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- PDB-3hp4: Crystal structure of psychrotrophic esterase EstA from Pseudoalte... -

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Basic information

Entry
Database: PDB / ID: 3hp4
TitleCrystal structure of psychrotrophic esterase EstA from Pseudoalteromonas sp. 643A inhibited by monoethylphosphonate
ComponentsGDSL-esterase
KeywordsHYDROLASE / esterase / psychrotrophic / monoethylphosphonate
Function / homology
Function and homology information


lysophospholipase activity
Similarity search - Function
: / SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudoalteromonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBrzuszkiewicz, A. / Nowak, E. / Dauter, Z. / Dauter, M. / Cieslinski, H. / Kur, J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of EstA esterase from psychrotrophic Pseudoalteromonas sp. 643A covalently inhibited by monoethylphosphonate.
Authors: Brzuszkiewicz, A. / Nowak, E. / Dauter, Z. / Dauter, M. / Cieslinski, H. / Dlugolecka, A. / Kur, J.
History
DepositionJun 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 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 / struct_conn / struct_ref_seq_dif
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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GDSL-esterase


Theoretical massNumber of molelcules
Total (without water)20,8041
Polymers20,8041
Non-polymers00
Water4,630257
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.820, 83.820, 130.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein GDSL-esterase


Mass: 20803.572 Da / Num. of mol.: 1 / Fragment: UNP residues 24-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas sp. (bacteria) / Strain: 643A / Gene: estA / Plasmid: pRCS69 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q1G1I7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 3.19 Å3/Da / Density % sol: 61.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 15 mg/ml Protein, 20 mM HEPES pH 7.5, 250 mM NaCl, 5 % Glycerol. Well solution: 1.6 M Na/K phosphate, 100 mM HEPES pH 7.5. Both solutions mixed 1:1 in drops, VAPOR ...Details: Protein solution: 15 mg/ml Protein, 20 mM HEPES pH 7.5, 250 mM NaCl, 5 % Glycerol. Well solution: 1.6 M Na/K phosphate, 100 mM HEPES pH 7.5. Both solutions mixed 1:1 in drops, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 2008 / Details: mirrors
RadiationMonochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 60202 / % possible obs: 100 % / Redundancy: 14 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 38.751
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.68 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
SERGUIdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IVN

1ivn


Resolution: 1.35→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.338 / SU ML: 0.025 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.18867 3052 5.1 %RANDOM
Rwork0.17228 ---
obs0.1731 60116 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.984 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.06 Å20 Å2
2---0.11 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1440 0 0 257 1697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221592
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.9782181
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8535218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55925.76978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51315300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.165157
X-RAY DIFFRACTIONr_chiral_restr0.1170.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211221
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0931.5970
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8721580
X-RAY DIFFRACTIONr_scbond_it3.0353622
X-RAY DIFFRACTIONr_scangle_it4.5514.5583
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 204 -
Rwork0.205 4141 -
obs--99.93 %
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)
12.60210.93780.23982.21050.74851.81120.03620.0195-0.0658-0.0558-0.1090.0311-0.0938-0.06440.07280.05510.0149-0.04910.0660.02060.062344.292840.279-1.9292
22.45581.9087-0.01786.88631.04921.1931-0.12650.440.1138-0.51490.0908-0.016-0.13950.01410.03570.11780.0064-0.03790.16860.01420.040747.703838.4898-12.4977
31.0749-0.05880.47840.4590.35541.4553-0.0342-0.07750.1178-0.0616-0.04530.05-0.1947-0.14070.07940.05670.0017-0.0330.0781-0.0020.086944.720644.06666.7039
42.49731.46030.14462.3350.2880.9477-0.0959-0.0639-0.00060.04410.132-0.0996-0.06420.0481-0.03620.0489-0.0133-0.01690.0724-0.00470.048957.729440.575514.561
51.22910.08420.20470.8959-0.71011.74560.03920.209-0.0215-0.1156-0.0971-0.1179-0.05630.21610.05790.073-0.00040.00660.12530.00770.072956.789936.3115-4.6665
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 12
2X-RAY DIFFRACTION2A13 - 38
3X-RAY DIFFRACTION3A39 - 114
4X-RAY DIFFRACTION4A115 - 137
5X-RAY DIFFRACTION5A138 - 185

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