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- PDB-3iii: 1.95 Angstrom Crystal Structure of CocE/NonD family hydrolase (SA... -

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Basic information

Entry
Database: PDB / ID: 3iii
Title1.95 Angstrom Crystal Structure of CocE/NonD family hydrolase (SACOL2612) from Staphylococcus aureus
ComponentsCocE/NonD family hydrolase
KeywordsHYDROLASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


dipeptidyl-peptidase activity
Similarity search - Function
alpha-amino acid ester hydrolase ( Helical cap domain) - #20 / alpha-amino acid ester hydrolase ( Helical cap domain) / CocE/Serine esterase / Xaa-Pro dipeptidyl-peptidase, C-terminal / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / Xaa-Pro dipeptidyl-peptidase-like domain / X-Pro dipeptidyl-peptidase (S15 family) / Galactose-binding domain-like / Galactose-binding-like domain superfamily ...alpha-amino acid ester hydrolase ( Helical cap domain) - #20 / alpha-amino acid ester hydrolase ( Helical cap domain) / CocE/Serine esterase / Xaa-Pro dipeptidyl-peptidase, C-terminal / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / Xaa-Pro dipeptidyl-peptidase-like domain / X-Pro dipeptidyl-peptidase (S15 family) / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Jelly Rolls / Sandwich / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / PALMITIC ACID / Hydrolase, CocE/NonD family / Hydrolase, CocE/NonD family
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsOsinski, T. / Chruszcz, M. / Domagalski, M.J. / Cymborowski, M. / Shumilin, I.A. / Skarina, T. / Onopriyenko, O. / Zimmerman, M.D. / Savchenko, A. / Edwards, A. ...Osinski, T. / Chruszcz, M. / Domagalski, M.J. / Cymborowski, M. / Shumilin, I.A. / Skarina, T. / Onopriyenko, O. / Zimmerman, M.D. / Savchenko, A. / Edwards, A. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.95 Angstrom Crystal Structure of CocE/NonD family hydrolase (SACOL2612) from Staphylococcus aureus
Authors: Osinski, T. / Chruszcz, M. / Domagalski, M.J. / Cymborowski, M. / Shumilin, I.A. / Skarina, T. / Onopriyenko, O. / Zimmerman, M.D. / Savchenko, A. / Edwards, A. / Anderson, W.F. / Minor, W. ...Authors: Osinski, T. / Chruszcz, M. / Domagalski, M.J. / Cymborowski, M. / Shumilin, I.A. / Skarina, T. / Onopriyenko, O. / Zimmerman, M.D. / Savchenko, A. / Edwards, A. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_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

Downloads & links

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Assembly

Deposited unit
A: CocE/NonD family hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3907
Polymers64,9331
Non-polymers4576
Water10,016556
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.498, 74.498, 210.681
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CocE/NonD family hydrolase


Mass: 64933.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Strain: Staphylococcus aureus subsp. aureus COL / Gene: SACOL2612 / Plasmid: pMCSG19c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q5HCV6, UniProt: A0A0H2WZL3*PLUS
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: suberic acid, sebacic acid, hexadecanedioic acid, dodecanedioic acid 12mM each, PEG3350 20%, Hepes 0.1M pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 18, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→42.14 Å / Num. all: 44452 / Num. obs: 44452 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 16.2 % / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 29.1
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 15.3 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.637 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000SOLVE/RESOLVEphasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
CCP4model building
Omodel building
Cootmodel building
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→42.14 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.237 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.127
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18336 2232 5 %RANDOM
Rwork0.14474 ---
obs0.14669 42010 99.91 %-
all-42010 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.694 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.95→42.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4506 0 15 556 5077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224719
X-RAY DIFFRACTIONr_bond_other_d0.0010.023188
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.9316416
X-RAY DIFFRACTIONr_angle_other_deg2.21737777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8545570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28324.958240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6315789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3271519
X-RAY DIFFRACTIONr_chiral_restr0.1070.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215313
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02952
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8991.52816
X-RAY DIFFRACTIONr_mcbond_other0.151.51136
X-RAY DIFFRACTIONr_mcangle_it1.46624572
X-RAY DIFFRACTIONr_scbond_it2.7731903
X-RAY DIFFRACTIONr_scangle_it3.9784.51844
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 158 -
Rwork0.169 3024 -
obs--99.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4354-0.883-0.72923.22520.58022.0665-0.03070.15810.4769-0.07960.0044-0.3712-0.30240.23050.02630.1692-0.0603-0.05550.20370.08580.206916.79136.102-9.502
21.03940.068-0.18290.5918-0.05231.5021-0.11030.07260.27650.09930.0365-0.0838-0.4131-0.06430.07380.262-0.0004-0.0980.11670.02030.1413.67442.3290.765
39.1127-8.9942.61921.9846-4.84651.1435-0.16840.17960.6717-0.4611-0.129-1.29040.04820.05270.29750.49780.0263-0.06110.41160.00210.476320.71731.417.546
40.4585-0.1126-0.00970.3955-0.1180.7207-0.0780.00280.06130.076-0.01040.0163-0.1119-0.07860.08850.1310.0018-0.03790.088-0.01950.031.23126.62910.427
50.619-0.2305-0.16981.09310.22621.059-0.1618-0.1281-0.07540.30990.03580.08630.1266-0.05490.12610.24110.02050.03110.11770.00880.04382.9616.59530.204
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 37
2X-RAY DIFFRACTION2A38 - 78
3X-RAY DIFFRACTION3A79 - 87
4X-RAY DIFFRACTION4A88 - 355
5X-RAY DIFFRACTION5A356 - 560

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