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- PDB-4o8c: Structure of the H170Y mutant of thermostable p-nitrophenylphosph... -

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Basic information

Entry
Database: PDB / ID: 4o8c
TitleStructure of the H170Y mutant of thermostable p-nitrophenylphosphatase from Bacillus Stearothermophilus
ComponentsThermostable NPPase
KeywordsHYDROLASE / Phosphatase
Function / homology
Function and homology information


phosphoglycolate phosphatase activity / alkaline phosphatase activity / metal ion binding
Similarity search - Function
HAD-superfamily hydrolase, subfamily IIA, hypothetical 1 / HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD-hyrolase-like / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShen, T. / Guo, Z. / Wang, F. / Gong, W. / Ji, C.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structure of a His170Tyr mutant of thermostable pNPPase from Geobacillus stearothermophilus.
Authors: Shen, T. / Guo, Z. / Ji, C.
History
DepositionDec 27, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Jan 1, 2020Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 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_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: Thermostable NPPase
B: Thermostable NPPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3994
Polymers58,2782
Non-polymers1202
Water4,648258
1
A: Thermostable NPPase


Theoretical massNumber of molelcules
Total (without water)29,1391
Polymers29,1391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thermostable NPPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2603
Polymers29,1391
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-17 kcal/mol
Surface area22540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.754, 83.245, 176.051
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 Thermostable NPPase / thermostable p-nitrophenylphosphatase


Mass: 29139.135 Da / Num. of mol.: 2 / Mutation: H170Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: pQE30a / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q8L1N9, alkaline phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M HEPES, 1.9M Ammonium sulphate, 3% PEG400, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2→40.506 Å / Num. all: 43178 / Num. obs: 38730 / % possible obs: 93.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 25.35 Å2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KN8

4kn8


Resolution: 2→40.506 Å / FOM work R set: 0.8634 / SU ML: 0.19 / σ(F): 1.34 / Phase error: 20.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2142 1948 5.03 %RANDOM
Rwork0.1708 ---
obs0.173 38730 97.84 %-
all-43178 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.67 Å2 / Biso mean: 24.22 Å2 / Biso min: 10.66 Å2
Refinement stepCycle: LAST / Resolution: 2→40.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3978 0 6 258 4242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114052
X-RAY DIFFRACTIONf_angle_d1.2375492
X-RAY DIFFRACTIONf_chiral_restr0.07634
X-RAY DIFFRACTIONf_plane_restr0.006704
X-RAY DIFFRACTIONf_dihedral_angle_d13.3211496
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9997-2.04970.23481130.16942375248889
2.0497-2.10510.20321250.16362455258095
2.1051-2.1670.22771300.16132582271296
2.167-2.2370.20711490.15392563271298
2.237-2.31690.20921450.15612641278699
2.3169-2.40970.21241470.149726442791100
2.4097-2.51930.22361410.157826342775100
2.5193-2.65210.20341210.164426702791100
2.6521-2.81830.24631350.169326772812100
2.8183-3.03580.23331610.183226612822100
3.0358-3.34120.22991330.190126962829100
3.3412-3.82430.21451450.176127162861100
3.8243-4.8170.17681310.15242665279696
4.817-40.51410.21711720.1932803297598
Refinement TLS params.Method: refined / Origin x: -18.5708 Å / Origin y: 1.725 Å / Origin z: -10.2131 Å
111213212223313233
T0.1283 Å2-0.0051 Å2-0.0135 Å2-0.135 Å2-0.0077 Å2--0.1678 Å2
L0.3696 °20.0512 °2-0.2004 °2-0.4185 °2-0.4085 °2--0.9424 °2
S0.0228 Å °0.0622 Å °0.0411 Å °-0.0271 Å °-0.0228 Å °-0.0174 Å °-0.0487 Å °0.0169 Å °-0.0065 Å °
Refinement TLS groupSelection details: ALL

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