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- PDB-7xhz: Crystal structure of SAV2152 from MRSA -

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Basic information

Entry
Database: PDB / ID: 7xhz
TitleCrystal structure of SAV2152 from MRSA
ComponentsPhosphatase, SAV2152
KeywordsHYDROLASE / Phosphatase
Function / homology
Function and homology information


phosphatase activity
Similarity search - Function
Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Cof family / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cof-type HAD-IIB family hydrolase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å
AuthorsPark, H.J. / Seok, S.H. / Kim, J.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of SAV2152 from MRSA
Authors: Park, H.J. / Seok, S.H. / Kim, J.H.
History
DepositionApr 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatase, SAV2152


Theoretical massNumber of molelcules
Total (without water)26,4951
Polymers26,4951
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.610, 63.060, 92.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

21A-415-

HOH

31A-431-

HOH

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Components

#1: Protein Phosphatase, SAV2152


Mass: 26494.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria)
Gene: SAV2152 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3JWK0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.1 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 17% PEG 8000, 0.1M CAPS pH 10.5, 0.3M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97957 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.92→27.76 Å / Num. obs: 24669 / % possible obs: 99.91 % / Redundancy: 7.4 % / Biso Wilson estimate: 28.17 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.031 / Rrim(I) all: 0.085 / Net I/av σ(I): 13.3 / Net I/σ(I): 14.4
Reflection shellResolution: 1.92→1.98 Å / Mean I/σ(I) obs: 4.85 / Num. unique obs: 24669 / Rpim(I) all: 0.031 / Rrim(I) all: 0.085 / % possible all: 99.91

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158phasing
HKL-2000data scaling
PHENIXmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.92→27.76 Å / SU ML: 0.1974 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.8549
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.218 1231 5 %
Rwork0.1877 23409 -
obs0.1892 24640 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.59 Å2
Refinement stepCycle: LAST / Resolution: 1.92→27.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 0 132 1981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01781884
X-RAY DIFFRACTIONf_angle_d1.43072542
X-RAY DIFFRACTIONf_chiral_restr0.0716278
X-RAY DIFFRACTIONf_plane_restr0.0106332
X-RAY DIFFRACTIONf_dihedral_angle_d5.4054246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-20.27861340.21822538X-RAY DIFFRACTION99.89
2-2.090.21671340.17712569X-RAY DIFFRACTION99.89
2.09-2.20.23261350.1762553X-RAY DIFFRACTION99.96
2.2-2.340.22941360.17632589X-RAY DIFFRACTION99.96
2.34-2.520.26691340.18072552X-RAY DIFFRACTION99.96
2.52-2.770.22641380.18822614X-RAY DIFFRACTION99.93
2.77-3.170.21461370.19682606X-RAY DIFFRACTION99.93
3.17-3.990.18191380.17832627X-RAY DIFFRACTION99.89
3.99-27.760.22031450.19492761X-RAY DIFFRACTION99.49
Refinement TLS params.Method: refined / Origin x: 27.8237100586 Å / Origin y: 48.6700310918 Å / Origin z: 26.3773340167 Å
111213212223313233
T0.201439439695 Å2-0.000465165121821 Å2-0.0133507148967 Å2-0.207356174546 Å20.0414753453539 Å2--0.201167291452 Å2
L0.994261201189 °20.0327693207451 °2-0.306196080904 °2-1.05642591674 °20.511517036735 °2--0.798590592687 °2
S-0.0761820335987 Å °0.0136416678279 Å °-0.129773349008 Å °-0.0256057543052 Å °0.0194330890635 Å °-0.0342058822549 Å °0.0154738382588 Å °-0.0646727471409 Å °-0.00134100589817 Å °
Refinement TLS groupSelection details: all

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