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- PDB-3l1w: The crystal structure of a functionally unknown conserved protein... -

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Basic information

Entry
Database: PDB / ID: 3l1w
TitleThe crystal structure of a functionally unknown conserved protein from Enterococcus faecalis V583
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / APC29019.2 / conserved protein / Enterococcus faecalis V583 / PSI-2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


3'-5'-RNA exonuclease activity
Similarity search - Function
: / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Endonuclease/exonuclease/phosphatase domain-containing protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsTan, K. / Rakowski, E. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a functionally unknown conserved protein from Enterococcus faecalis V583
Authors: Tan, K. / Rakowski, E. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionDec 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 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
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,68648
Polymers178,4566
Non-polymers3,23042
Water27,3291517
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,56216
Polymers59,4852
Non-polymers1,07714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-89 kcal/mol
Surface area20550 Å2
MethodPISA
2
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,56216
Polymers59,4852
Non-polymers1,07714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-88 kcal/mol
Surface area20520 Å2
MethodPISA
3
E: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,56216
Polymers59,4852
Non-polymers1,07714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-90 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.565, 68.558, 104.245
Angle α, β, γ (deg.)89.88, 89.79, 60.07
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Uncharacterized protein


Mass: 29742.707 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_1237 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q835Y1
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1517 / 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: 2.38 Å3/Da / Density % sol: 48.31 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.0M (NH4)2SO4, 0.1M Bis-Tris, 1%w/v PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2009 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.6→33 Å / Num. all: 210181 / Num. obs: 210181 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 21.6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 1.3 / Num. unique all: 10273 / % possible all: 94.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→32.61 Å / SU ML: 0.21 / σ(F): 1.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 20547 5.03 %random
Rwork0.1666 ---
obs0.1681 408196 94.04 %-
all-408196 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.044 Å2 / ksol: 0.359 e/Å3
Refinement stepCycle: LAST / Resolution: 1.6→32.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12474 0 180 1517 14171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612983
X-RAY DIFFRACTIONf_angle_d1.05217709
X-RAY DIFFRACTIONf_dihedral_angle_d16.8374659
X-RAY DIFFRACTIONf_chiral_restr0.081877
X-RAY DIFFRACTIONf_plane_restr0.0042304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.65720.321120320.29436742X-RAY DIFFRACTION90
1.6572-1.72360.287819940.262838222X-RAY DIFFRACTION93
1.7236-1.8020.249320760.218438440X-RAY DIFFRACTION93
1.802-1.8970.212120230.18538429X-RAY DIFFRACTION94
1.897-2.01580.196920170.159539156X-RAY DIFFRACTION94
2.0158-2.17150.188920590.151338758X-RAY DIFFRACTION95
2.1715-2.38990.190321300.150439339X-RAY DIFFRACTION95
2.3899-2.73560.201421680.161739476X-RAY DIFFRACTION96
2.7356-3.4460.194420470.16339625X-RAY DIFFRACTION96
3.446-32.61670.161720010.141439462X-RAY DIFFRACTION96
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.70830.00140.23811.17990.26790.9019-0.04460.01160.06670.0365-0.0030.0059-0.1230.02070.04570.1569-0.0115-0.01920.1108-0.00650.126721.764551.19161.8881
20.7213-0.0341-0.20741.23570.28890.8776-0.0322-0.0182-0.0517-0.052-0.00550.01420.11930.02450.03630.16150.01030.01610.1152-0.00750.1255
31.12570.2782-0.35540.76330.11230.8440.02190.0008-0.03320.0048-0.05780.04310.0309-0.10630.03510.1122-0.01710.01380.1509-0.01340.126
41.05260.2899-0.09670.7981-0.32350.8162-0.03610.04370.00170.0235-0.0042-0.0509-0.05160.07550.03990.125-0.026-0.00310.13590.01660.1281
51.1204-0.32360.04670.828-0.30790.8404-0.038-0.0495-0.0146-0.0051-0.0009-0.03690.07190.07960.03770.13740.0270.00230.14160.0170.1239
61.1169-0.22920.36670.8680.07010.86810.01290.01360.0243-0.0139-0.05220.0305-0.0295-0.11440.03780.09940.0169-0.01310.1424-0.01370.1031
Refinement TLS groupSelection details: chain F

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