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- PDB-1z5g: Crystal structure of Salmonella typhimurium AphA protein -

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Basic information

Entry
Database: PDB / ID: 1z5g
TitleCrystal structure of Salmonella typhimurium AphA protein
ComponentsAphA protein
KeywordsHYDROLASE / Class-B bacterial non-specific acid phosphatases / AphA protein / metalloenzyme
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
HAD-superfamily phosphatase, subfamily IIIB, AphA / Acid phosphatase, class B-like / HAD superfamily, subfamily IIIB (Acid phosphatase) / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Class B acid phosphatase / Class B acid phosphatase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMakde, R.D. / Kumar, V.
Citation
Journal: Arch.Biochem.Biophys. / Year: 2007
Title: Structural and mutational analyses reveal the functional role of active-site Lys-154 and Asp-173 of Salmonella typhimurium AphA protein.
Authors: Makde, R.D. / Gupta, G.D. / Mahajan, S.K. / Kumar, V.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003
Title: Expression, purification, crystallization and preliminary X-ray diffraction studies of recombinant class B non-specific acid phosphatase of Salmonella typhimurium
Authors: Makde, R.D. / Kumar, V. / Gupta, G.D. / Jasti, J. / Singh, T.P. / Mahajan, S.K.
History
DepositionMar 18, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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_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_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: AphA protein
B: AphA protein
C: AphA protein
D: AphA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6759
Polymers95,4834
Non-polymers1925
Water10,305572
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12150 Å2
ΔGint-115 kcal/mol
Surface area34230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.840, 84.590, 149.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
AphA protein


Mass: 23870.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: aphA / Plasmid: pET21(a) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q5MB24, UniProt: Q540U1*PLUS, acid phosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 2.4 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: PEG 6000, magnesium chloride, sodium acetate, glycerol, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 17, 2004 / Details: OSMIC Mirrors
RadiationMonochromator: Ni Mirror + Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 56804 / Num. obs: 56804 / % possible obs: 92.7 % / Observed criterion σ(I): 0 / Redundancy: 2.93 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 15.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 4.03 / Num. unique all: 5311 / % possible all: 88.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
DMmodel building
CNS1.1refinement
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N8N

1n8n


Resolution: 2→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2843 -RANDOM
Rwork0.165 ---
all-56804 --
obs-56804 92.7 %-
Solvent computationSolvent model: Flat model / Bsol: 48.2 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso mean: 28.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6587 0 9 572 7168
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.35
X-RAY DIFFRACTIONc_mcangle_it2.11
X-RAY DIFFRACTIONc_scbond_it2.05
X-RAY DIFFRACTIONc_scangle_it3.14
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection
Rfree0.239 238
Rwork0.222 -
obs-5097
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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