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- PDB-2qru: Crystal structure of an alpha/beta hydrolase superfamily protein ... -

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Basic information

Entry
Database: PDB / ID: 2qru
TitleCrystal structure of an alpha/beta hydrolase superfamily protein from Enterococcus faecalis
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Enterococcus faecalis / alpha/beta-hydrolase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


: / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Alpha/beta hydrolase fold-3 domain-containing protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsCuff, M.E. / Volkart, L. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Structure of an alpha/beta hydrolase superfamily protein from Enterococcus faecalis.
Authors: Cuff, M.E. / Volkart, L. / Moy, S. / Joachimiak, A.
History
DepositionJul 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
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 / _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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8448
Polymers31,3761
Non-polymers4677
Water6,467359
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.352, 50.413, 64.683
Angle α, β, γ (deg.)90.000, 110.270, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-412-

HOH

DetailsAuthors state that the biological unit assembly has not been determined experimentally and that the monomeric prediction is based on crystal packing.

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Components

#1: Protein Uncharacterized protein


Mass: 31376.150 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_0381 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q838Q5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.01M MgCl2, 10% PEG 6000, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97878, 0.97894
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 20, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978781
20.978941
ReflectionRedundancy: 6.8 % / Av σ(I) over netI: 9.1 / Number: 246257 / Rmerge(I) obs: 0.068 / Χ2: 1.38 / D res high: 1.65 Å / D res low: 50 Å / Num. obs: 36066 / % possible obs: 99
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.555097.110.052.9116.4
2.823.5599.510.0562.1196.7
2.462.8299.910.0711.7227
2.242.4699.910.0841.387.1
2.082.2499.910.0981.2367.1
1.962.0899.910.1371.0857.1
1.861.9610010.21.0067.1
1.781.8699.810.2790.7967
1.711.7899.110.3930.7986.6
1.651.7194.510.4910.8066
ReflectionResolution: 1.65→50 Å / Num. all: 36066 / Num. obs: 36066 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.068 / Χ2: 1.384 / Net I/σ(I): 9.1
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 6 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 1.92 / Num. unique all: 3433 / Χ2: 0.806 / % possible all: 94.5

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 1.65 Å / D res low: 50 Å / FOM : 0.318 / FOM acentric: 0.325 / FOM centric: 0.172 / Reflection: 35870 / Reflection acentric: 34208 / Reflection centric: 1662
Phasing MAD set

Highest resolution: 1.65 Å / Lowest resolution: 50 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
11.7710000342081662
20.970.933.75.10.40.36338441578
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
110.72-501.110.10.1007516
16.01-10.721.5710.10.10054381
14.17-6.011.1410.10.1001389135
13.19-4.171.1710.10.1002591183
12.59-3.191.7210.10004142237
12.18-2.592.09100006111290
11.88-2.182.19100008401348
11.65-1.884.051000010956372
210.72-500.870.976.15.61.011.057015
26.01-10.720.820.644.34.91.241.0154181
24.17-6.010.880.784.55.30.970.841387134
23.19-4.170.950.9655.70.650.542569166
22.59-3.190.950.923.95.20.590.394113226
22.18-2.590.980.993.54.70.430.296079277
21.88-2.180.990.993.75.50.260.158359335
21.65-1.88113.44.40.170.110726344
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se34.556740.1830.5550.3080
2Se30.721880.2270.3930.1870
3Se34.142050.1830.5550.308-0.071
4Se31.823810.2270.3940.187-0.025
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
10.72-500.5720.610.392917516
6.01-10.720.6710.6930.52362454381
4.17-6.010.6280.6450.45815241389135
3.19-4.170.5090.5280.23227742591183
2.59-3.190.5270.5430.23843794142237
2.18-2.590.4150.4280.13764016111290
1.88-2.180.2560.2630.07587498401348
1.65-1.880.1210.1240.0271132810956372
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 35870
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.68-10054.20.859508
5.35-6.6845.20.906532
4.59-5.3542.60.923618
4.08-4.5948.60.92719
3.72-4.0851.40.891789
3.43-3.7253.70.884872
3.2-3.4351.10.889936
3.02-3.250.80.885973
2.86-3.0247.60.8941036
2.72-2.8649.90.8891096
2.6-2.7251.30.8821145
2.5-2.653.40.8751191
2.41-2.554.40.871236
2.33-2.41530.8561287
2.25-2.3355.70.8541341
2.18-2.2556.70.8731384
2.12-2.1860.50.8691400
2.06-2.12640.8721446
2.01-2.0663.80.8611491
1.96-2.0164.50.8461540
1.92-1.9667.40.8371553
1.87-1.9266.30.8231589
1.83-1.8769.40.8131662
1.8-1.8372.40.8131637
1.76-1.874.80.8221740
1.73-1.7674.50.8011707
1.7-1.7377.50.7971717
1.65-1.7800.7492725

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT3data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.65→33.3 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.285 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.094
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1804 5 %RANDOM
Rwork0.167 ---
all0.168 35870 --
obs0.168 35870 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.619 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å21.46 Å2
2---0.88 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.65→33.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 29 359 2586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222376
X-RAY DIFFRACTIONr_angle_refined_deg1.351.9813238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8945292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.40725108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66415402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.474157
X-RAY DIFFRACTIONr_chiral_restr0.0940.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021815
X-RAY DIFFRACTIONr_nbd_refined0.2150.21243
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21657
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2301
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.221
X-RAY DIFFRACTIONr_mcbond_it0.8151.51462
X-RAY DIFFRACTIONr_mcangle_it1.26322332
X-RAY DIFFRACTIONr_scbond_it2.04431037
X-RAY DIFFRACTIONr_scangle_it3.084.5906
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 131 -
Rwork0.283 2372 -
all-2503 -
obs--93.85 %
Refinement TLS params.Method: refined / Origin x: 12.2237 Å / Origin y: 22.0434 Å / Origin z: 12.9173 Å
111213212223313233
T-0.1228 Å2-0.0512 Å20.0041 Å2--0.0675 Å2-0.0596 Å2---0.0826 Å2
L1.0796 °20.1059 °2-0.6147 °2-2.9093 °20.7106 °2--1.9677 °2
S0.1166 Å °0.0254 Å °-0.0112 Å °0.3019 Å °-0.3421 Å °0.363 Å °0.017 Å °-0.1425 Å °0.2255 Å °

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