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- PDB-3cex: Crystal structure of the conserved protein of locus EF_3021 from ... -

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Basic information

Entry
Database: PDB / ID: 3cex
TitleCrystal structure of the conserved protein of locus EF_3021 from Enterococcus faecalis
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Enterococcus faecalis / EF_3021 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyProtein of unknown function DUF664 / Protein of unknown function (DUF664) / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / ACETIC ACID / Uncharacterized protein
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2 Å
AuthorsCuff, M.E. / Wu, R. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Structure of the conserved protein of locus EF_3021 from Enterococcus faecalis.
Authors: Cuff, M.E. / Wu, R. / Moy, S. / Joachimiak, A.
History
DepositionFeb 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8816
Polymers39,5772
Non-polymers3044
Water3,387188
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8816
Polymers39,5772
Non-polymers3044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3350 Å2
ΔGint-17.1 kcal/mol
Surface area16110 Å2
MethodPISA
2
B: Uncharacterized protein
hetero molecules

B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8816
Polymers39,5772
Non-polymers3044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3370 Å2
ΔGint-18.3 kcal/mol
Surface area15260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.191, 55.137, 62.429
Angle α, β, γ (deg.)90.000, 108.200, 90.000
Int Tables number3
Space group name H-MP121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein Uncharacterized protein


Mass: 19788.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_3021 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q82ZN0
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1M Trisodium citrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→35.9 Å / Num. all: 23947 / Num. obs: 23947 / % possible obs: 98.91 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 6.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1506 / % possible all: 89.32

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.01 Å / D res low: 50 Å / FOM : 0.168 / FOM acentric: 0.177 / FOM centric: 0 / Reflection: 23729 / Reflection acentric: 22468 / Reflection centric: 1261
Phasing MAD setR cullis acentric: 1.62 / R cullis centric: 1 / Highest resolution: 2.01 Å / Lowest resolution: 50 Å / Loc acentric: 0.1 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 22468 / Reflection centric: 1261
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
12.55-501.740.30.17728
7.17-12.551.470.30.238258
5.02-7.172.190.30.1925102
3.86-5.021.180.20.11719142
3.14-3.861.20.10.12748177
2.64-3.141.73004003215
2.28-2.645.12005512254
2.01-2.282.06007102285
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se63.34233-0.11-0.804-0.0240
2Se59.75295-0.556-0.623-0.3240
3Se74.54069-0.612-0.279-0.5120
4Se85.73228-0.091-1.1530.1580
5Se74.23188-0.58-0.857-0.4730
6Se85.10638-0.089-1.3860.0150
7Se51.7496-0.356-0.828-0.2780
8Se47.3514-0.321-0.703-0.3240
9Se50.790560.107-1.3530.2310
10Se63.154790.149-1.2280.1910
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.55-500.3050.41601057728
7.17-12.550.3870.445044038258
5.02-7.170.4230.4701027925102
3.86-5.020.3150.341018611719142
3.14-3.860.2670.285029252748177
2.64-3.140.2170.228042184003215
2.28-2.640.1180.124057665512254
2.01-2.280.0510.053073877102285
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 23729
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.39-10070.60.599504
5.85-7.3965.20.81501
5.09-5.8566.80.833515
4.61-5.0962.50.861507
4.24-4.6159.90.836561
3.96-4.2464.50.84605
3.72-3.9663.80.831653
3.52-3.7263.50.812690
3.35-3.5263.30.802723
3.2-3.35660.794749
3.07-3.262.60.796775
2.96-3.0764.80.795813
2.85-2.9664.40.786846
2.76-2.8564.50.82852
2.68-2.7670.70.786921
2.6-2.6868.40.824911
2.53-2.671.10.81953
2.46-2.5369.20.7931006
2.4-2.4671.60.758988
2.34-2.4750.791055
2.29-2.34740.7991026
2.24-2.2974.70.7971084
2.2-2.2477.70.7641098
2.15-2.280.30.7431114
2.11-2.1581.50.771137
2.07-2.1183.70.7431152
2.01-2.07840.6871990

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Processing

Software
NameVersionClassificationNB
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
DENZOdata reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→35.9 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 7.472 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.151
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1222 5.1 %RANDOM
Rwork0.162 ---
all0.164 22725 --
obs0.164 22725 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.04 Å2
2--1.84 Å20 Å2
3----1.84 Å2
Refinement stepCycle: LAST / Resolution: 2→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 20 188 2930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222845
X-RAY DIFFRACTIONr_bond_other_d0.0010.021859
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.9463884
X-RAY DIFFRACTIONr_angle_other_deg0.95634570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8815348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65424.885131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58315496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4631515
X-RAY DIFFRACTIONr_chiral_restr0.0770.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023119
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02527
X-RAY DIFFRACTIONr_nbd_refined0.2070.2630
X-RAY DIFFRACTIONr_nbd_other0.1860.21871
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21405
X-RAY DIFFRACTIONr_nbtor_other0.0880.21313
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2144
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3410.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.221
X-RAY DIFFRACTIONr_mcbond_it1.2191.52162
X-RAY DIFFRACTIONr_mcbond_other0.2321.5674
X-RAY DIFFRACTIONr_mcangle_it1.43622819
X-RAY DIFFRACTIONr_scbond_it2.45731265
X-RAY DIFFRACTIONr_scangle_it3.6794.51061
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 89 -
Rwork0.184 1508 -
all-1597 -
obs--89.32 %
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)
12.21890.2150.36921.4310.63921.5569-0.0947-0.40120.02950.09680.01030.04930.0784-0.1140.0844-0.09880.03040.002-0.02460.0028-0.098323.34014.622711.288
21.6251-0.4161-0.23921.9756-1.09882.50830.07670.23740.22880.0207-0.1196-0.1028-0.29550.1490.0429-0.082-0.01140.0022-0.02120.0296-0.0963-3.810330.647919.1918
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1693 - 172
2X-RAY DIFFRACTION2BB0 - 1693 - 172

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