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- PDB-2dg1: Crystal structure of Drp35, a 35kDa drug responsive protein from ... -

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Basic information

Entry
Database: PDB / ID: 2dg1
TitleCrystal structure of Drp35, a 35kDa drug responsive protein from Staphylococcus aureus, complexed with Ca2+
ComponentsDrP35
KeywordsHYDROLASE / BETA PROPELLER
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity / response to antibiotic / 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
Lactonase drp35 / Lactonase drp35
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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
DepositionMar 7, 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 1.3Oct 25, 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_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

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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)224,41230
Polymers222,8266
Non-polymers1,58624
Water38,5702141
1
A: DrP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4025
Polymers37,1381
Non-polymers2644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: DrP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4025
Polymers37,1381
Non-polymers2644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: DrP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4025
Polymers37,1381
Non-polymers2644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: DrP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4025
Polymers37,1381
Non-polymers2644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: DrP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4025
Polymers37,1381
Non-polymers2644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: DrP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4025
Polymers37,1381
Non-polymers2644
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)112,20615
Polymers111,4133
Non-polymers79312
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation1_655x+1,y,z1
identity operation1_555x,y,z1
Buried area8720 Å2
ΔGint-90 kcal/mol
Surface area31180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.527, 181.978, 81.803
Angle α, β, γ (deg.)90.00, 115.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DrP35 / Lactonase


Mass: 37137.711 Da / Num. of mol.: 6
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: Q9S0S3, UniProt: Q99QV3*PLUS, 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2141 / 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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 1M succinic acid, 1% PEG MME2000, 5mM CaCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 211193 / % possible obs: 99.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 15.3 Å2 / Rsym value: 0.063
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 3.4 % / Num. unique all: 20225 / Rsym value: 0.395 / % possible all: 95

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DG0

2dg0


Resolution: 1.72→19.99 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 2322719.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.197 20975 9.9 %RANDOM
Rwork0.169 ---
obs0.169 211106 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.3322 Å2 / ksol: 0.388611 e/Å3
Displacement parametersBiso mean: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20 Å22.33 Å2
2---4.4 Å20 Å2
3---3.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.72→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15076 0 84 2141 17301
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_d26
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_it0.991.5
X-RAY DIFFRACTIONc_mcangle_it1.472
X-RAY DIFFRACTIONc_scbond_it1.622
X-RAY DIFFRACTIONc_scangle_it2.312.5
LS refinement shellResolution: 1.72→1.83 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 3324 9.8 %
Rwork0.251 30557 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cis_peptide.paramion.top
X-RAY DIFFRACTION3ion.paramwater.top
X-RAY DIFFRACTION4water_rep.paramgol_xplor_2.top
X-RAY DIFFRACTION5gol_xplor_2.param

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