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- PDB-4i3f: Crystal structure of serine hydrolase CCSP0084 from the polyaroma... -

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Basic information

Entry
Database: PDB / ID: 4i3f
TitleCrystal structure of serine hydrolase CCSP0084 from the polyaromatic hydrocarbon (PAH)-degrading bacterium Cycloclasticus zankles
Componentsserine hydrolase CCSP0084
KeywordsHYDROLASE / alpha and beta proteins / alpha/beta hydrolase fold / alpha/beta-hydrolases superfamily / carbon-carbon bond hydrolase family / serine hydrolase / esterase / meta-cleavage product (MCP) hydrolase
Function / homology
Function and homology information


Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Alpha/beta hydrolase fold-containing protein
Similarity search - Component
Biological speciesCycloclasticus sp. P1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsStogios, P.J. / Xu, X. / Dong, A. / Cui, H. / Alcaide, M. / Tornes, J. / Gertler, C. / Yakimov, M.M. / Golyshin, P.N. / Ferrer, M. / Savchenko, A.
CitationJournal: Biochem.J. / Year: 2013
Title: Single residues dictate the co-evolution of dual esterases: MCP hydrolases from the alpha / beta hydrolase family.
Authors: Alcaide, M. / Tornes, J. / Stogios, P.J. / Xu, X. / Gertler, C. / Di Leo, R. / Bargiela, R. / Lafraya, A. / Guazzaroni, M.E. / Lopez-Cortes, N. / Chernikova, T.N. / Golyshina, O.V. / ...Authors: Alcaide, M. / Tornes, J. / Stogios, P.J. / Xu, X. / Gertler, C. / Di Leo, R. / Bargiela, R. / Lafraya, A. / Guazzaroni, M.E. / Lopez-Cortes, N. / Chernikova, T.N. / Golyshina, O.V. / Nechitaylo, T.Y. / Plumeier, I. / Pieper, D.H. / Yakimov, M.M. / Savchenko, A. / Golyshin, P.N. / Ferrer, M.
History
DepositionNov 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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: serine hydrolase CCSP0084
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2125
Polymers34,0121
Non-polymers2004
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.543, 49.691, 67.995
Angle α, β, γ (deg.)90.00, 105.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein serine hydrolase CCSP0084


Mass: 34012.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cycloclasticus sp. P1 (bacteria) / Gene: Q91_2195 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: K0C6T6*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 1.95 Å3/Da / Density % sol: 36.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.2 M magnesium chloride, 25% PEG3350. , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 13, 2012
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.61→19.61 Å / Num. obs: 31991 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 13.4
Reflection shellResolution: 1.61→1.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3926 / % possible all: 79.1

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHENIX(phenix.phaser)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CR6

1cr6


Resolution: 1.69→19.606 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1866 1368 5.04 %random
Rwork0.1463 ---
obs0.1484 28176 94.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→19.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2231 0 10 413 2654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082345
X-RAY DIFFRACTIONf_angle_d1.0283189
X-RAY DIFFRACTIONf_dihedral_angle_d13.781854
X-RAY DIFFRACTIONf_chiral_restr0.074339
X-RAY DIFFRACTIONf_plane_restr0.005425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6901-1.71920.2885700.1972473X-RAY DIFFRACTION90
1.7192-1.75040.2253750.18982467X-RAY DIFFRACTION90
1.7504-1.78410.2657610.19742503X-RAY DIFFRACTION91
1.7841-1.82050.239620.18452466X-RAY DIFFRACTION91
1.8205-1.860.2554680.17822489X-RAY DIFFRACTION92
1.86-1.90330.2399510.16722593X-RAY DIFFRACTION92
1.9033-1.95080.2038630.17212513X-RAY DIFFRACTION93
1.9508-2.00350.1985660.15752557X-RAY DIFFRACTION93
2.0035-2.06240.1986610.1432555X-RAY DIFFRACTION93
2.0624-2.12890.185660.13872551X-RAY DIFFRACTION94
2.1289-2.20490.177610.14432583X-RAY DIFFRACTION94
2.2049-2.2930.161700.14832639X-RAY DIFFRACTION95
2.293-2.39720.1794650.14852573X-RAY DIFFRACTION95
2.3972-2.52340.1586700.1432623X-RAY DIFFRACTION96
2.5234-2.68110.1859890.1432579X-RAY DIFFRACTION96
2.6811-2.88750.169750.15212621X-RAY DIFFRACTION97
2.8875-3.1770.21356010.14922714X-RAY DIFFRACTION98
3.177-3.63420.1798840.1272645X-RAY DIFFRACTION98
3.6342-4.56910.1552780.11242670X-RAY DIFFRACTION99
4.5691-19.60770.1756800.14582708X-RAY DIFFRACTION99
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)
11.66220.35750.87121.48630.05572.3018-0.04020.08930.1286-0.1136-0.0640.08-0.161-0.07280.09280.08980.0254-0.01050.10.00410.0751-19.5875-2.693311.3796
23.89670.56760.60491.08950.66144.6012-0.01650.09640.4878-0.1035-0.04520.1875-0.3502-0.75790.05150.1628-0.0106-0.01320.22830.02870.2118-35.0298-12.774523.2488
31.6430.30770.42260.594-0.16451.66440.01860.0999-0.0412-0.065-0.0058-0.03380.12290.0046-0.00860.0720.00330.00090.0715-0.00160.0735-15.1985-11.093223.1885
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 0:131
2X-RAY DIFFRACTION2chain A and resi 132:189
3X-RAY DIFFRACTION3chain A and resi 190:282

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