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- PDB-3bwx: Crystal structure of an alpha/beta hydrolase (YP_496220.1) from N... -

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Basic information

Entry
Database: PDB / ID: 3bwx
TitleCrystal structure of an alpha/beta hydrolase (YP_496220.1) from Novosphingobium aromaticivorans DSM 12444 at 1.50 A resolution
ComponentsAlpha/beta hydrolase
KeywordsHYDROLASE / YP_496220.1 / An Alpha/Beta Hydrolase / alpha/beta hydrolase fold / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
: / Alpha/beta hydrolase family / 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
Alpha/beta hydrolase
Similarity search - Component
Biological speciesNovosphingobium aromaticivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an alpha/beta hydrolase (YP_496220.1) from Novosphingobium aromaticivorans DSM 12444 at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Jan 25, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.6Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999 SEQUENCE 1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. 2. THE CONSTRUCT WAS ENGINEERED WITH THE FOLLOWING MUTATION: A209V.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,04619
Polymers32,0261
Non-polymers1,02018
Water6,053336
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.480, 69.950, 82.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha/beta hydrolase


Mass: 32025.805 Da / Num. of mol.: 1 / Mutation: A209V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Novosphingobium aromaticivorans (bacteria)
Strain: DSM 12444 / Gene: YP_496220.1, Saro_0941 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2G9T7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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 Å3/Da / Density % sol: 38.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: NANODROP, 0.2M CaCl2, 20.0% PEG 3350, No Buffer pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97908 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 25, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 1.5→27.714 Å / Num. obs: 41517 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 11.671 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.5-1.550.7041.5175467266197.4
1.55-1.620.5821.8215918782198.3
1.62-1.690.5062.1183057432198.5
1.69-1.780.3972.7194007863198.7
1.78-1.890.2933.7192747752198.8
1.89-2.040.1925.5199468048199.1
2.04-2.240.1258.1191417695199.3
2.24-2.560.09410.5194657802199.5
2.56-3.230.06114.9200708005199.6
3.23-27.7140.0326.7199207918199.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→27.714 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.96 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.08
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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. 4. CA IONS AND CL IONS WERE MODELED BASED ON CRYSTALLIZATION CONDITION, ETHYLENE GLYCOL (EDO) MOLECULES WERE MODELED BASED ON CRYO CONDITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2095 5.1 %RANDOM
Rwork0.161 ---
obs0.163 41469 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.006 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2--0.46 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.5→27.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 60 336 2581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222303
X-RAY DIFFRACTIONr_bond_other_d0.0020.021617
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.9863110
X-RAY DIFFRACTIONr_angle_other_deg1.04133893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7755290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23122.44998
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55115356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1911524
X-RAY DIFFRACTIONr_chiral_restr0.0960.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022572
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02478
X-RAY DIFFRACTIONr_nbd_refined0.2210.2484
X-RAY DIFFRACTIONr_nbd_other0.2110.21859
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21119
X-RAY DIFFRACTIONr_nbtor_other0.0870.21173
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2244
X-RAY DIFFRACTIONr_metal_ion_refined0.0910.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.223
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.020.21
X-RAY DIFFRACTIONr_mcbond_it2.06131495
X-RAY DIFFRACTIONr_mcbond_other0.5263580
X-RAY DIFFRACTIONr_mcangle_it2.60552300
X-RAY DIFFRACTIONr_scbond_it4.0658947
X-RAY DIFFRACTIONr_scangle_it5.44511810
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 169 -
Rwork0.228 2838 -
all-3007 -
obs--98.14 %
Refinement TLS params.Method: refined / Origin x: 37.0076 Å / Origin y: 36.5432 Å / Origin z: 13.1223 Å
111213212223313233
T-0.0244 Å20.0009 Å2-0.0031 Å2--0.0166 Å20.0036 Å2---0.0189 Å2
L0.2816 °2-0.1384 °20.0239 °2-0.4219 °2-0.0571 °2--0.3725 °2
S0.0056 Å °0.0151 Å °-0.0262 Å °-0.0119 Å °0.0036 Å °0.0211 Å °0.005 Å °-0.0327 Å °-0.0092 Å °

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