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- PDB-2akc: Crystal structure of tungstate complex of the PhoN protein from S... -

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Basic information

Entry
Database: PDB / ID: 2akc
TitleCrystal structure of tungstate complex of the PhoN protein from S. typhimurium
Componentsclass A nonspecific acid phosphatase PhoN
KeywordsHYDROLASE / Class-A bacterial non-specific acid phosphatase / tungstate complex of 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 / Acid phosphatase homologues / Phosphatidic acid phosphatase type 2/haloperoxidase / Vanadium-containing Chloroperoxidase; domain 1 / Phosphatidic acid phosphatase type 2/haloperoxidase / PAP2 superfamily / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
TUNGSTATE(VI)ION / : / Acid phosphatase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 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.
History
DepositionAug 3, 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
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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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

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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)105,3528
Polymers104,3614
Non-polymers9914
Water5,873326
1
A: class A nonspecific acid phosphatase PhoN
B: class A nonspecific acid phosphatase PhoN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6764
Polymers52,1802
Non-polymers4962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-30 kcal/mol
Surface area18000 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)52,6764
Polymers52,1802
Non-polymers4962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-29 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.800, 45.200, 112.700
Angle α, β, γ (deg.)90.00, 111.40, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe entry contains 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: 26090.242 Da / Num. of mol.: 4 / Fragment: Periplasmic (mature) PhoN (residues 21-250)
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-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: WO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG-6000 15%, Glycerol 2%, 1mM sodium tungstate, 25mM sodium acetate, pH 5.6, 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: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 3, 2002 / Details: OSMIC 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: 2.3→30 Å / Num. all: 37751 / Num. obs: 37069 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 30.34 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5148 / % possible all: 89.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
CCP4model building
CNS1.1refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2A96

2a96


Resolution: 2.3→20 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The submission is the structure of periplasmic (mature) PhoN protein constituted of 230 amino acid residues. The 20 N-terminus signal peptide residues corresponding to the GenBank entry ...Details: The submission is the structure of periplasmic (mature) PhoN protein constituted of 230 amino acid residues. The 20 N-terminus signal peptide residues corresponding to the GenBank entry 21913311 (AAM81208) are known to be cleaved and thus not observed in the mature protein. The residue numbering in the deposited structure however is as the full length CDS in the Genbank entry.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1884 5 %RANDOM
Rwork0.164 ---
all-37038 --
obs-37038 92.3 %-
Solvent computationSolvent model: Bulk Solvent modeling, Flat model / Bsol: 39.6 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso mean: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.53 Å20 Å2-5.08 Å2
2--4.82 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6982 0 20 326 7328
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.282.5
LS refinement shellResolution: 2.3→2.38 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.256 180 5 %
Rwork0.214 3361 -
obs-3541 88 %
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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