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- PDB-4i4c: Crystal structure of the protein frsA complexed with unknown ligand -

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Basic information

Entry
Database: PDB / ID: 4i4c
TitleCrystal structure of the protein frsA complexed with unknown ligand
ComponentsUPF0255 protein frsA
KeywordsUNKNOWN FUNCTION / two-domain protein frsA / unknown ligand
Function / homology
Function and homology information


methyl indole-3-acetate esterase activity / carboxylesterase
Similarity search - Function
Esterase FrsA / Esterase FrsA-like / Esterase FrsA-like / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1PG / HEXANOIC ACID / Esterase FrsA
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Desai, B. / Gerlt, J.A. / Richards, N. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2013
Title: Computational, structural, and kinetic evidence that Vibrio vulnificus FrsA is not a cofactor-independent pyruvate decarboxylase.
Authors: Kellett, W.F. / Brunk, E. / Desai, B.J. / Fedorov, A.A. / Almo, S.C. / Gerlt, J.A. / Rothlisberger, U. / Richards, N.G.
History
DepositionNov 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: UPF0255 protein frsA
B: UPF0255 protein frsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9777
Polymers94,1482
Non-polymers8295
Water4,936274
1
A: UPF0255 protein frsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4423
Polymers47,0741
Non-polymers3682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UPF0255 protein frsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5344
Polymers47,0741
Non-polymers4613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.659, 104.542, 82.302
Angle α, β, γ (deg.)90.00, 91.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UPF0255 protein frsA


Mass: 47073.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: frsA / Production host: Escherichia coli (E. coli) / References: UniProt: D9IR22
#2: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24O6
#3: Chemical ChemComp-6NA / HEXANOIC ACID


Mass: 116.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 36.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG monomethyl ether 2000, 0.1M Tris, 0.2M Trimethylamine N-oxide, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.95→38.284 Å / Num. all: 51363 / Num. obs: 51363 / % possible obs: 97.79 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CBASSdata collection
BALBESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MVE

3mve


Resolution: 1.95→38.284 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 25.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2273 2608 5.08 %RANDOM
Rwork0.1794 ---
all0.1819 51363 --
obs0.1819 51363 97.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→38.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6385 0 56 274 6715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086609
X-RAY DIFFRACTIONf_angle_d1.0538925
X-RAY DIFFRACTIONf_dihedral_angle_d15.0812469
X-RAY DIFFRACTIONf_chiral_restr0.072972
X-RAY DIFFRACTIONf_plane_restr0.0041125
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.98550.28821240.24652540X-RAY DIFFRACTION98
1.9855-2.02360.30021310.23462571X-RAY DIFFRACTION98
2.0236-2.06490.30611300.2292567X-RAY DIFFRACTION98
2.0649-2.10980.31821530.21932567X-RAY DIFFRACTION98
2.1098-2.15890.27831290.21252553X-RAY DIFFRACTION98
2.1589-2.21290.28061520.20442550X-RAY DIFFRACTION98
2.2129-2.27270.26331150.2052567X-RAY DIFFRACTION98
2.2727-2.33960.28381390.20492556X-RAY DIFFRACTION97
2.3396-2.41510.30441350.20672550X-RAY DIFFRACTION98
2.4151-2.50140.23971430.2112574X-RAY DIFFRACTION98
2.5014-2.60150.30091400.2062511X-RAY DIFFRACTION97
2.6015-2.71990.26021300.19652549X-RAY DIFFRACTION97
2.7199-2.86330.22581580.20152529X-RAY DIFFRACTION96
2.8633-3.04260.24321280.1892526X-RAY DIFFRACTION96
3.0426-3.27740.22791460.19222522X-RAY DIFFRACTION96
3.2774-3.6070.24311170.17512606X-RAY DIFFRACTION98
3.607-4.12840.1791430.14872611X-RAY DIFFRACTION100
4.1284-5.19930.18271530.13422634X-RAY DIFFRACTION100
5.1993-38.29160.15861420.14652672X-RAY DIFFRACTION100
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)
10.9237-0.236-0.16981.49850.5781.20910.06160.0112-0.0899-0.23860.0031-0.03970.0035-0.0474-0.05440.1446-0.0025-0.02060.11830.01670.149710.310717.115681.7416
20.76790.08770.21431.6510.1930.64160.0387-0.07080.03290.2413-0.0406-0.02780.0369-0.06820.00430.1432-0.01590.01540.1457-0.0040.1266-9.506636.799441.7463
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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