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- PDB-3esh: Crystal structure of a probable metal-dependent hydrolase from St... -

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Basic information

Entry
Database: PDB / ID: 3esh
TitleCrystal structure of a probable metal-dependent hydrolase from Staphylococcus aureus. Northeast Structural Genomics target ZR314
ComponentsProtein similar to metal-dependent hydrolase
KeywordsHYDROLASE / Similar to metal-dependent hydrolase / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Similar to metal-dependent hydrolase / Similar to metal-dependent hydrolase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsSeetharaman, J. / Chen, Y. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. ...Seetharaman, J. / Chen, Y. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of a probable metal-dependent hydrolase from Staphylococcus aureus. Northeast Structural Genomics target ZR314
Authors: Seetharaman, J. / Chen, Y. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionOct 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein similar to metal-dependent hydrolase
B: Protein similar to metal-dependent hydrolase
C: Protein similar to metal-dependent hydrolase


Theoretical massNumber of molelcules
Total (without water)97,9053
Polymers97,9053
Non-polymers00
Water2,990166
1
A: Protein similar to metal-dependent hydrolase
B: Protein similar to metal-dependent hydrolase
C: Protein similar to metal-dependent hydrolase

A: Protein similar to metal-dependent hydrolase
B: Protein similar to metal-dependent hydrolase
C: Protein similar to metal-dependent hydrolase


Theoretical massNumber of molelcules
Total (without water)195,8116
Polymers195,8116
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area12030 Å2
ΔGint-71 kcal/mol
Surface area61050 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.110, 113.110, 155.807
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Protein similar to metal-dependent hydrolase


Mass: 32635.135 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Gene: SAV1747 / Plasmid: PET 21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99TB7, UniProt: A0A0H3JZW1*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.54 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.17% 2,6-Naphthalenedisulfonic acid 0.17% 2,7-Naphthalenedisulfonic acid 0.17% Anthraquinone-2,6-disulfonic acid 25 mM HEPES sodium pH 6.8 6.25% PEG 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 25, 2008 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 449114 / Num. obs: 85257 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.076 / Net I/σ(I): 11.7
Reflection shellResolution: 2.39→2.5 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 11.2 / Rsym value: 0.23 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→45.77 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 150252.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.274 3098 4.9 %RANDOM
Rwork0.228 ---
obs0.228 62800 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.7971 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 44.2 Å2
Baniso -1Baniso -2Baniso -3
1-6.79 Å20 Å20 Å2
2--6.79 Å20 Å2
3----13.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.5→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6723 0 0 166 6889
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
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: 2.5→2.66 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 416 4.4 %
Rwork0.301 9103 -
obs--85.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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