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- PDB-3dev: Crystal structure of SH1221 protein from Staphylococcus haemolyti... -

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Basic information

Entry
Database: PDB / ID: 3dev
TitleCrystal structure of SH1221 protein from Staphylococcus haemolyticus, Northeast Structural Genomics Consortium Target ShR87
ComponentsSH1221
Keywordsstructural genomics / unknown function / alpha-beta protein. / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


nucleic acid binding / metal ion binding
Similarity search - Function
inorganic pyrophosphatase (n-terminal core) / Diaminopimelate Epimerase; Chain A, domain 1 - #30 / : / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Diaminopimelate Epimerase; Chain A, domain 1 ...inorganic pyrophosphatase (n-terminal core) / Diaminopimelate Epimerase; Chain A, domain 1 - #30 / : / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DHH family phosphoesterase
Similarity search - Component
Biological speciesStaphylococcus haemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsForouhar, F. / Neely, H. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Wang, D. / Everett, J.K. / Acton, T.B. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of SH1221 protein from Staphylococcus haemolyticus, Northeast Structural Genomics Consortium Target ShR87
Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJun 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.pdbx_leaving_atom_flag / _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: SH1221
B: SH1221
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5167
Polymers73,1802
Non-polymers3375
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-76 kcal/mol
Surface area27540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.087, 106.087, 86.092
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein SH1221


Mass: 36589.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus haemolyticus (bacteria) / Strain: JCSC1435 / Gene: SH1221 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q4L745
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.82 Å3/Da / Density % sol: 67.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100 mM sodium citrate (pH 5.2), 1.25 M lithium sulfate, and 0.5 M ammonium sulfate., VAPOR ...Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100 mM sodium citrate (pH 5.2), 1.25 M lithium sulfate, and 0.5 M ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97931 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 21, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 39168 / Num. obs: 38268 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.104 / Rsym value: 0.081 / Net I/σ(I): 13.83
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.44 / Rsym value: 0.284 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SHELXthen SOLVE/RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→19.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 347555.58 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 3120 9.7 %RANDOM
Rwork0.193 ---
obs0.193 32319 82.7 %-
all-39079 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.1602 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 68.1 Å2
Baniso -1Baniso -2Baniso -3
1-13.87 Å20 Å20 Å2
2--13.87 Å20 Å2
3----27.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 3.1→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5036 0 17 36 5089
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.1→3.21 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.36 200 10.1 %
Rwork0.331 1773 -
obs--50.5 %

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