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- PDB-2dg0: Crystal structure of Drp35, a 35kDa drug responsive protein from ... -

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Basic information

Entry
Database: PDB / ID: 2dg0
TitleCrystal structure 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 / 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 / SAD / Resolution: 2.4 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 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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
G: DrP35
H: DrP35
I: DrP35
J: DrP35
K: DrP35
L: DrP35


Theoretical massNumber of molelcules
Total (without water)449,59212
Polymers449,59212
Non-polymers00
Water23,3291295
1
A: DrP35


Theoretical massNumber of molelcules
Total (without water)37,4661
Polymers37,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: DrP35


Theoretical massNumber of molelcules
Total (without water)37,4661
Polymers37,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: DrP35


Theoretical massNumber of molelcules
Total (without water)37,4661
Polymers37,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: DrP35


Theoretical massNumber of molelcules
Total (without water)37,4661
Polymers37,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: DrP35


Theoretical massNumber of molelcules
Total (without water)37,4661
Polymers37,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: DrP35


Theoretical massNumber of molelcules
Total (without water)37,4661
Polymers37,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
G: DrP35


Theoretical massNumber of molelcules
Total (without water)37,4661
Polymers37,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
8
H: DrP35


Theoretical massNumber of molelcules
Total (without water)37,4661
Polymers37,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
9
I: DrP35


Theoretical massNumber of molelcules
Total (without water)37,4661
Polymers37,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
10
J: DrP35


Theoretical massNumber of molelcules
Total (without water)37,4661
Polymers37,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
11
K: DrP35


Theoretical massNumber of molelcules
Total (without water)37,4661
Polymers37,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
12
L: DrP35


Theoretical massNumber of molelcules
Total (without water)37,4661
Polymers37,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
13
E: DrP35
G: DrP35
H: DrP35


Theoretical massNumber of molelcules
Total (without water)112,3983
Polymers112,3983
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-35 kcal/mol
Surface area31720 Å2
MethodPISA
14
B: DrP35

A: DrP35
K: DrP35


Theoretical massNumber of molelcules
Total (without water)112,3983
Polymers112,3983
Non-polymers00
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation2_545-x,y-1/2,-z1
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-34 kcal/mol
Surface area31700 Å2
MethodPISA
15
I: DrP35
J: DrP35
L: DrP35


Theoretical massNumber of molelcules
Total (without water)112,3983
Polymers112,3983
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-34 kcal/mol
Surface area31830 Å2
MethodPISA
16
C: DrP35

D: DrP35
F: DrP35


Theoretical massNumber of molelcules
Total (without water)112,3983
Polymers112,3983
Non-polymers00
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation1_655x+1,y,z1
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-35 kcal/mol
Surface area31630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.089, 146.062, 151.947
Angle α, β, γ (deg.)90.00, 93.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DrP35 / Lactonase


Mass: 37465.977 Da / Num. of mol.: 12
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1295 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.1M Tris, 23% PEG4000, 0.1M lithium sulfate, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97908 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 145982 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 31.2 Å2 / Rsym value: 0.103
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 10.2 % / Num. unique all: 14540 / Rsym value: 0.466 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2581460.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.222 13838 10 %RANDOM
Rwork0.2 ---
obs0.2 138199 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.5948 Å2 / ksol: 0.322615 e/Å3
Displacement parametersBiso mean: 39.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å2-3.52 Å2
2---1.01 Å20 Å2
3---2.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30096 0 0 1295 31391
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it1.932
X-RAY DIFFRACTIONc_scangle_it2.82.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 2092 10.1 %
Rwork0.251 18595 -
obs--85.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cis_peptide.param
X-RAY DIFFRACTION3water.param

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