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- PDB-2a96: Crystal structure of phosphate tethered PhoN of S. typhimurium -

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Basic information

Entry
Database: PDB / ID: 2a96
TitleCrystal structure of phosphate tethered PhoN of S. typhimurium
Componentsclass A nonspecific acid phosphatase PhoN
KeywordsHYDROLASE / Class-A bacterial non-specific acid phosphatase / PhoN protein
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / outer membrane-bounded periplasmic space
Similarity search - Function
Acid phosphatase, class A, bacterial, conserved site / Class A bacterial acid phosphatases signature. / Acid phosphatase, class A, bacterial / Vanadium-containing Chloroperoxidase; domain 1 / Phosphatidic acid phosphatase type 2/haloperoxidase / Acid phosphatase homologues / Phosphatidic acid phosphatase type 2/haloperoxidase / PAP2 superfamily / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / : / Acid phosphatase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Molecular replacement, Non-crystallographic symmetry averaging / Resolution: 2.5 Å
AuthorsMakde, R.D. / Mahajan, S.K. / Kumar, V.
Citation
Journal: Biochemistry / Year: 2007
Title: Structure and Mutational Analysis of the PhoN Protein of Salmonella typhimurium Provide Insight into Mechanistic Details.
Authors: Makde, R.D. / Mahajan, S.K. / Kumar, V.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Purification, crystallization and preliminary x-ray diffraction studies of recombinant class A non-specific acid phosphatase of Salmonella typhimurium.
Authors: Makde, R.D. / Kumar, V. / Rao, A.S. / Yadava, V.S. / Mahajan, S.K.
History
DepositionJul 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Aug 23, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: class A nonspecific acid phosphatase PhoN
B: class A nonspecific acid phosphatase PhoN
C: class A nonspecific acid phosphatase PhoN
D: class A nonspecific acid phosphatase PhoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1288
Polymers113,7494
Non-polymers3804
Water4,954275
1
A: class A nonspecific acid phosphatase PhoN
B: class A nonspecific acid phosphatase PhoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0644
Polymers56,8742
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-44 kcal/mol
Surface area17740 Å2
MethodPISA
2
C: class A nonspecific acid phosphatase PhoN
D: class A nonspecific acid phosphatase PhoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0644
Polymers56,8742
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-44 kcal/mol
Surface area17730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.870, 45.080, 112.470
Angle α, β, γ (deg.)90.00, 111.58, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2
DetailsThe entry contains the crystallographic asymmetric unit consisting of four chains (two dimers). A dimer is the known biologically active state of the PHON protein. Chains A and B form one dimer while the chains C and D form the other dimer.

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Components

#1: Protein
class A nonspecific acid phosphatase PhoN


Mass: 28437.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: phoN / Plasmid: pSK- / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: GenBank: 21913311, UniProt: Q8KRU6*PLUS, acid phosphatase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG-6000 12%, Glycerol 2%, 25mM phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 18, 2001 / Details: OSMIC mirror
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 27475 / Num. obs: 27475 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 1.4 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 8.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4028 / % possible all: 89.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA/ TRUNCATEdata scaling
AMoREphasing
DMmodel building
CNS1.1refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
DMphasing
RefinementMethod to determine structure: Molecular replacement, Non-crystallographic symmetry averaging
Starting model: PDB entry 1D2T

1d2t


Resolution: 2.5→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: NCS restraints for equivalence of chain A and Chain C, and for chain B and Chain D.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1400 -RANDOM
Rwork0.17 ---
all-27448 --
obs-27448 88.2 %-
Solvent computationSolvent model: Flat Model / Bsol: 50.4 Å2
Displacement parametersBiso mean: 28.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6960 0 20 275 7255
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.25
X-RAY DIFFRACTIONc_mcangle_it2.1
X-RAY DIFFRACTIONc_scbond_it2.13
X-RAY DIFFRACTIONc_scangle_it3.3
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDWeight Biso Weight position
11X-RAY DIFFRACTION5300
22X-RAY DIFFRACTION5300
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection% reflection
Rfree0.312 140 -
Rwork0.258 --
obs-2737 89.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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