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- PDB-3pdw: Crystal structure of putative p-nitrophenyl phosphatase from Baci... -

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Basic information

Entry
Database: PDB / ID: 3pdw
TitleCrystal structure of putative p-nitrophenyl phosphatase from Bacillus subtilis
ComponentsUncharacterized hydrolase yutF
KeywordsHYDROLASE / structural genomics / PSI2 / NYSGXRC / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / phosphatase fold / p-nitrophenyl phosphatase
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / 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 superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Acid sugar phosphatase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.596 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of putative p-nitrophenyl phosphatase from Bacillus subtilis
Authors: Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionOct 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized hydrolase yutF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4424
Polymers29,1981
Non-polymers2443
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.190, 38.878, 81.031
Angle α, β, γ (deg.)90.00, 93.04, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-437-

HOH

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Components

#1: Protein Uncharacterized hydrolase yutF


Mass: 29197.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yutF, BSU32290 / Production host: Escherichia coli (E. coli) / References: UniProt: O32125
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG 4000, 0.1M Sodium citrate, 0.2M Ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 26, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.596→32.594 Å / Num. all: 36822 / Num. obs: 36822 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.5_2) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 1.596→32.594 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 23.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 1841 5 %RANDOM
Rwork0.184 ---
all0.1855 36822 --
obs0.1855 36822 93.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.629 Å2 / ksol: 0.384 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.3169 Å2-0 Å2-2.5494 Å2
2---4.4524 Å2-0 Å2
3----3.8645 Å2
Refinement stepCycle: LAST / Resolution: 1.596→32.594 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 16 199 2179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072017
X-RAY DIFFRACTIONf_angle_d1.012731
X-RAY DIFFRACTIONf_dihedral_angle_d16.215725
X-RAY DIFFRACTIONf_chiral_restr0.067317
X-RAY DIFFRACTIONf_plane_restr0.004354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5964-1.63960.3283880.29571681X-RAY DIFFRACTION59
1.6396-1.68780.28391220.27192117X-RAY DIFFRACTION75
1.6878-1.74230.26671370.25552456X-RAY DIFFRACTION87
1.7423-1.80460.28341440.22842775X-RAY DIFFRACTION97
1.8046-1.87680.23231200.21292908X-RAY DIFFRACTION100
1.8768-1.96220.2531430.18742853X-RAY DIFFRACTION100
1.9622-2.06570.1941320.17712840X-RAY DIFFRACTION100
2.0657-2.19510.20461630.16682870X-RAY DIFFRACTION100
2.1951-2.36450.2011470.17482852X-RAY DIFFRACTION100
2.3645-2.60240.19011340.182907X-RAY DIFFRACTION100
2.6024-2.97870.2041410.18592905X-RAY DIFFRACTION100
2.9787-3.7520.22151870.17442859X-RAY DIFFRACTION100
3.752-32.60070.18011830.16382958X-RAY DIFFRACTION100

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