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- PDB-2ipb: Crystal structure of T159D mutant of S. Typhimurium PhoN protein -

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Basic information

Entry
Database: PDB / ID: 2ipb
TitleCrystal structure of T159D mutant of S. Typhimurium PhoN protein
ComponentsClass A nonspecific acid phosphatase PhoN
KeywordsHYDROLASE / Class-A bacterial non-specific acid phosphatase / T159D mutant of the 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
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.23 Å
AuthorsMakde, R.D. / 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.
#2: Journal: Biomol.Eng. / Year: 2006
Title: Protein engineering of class-A non-specific acid phosphatase (PhoN) of Salmonella typhimurium: modulation of the pH-activity profile
Authors: Makde, R.D. / Dikshit, K. / Kumar, V.
History
DepositionOct 12, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 30, 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


Theoretical massNumber of molelcules
Total (without water)104,6534
Polymers104,6534
Non-polymers00
Water5,278293
1
A: Class A nonspecific acid phosphatase PhoN
B: Class A nonspecific acid phosphatase PhoN


Theoretical massNumber of molelcules
Total (without water)52,3272
Polymers52,3272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-28 kcal/mol
Surface area18070 Å2
MethodPISA
2
C: Class A nonspecific acid phosphatase PhoN
D: Class A nonspecific acid phosphatase PhoN


Theoretical massNumber of molelcules
Total (without water)52,3272
Polymers52,3272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-27 kcal/mol
Surface area18140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.273, 45.113, 112.945
Angle α, β, γ (deg.)90.00, 112.05, 90.00
Int Tables number5
Space group name H-MC121
DetailsA dimer is the known biologically active state of the PhoN protein of Salmonella Typhimurium. The entry contains crystallographic asymmetric unit consisting of four chains (two dimers). Chains A and B form one dimer while chains C and D form the other dimer in the asymmetric unit.

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Components

#1: Protein
Class A nonspecific acid phosphatase PhoN / PhoN protein


Mass: 26163.316 Da / Num. of mol.: 4 / Mutation: T159D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: MD6001 isolate / Gene: phoN / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q71EB8, acid phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 42.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% PEG-6000, 25mM potassium chloride, 5mM magnesium sulphate, 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 RU200HB / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 10, 2005 / Details: mirrors
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.21→30 Å / Num. all: 43054 / Num. obs: 43054 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.7
Reflection shellResolution: 2.21→2.33 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 4.7 / Num. unique all: 4944 / % possible all: 75.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
CCP4model building
REFMAC5.2.0005refinement
MAR345345DTBdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2A96

2a96


Resolution: 2.23→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.322 / SU ML: 0.136 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.271 / ESU R Free: 0.2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2167 5 %RANDOM
Rwork0.151 ---
all0.154 40837 --
obs0.154 40837 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: Babinet model with mask
Displacement parametersBiso mean: 29.06 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å20.63 Å21.43 Å2
2--0 Å20.43 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.271 Å
Luzzati sigma a-0.136 Å
Refinement stepCycle: LAST / Resolution: 2.23→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7012 0 0 293 7305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227208
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9291.9519774
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4215872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46223.516364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.062151174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.831560
X-RAY DIFFRACTIONr_chiral_restr0.0810.2994
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025684
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.33118
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.54985
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.5661
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.341
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.513
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.02924479
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.10237054
X-RAY DIFFRACTIONr_scbond_it2.25123107
X-RAY DIFFRACTIONr_scangle_it3.44832720
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.232→2.29 Å
RfactorNum. reflection% reflection
Rfree0.24 133 -
Rwork0.175 2759 -
obs-2759 100 %

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