetamidase/Formamidase / Acetamidase/Formamidase family / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / metal ion binding / Acetamidase
Function and homology information
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal Structure of Acetamidase (10172637) from Bacillus Halodurans at 1.95 A Resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jan 24, 2018Group: Advisory / Database references / Category: citation_author / pdbx_unobs_or_zero_occ_atoms / Item: _citation_author.name
Revision 1.4Dec 25, 2019Group: Advisory / Database references / Derived calculations
Category: database_PDB_caveat / pdbx_struct_assembly ...database_PDB_caveat / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn / struct_ref_seq_dif
Item: _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value ..._pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetamidase
B: Acetamidase
C: Acetamidase
D: Acetamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,26719
Polymers129,6664
Non-polymers60115
Water7,981443
1
A: Acetamidase
D: Acetamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0337
Polymers64,8332
Non-polymers2005
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-103 kcal/mol
Surface area20810 Å2
MethodPISA
2
B: Acetamidase
C: Acetamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,23412
Polymers64,8332
Non-polymers40110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-128 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.759, 69.605, 94.984
Angle α, β, γ (deg.)73.95, 88.91, 86.63
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEVALAA10 - 20811 - 209
21ILEVALBB10 - 20811 - 209
31ILEVALCC10 - 20811 - 209
41ILEVALDD10 - 20811 - 209
12PROLYSAA215 - 280216 - 281
22PROLYSBB215 - 280216 - 281
32PROLYSCC215 - 280216 - 281
42PROLYSDD215 - 280216 - 281

NCS ensembles :
ID
1
2

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Components

#1: Protein
Acetamidase


Mass: 32416.439 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: 10172637 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KGN3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.15 Å3/Da / Density % sol: 42.27 %
Crystal growDetails: 20.0% POLYETHYLENE GLYCOL 3350, 0.2M CALCIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, NANODROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9797
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 31, 2006
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.898→28.892 Å / Num. obs: 70889 / % possible obs: 90.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.116 / Net I/σ(I): 6.1
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 1.1 / Rsym value: 0.681 / % possible all: 89.3

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Processing

Software
NameVersionClassification
SHELXDphasing
SHARPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→28.89 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.164 / SU ML: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.174
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. CA ATOMS MODELED BASED ON DENSITY AND GEOMETRY. 5. MSE B1 AND ILE 193 FROM ALL CHAINS ARE RAMACHANDRAN OUTLIERS. ALL ARE SUPPORTED BY THE ELECTRON DENSITY. 6. RESIDUES 297-300 FROM CHAINS A AND B, AND RESIDUES 298-300 FROM CHAINS C AND D WERE NOT MODELED DUE TO LACK OF DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3594 5.1 %RANDOM
Rwork0.175 ---
obs0.17761 70887 90.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å21.22 Å2-1.58 Å2
2--0.06 Å2-0.71 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.95→28.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8747 0 15 443 9205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228929
X-RAY DIFFRACTIONr_bond_other_d0.0010.025822
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9912160
X-RAY DIFFRACTIONr_angle_other_deg0.976314443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48751193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47925.831331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.382151481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7321529
X-RAY DIFFRACTIONr_chiral_restr0.1120.21467
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029981
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021564
X-RAY DIFFRACTIONr_nbd_refined0.2170.21578
X-RAY DIFFRACTIONr_nbd_other0.1890.26063
X-RAY DIFFRACTIONr_nbtor_refined0.1650.24185
X-RAY DIFFRACTIONr_nbtor_other0.0840.24720
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2470
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2240.248
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.070.24
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.88736050
X-RAY DIFFRACTIONr_mcbond_other0.4732418
X-RAY DIFFRACTIONr_mcangle_it2.54959522
X-RAY DIFFRACTIONr_scbond_it4.8783165
X-RAY DIFFRACTIONr_scangle_it6.406112632
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2356loose positional0.345
12B2356loose positional0.315
13C2356loose positional0.335
14D2356loose positional0.35
21A749loose positional0.315
22B749loose positional0.225
23C749loose positional0.225
24D749loose positional0.255
11A2356loose thermal1.9910
12B2356loose thermal2.0910
13C2356loose thermal3.2710
14D2356loose thermal3.3110
21A749loose thermal2.2110
22B749loose thermal2.5610
23C749loose thermal1.8410
24D749loose thermal2.1610
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 235 -
Rwork0.223 4861 -
obs--87.23 %
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)
10.6503-0.21110.12191.15260.25171.21770.02560.0055-0.05950.0126-0.0034-0.06640.10.0415-0.02220.03-0.00730.01320.0078-0.00590.057527.140740.463212.4605
21.5371-1.05070.57231.0599-0.18231.05410.02470.0497-0.0062-0.1146-0.0280.03120.0036-0.06370.00330.034-0.0310.02230.03640.00250.052314.060256.22184.2784
31.1412-0.20290.66280.8223-0.40871.73280.0884-0.0005-0.1165-0.0625-0.073-0.01350.10850.0593-0.01540.0142-0.00610.00330.01560.01280.04930.221763.0886-27.946
40.7435-0.33360.20821.28350.2551.1228-0.0197-0.16880.0737-0.00070.0092-0.0863-0.1236-0.12550.01050.03110.0048-0.00080.0541-0.00780.008123.316982.2444-19.4407
51.3592-0.19010.51050.6881-0.23760.8304-0.1352-0.17140.16850.07080.0761-0.0184-0.2018-0.10130.05910.0720.0348-0.00420.0398-0.02620.02256.426997.2838-32.3397
60.8522-0.4444-0.0511.07660.32381.68620.0947-0.0075-0.0577-0.1219-0.02690.0010.0067-0.0639-0.06780.0262-0.0013-0.00670.03920.01010.033312.674477.7074-40.3144
70.5980.11330.19831.03550.18551.1102-0.04330.00480.06720.00230.0220.0672-0.0696-0.05040.02130.0249-0.00410.01690.0250.00520.05619.491978.608816.7895
81.1333-0.60380.45121.7905-0.57620.4206-0.0253-0.11860.01720.23490.0427-0.08710.02620.014-0.01740.0344-0.01940.00890.0317-0.01240.041923.487563.319325.1472
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 2161 - 217
2X-RAY DIFFRACTION2AA217 - 296218 - 297
3X-RAY DIFFRACTION3BB1 - 2152 - 216
4X-RAY DIFFRACTION4BB216 - 296217 - 297
5X-RAY DIFFRACTION5CC2 - 2183 - 219
6X-RAY DIFFRACTION6CC219 - 297220 - 298
7X-RAY DIFFRACTION7DD1 - 2132 - 214
8X-RAY DIFFRACTION8DD214 - 297215 - 298

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