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- PDB-2dso: Crystal structure of D138N mutant of Drp35, a 35kDa drug responsi... -

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Basic information

Entry
Database: PDB / ID: 2dso
TitleCrystal structure of D138N mutant of Drp35, a 35kDa drug responsive protein from Staphylococcus aureus
ComponentsDrp35
KeywordsHYDROLASE / BETA PROPELLER
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity / metal ion binding / cytoplasm
Similarity search - Function
: / SMP-30/Gluconolactonase/LRE-like region / SMP-30/Gluconolactonase/LRE-like region / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTanaka, Y. / Ohki, Y. / Morikawa, K. / Yao, M. / Watanabe, N. / Ohta, T. / Tanaka, I.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural and Mutational Analyses of Drp35 from Staphylococcus aureus: A POSSIBLE MECHANISM FOR ITS LACTONASE ACTIVITY
Authors: Tanaka, Y. / Morikawa, K. / Ohki, Y. / Yao, M. / Tsumoto, K. / Watanabe, N. / Ohta, T. / Tanaka, I.
History
DepositionJul 4, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 10, 2021Group: 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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Drp35
B: Drp35
C: Drp35
D: Drp35
E: Drp35
F: Drp35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,57821
Polymers222,8206
Non-polymers75715
Water15,781876
1
A: Drp35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3094
Polymers37,1371
Non-polymers1723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Drp35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2173
Polymers37,1371
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Drp35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2173
Polymers37,1371
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: Drp35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4015
Polymers37,1371
Non-polymers2644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: Drp35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2173
Polymers37,1371
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: Drp35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2173
Polymers37,1371
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
A: Drp35
hetero molecules

B: Drp35
C: Drp35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,74310
Polymers111,4103
Non-polymers3337
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation1_655x+1,y,z1
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-73 kcal/mol
Surface area31730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.548, 182.432, 81.454
Angle α, β, γ (deg.)90.00, 115.58, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is monomer. Six molecules of monomers are included in an asymmetric unit.

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Components

#1: Protein
Drp35


Mass: 37136.727 Da / Num. of mol.: 6 / Mutation: D138N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q99QV3, 1,4-lactonase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 876 / 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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 100mM HEPES, 1M succinic acid, 1% polyethylene glycol mono methyl ether 2000, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 116543 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 15.5 Å2 / Rsym value: 0.105

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DG1

2dg1


Resolution: 2.1→19.99 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2606129.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.202 11651 10 %RANDOM
Rwork0.168 ---
obs0.168 116380 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.2612 Å2 / ksol: 0.415262 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å23.88 Å2
2---5.96 Å20 Å2
3---4.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15082 0 30 876 15988
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.892.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.239 1800 9.5 %
Rwork0.202 17144 -
obs--97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramion.top
X-RAY DIFFRACTION3cis_peptide.paramwater.top
X-RAY DIFFRACTION4ion.paramgol_xplor_2.top
X-RAY DIFFRACTION5gol_xplor_2.param

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