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- PDB-4x00: X-ray crystal structure of a putative aryl esterase from Burkhold... -

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Basic information

Entry
Database: PDB / ID: 4x00
TitleX-ray crystal structure of a putative aryl esterase from Burkholderia cenocepacia
ComponentsPutative hydrolase
KeywordsHYDROLASE / aryl esterase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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
FLUORIDE ION / Putative hydrolase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.38 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: to be published
Title: X-ray crystal structure of a putative aryl esterase from Burkholderia cenocepacia
Authors: Fairman, J.W. / Edwards, T.E. / Lorimer, D.
History
DepositionNov 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative hydrolase
B: Putative hydrolase
C: Putative hydrolase
D: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,83624
Polymers124,6344
Non-polymers1,20220
Water23,2211289
1
A: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6859
Polymers31,1581
Non-polymers5278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3645
Polymers31,1581
Non-polymers2054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3945
Polymers31,1581
Non-polymers2354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3945
Polymers31,1581
Non-polymers2354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.720, 80.370, 99.400
Angle α, β, γ (deg.)90.000, 93.070, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is a monomer

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Components

#1: Protein
Putative hydrolase /


Mass: 31158.381 Da / Num. of mol.: 4 / Fragment: UNP residues 28-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: BCAL2527 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4E794
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-F / FLUORIDE ION / Fluoride


Mass: 18.998 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: F
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1289 / 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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MCSG1 H1: 0.2 M potassium fluoride, 20% PEG3350, BuceA.00095.a.B1.PW37307 at 26.4 mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9774 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 13, 2013
RadiationMonochromator: DIAMOND[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionNumber: 959091 / Rmerge(I) obs: 0.11 / Χ2: 1.07 / D res high: 2 Å / Num. obs: 138657 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
22.05974810.309
2.052.11991010.274
2.112.17973710.266
2.172.24948510.392
2.242.31913510.368
2.312.39886010.214
2.392.48864710.167
2.482.58831010.149
2.582.7789310.139
2.72.83758710.119
2.832.98724910.102
2.983.16683810.087
3.163.38639410.073
3.383.65598810.078
3.654548410.086
44.47494910.058
4.475.16438610.054
5.166.32365710.058
6.328.94286310.052
ReflectionResolution: 1.38→50 Å / Num. all: 211621 / Num. obs: 211257 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.76 % / Biso Wilson estimate: 11.06 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.065 / Χ2: 0.974 / Net I/σ(I): 14.95 / Num. measured all: 795627
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.38-1.420.7930.5762.275743215566155350.67599.8
1.42-1.450.8470.4662.815643415255152300.54699.8
1.45-1.50.8980.3743.55495014787147600.43899.8
1.5-1.540.930.2994.335342414329143110.3599.9
1.54-1.590.9510.245.335197413911138910.28199.9
1.59-1.650.9640.2036.345068213510134910.23799.9
1.65-1.710.9750.1667.694892613017129920.19399.8
1.71-1.780.9820.1359.34725112527125090.15899.9
1.78-1.860.9880.10911.424535411996119730.12799.8
1.86-1.950.9920.08414.374363111510114990.09899.9
1.95-2.060.9950.06517.994156310946109360.07699.9
2.06-2.180.9970.05421.593926910321103150.06399.9
2.18-2.330.9970.04624.8737108974297350.05499.9
2.33-2.520.9980.0428.5934579907790680.04799.9
2.52-2.760.9980.03731.3831850835383400.04399.8
2.76-3.090.9980.03335.4728697753275230.03899.9
3.09-3.560.9990.02740.7125476669366810.03299.8
3.56-4.360.9990.02444.821587567156550.02899.7
4.36-6.170.9990.02445.9516715441344050.02899.8
6.170.9990.02346.018725246524080.02797.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementResolution: 1.38→46.025 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1662 10430 4.94 %RANDOM
Rwork0.1367 200809 --
obs0.1381 211239 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.26 Å2 / Biso mean: 16.6079 Å2 / Biso min: 6.41 Å2
Refinement stepCycle: final / Resolution: 1.38→46.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8278 0 77 1289 9644
Biso mean--25.77 28.07 -
Num. residues----1090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018774
X-RAY DIFFRACTIONf_angle_d1.29111980
X-RAY DIFFRACTIONf_chiral_restr0.0571345
X-RAY DIFFRACTIONf_plane_restr0.0081569
X-RAY DIFFRACTIONf_dihedral_angle_d12.6343235
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.38-1.39560.24283550.195666176972100
1.3956-1.4120.25643290.202466947023100
1.412-1.42930.23243560.191766817037100
1.4293-1.44730.22723650.171366306995100
1.4473-1.46640.19943660.169166316997100
1.4664-1.48650.19523760.163167177093100
1.4865-1.50770.20123500.153266226972100
1.5077-1.53020.18193750.142966517026100
1.5302-1.55410.18173470.139166897036100
1.5541-1.57960.1723340.130866646998100
1.5796-1.60690.16953260.129867177043100
1.6069-1.63610.18483660.130566577023100
1.6361-1.66750.17983520.124266236975100
1.6675-1.70160.18353450.122767277072100
1.7016-1.73860.17043240.121866656989100
1.7386-1.7790.15433410.122167037044100
1.779-1.82350.16822960.12267597055100
1.8235-1.87280.1713410.126366867027100
1.8728-1.92790.17723300.126367037033100
1.9279-1.99020.1583340.125567307064100
1.9902-2.06130.15583350.126467117046100
2.0613-2.14380.163720.126466647036100
2.1438-2.24140.15353560.122466747030100
2.2414-2.35960.16733300.132667727102100
2.3596-2.50740.15733350.13366837018100
2.5074-2.7010.17183690.13867127081100
2.701-2.97270.1673830.143567197102100
2.9727-3.40280.14773450.143467007045100
3.4028-4.28670.14963530.13467867139100
4.2867-46.05010.14443440.13866822716699

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