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- PDB-2gmq: Crystal structure of protein EF0006 from Enterococcus faecalis -

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Basic information

Entry
Database: PDB / ID: 2gmq
TitleCrystal structure of protein EF0006 from Enterococcus faecalis
ComponentsHypothetical protein EF0006
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Enterococcus faecalis / Hypothetical protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


PUA domain-like fold / PUA domain-like domain / Pheromone response, PrgU-like domain / PrgU-like superfamily / PrgU-like protein / PUA-like superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Pheromone response PrgU-like domain-containing protein / EF0006
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.76 Å
AuthorsChang, C. / Volkart, L. / Moy, S.F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of protein EF0006 from Enterococcus faecalis
Authors: Chang, C. / Volkart, L. / Moy, S. / Joachimiak, A.
History
DepositionApr 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein EF0006
B: Hypothetical protein EF0006


Theoretical massNumber of molelcules
Total (without water)27,6612
Polymers27,6612
Non-polymers00
Water3,189177
1
A: Hypothetical protein EF0006
B: Hypothetical protein EF0006

A: Hypothetical protein EF0006
B: Hypothetical protein EF0006


Theoretical massNumber of molelcules
Total (without water)55,3224
Polymers55,3224
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y+1/2,z1
Unit cell
Length a, b, c (Å)83.122, 83.400, 83.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-119-

HOH

21B-119-

HOH

DetailsEach of molecule A and B makes dimer with symmetry pair using operator (1-x, 1/2-y, z)

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Components

#1: Protein Hypothetical protein EF0006


Mass: 13830.537 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Plasmid: pMCSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q82YS4, UniProt: Q8KUD5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 20% PEG 3350, 0.2 M CaCl2, 0.1 M Tris, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929, 0.97940
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2005
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979291
20.97941
ReflectionResolution: 1.75→50 Å / Num. all: 29350 / Num. obs: 28088 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 32.09
Reflection shellResolution: 1.75→1.76 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 1.82 / % possible all: 90.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.76→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.876 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21663 1401 5.1 %RANDOM
Rwork0.1906 ---
obs0.19194 26281 93.75 %-
all-26281 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.802 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å20 Å20 Å2
2--1.03 Å20 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1611 0 0 177 1788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221846
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0251.9742532
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3885251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72725.34986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65915392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.31510
X-RAY DIFFRACTIONr_chiral_restr0.1490.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021366
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.240.2894
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21259
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2165
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3330.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2790.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6441.51124
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.06421786
X-RAY DIFFRACTIONr_scbond_it3.4193854
X-RAY DIFFRACTIONr_scangle_it4.7594.5716
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.801 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 98 -
Rwork0.295 1713 -
obs--83.8 %
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)
14.72182.9608-0.32517.4823-2.48942.5781-0.13970.0901-0.2199-0.41780.0151-0.06730.194-0.03530.12460.0442-0.02850.0005-0.2025-0.0086-0.130935.23410.33413.571
23.40252.07-1.64184.921-2.18063.45860.13750.01750.89310.04260.13751.0326-0.2339-0.1695-0.2750.02360.01530.0047-0.1818-0.00240.135426.11917.19217.985
32.96993.0668-0.74274.7068-0.96131.1694-0.18220.23510.5903-0.28130.27650.6297-0.0624-0.1102-0.09430.0765-0.0109-0.0424-0.14990.00050.02133.4416.96514.619
46.88443.91030.72255.2111-0.02862.4737-0.0782-0.19940.05910.041-0.06410.144-0.0215-0.14860.1423-0.0676-0.02820.0018-0.1350.003-0.147731.23214.70448.604
55.34422.49181.40753.21130.90583.08840.12980.0808-0.8507-0.00330.0925-0.69950.10670.1799-0.2223-0.06390.01050.0253-0.1855-0.02180.033535.6326.27743.683
66.22634.7241.84173.66721.01692.28870.5453-0.542-1.01770.4277-0.4168-0.90220.19580.0218-0.12840.0332-0.042-0.0791-0.04640.08820.086743.31914.09452.242
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 21
2X-RAY DIFFRACTION1A61 - 78
3X-RAY DIFFRACTION2A22 - 41
4X-RAY DIFFRACTION2A79 - 100
5X-RAY DIFFRACTION3A42 - 60
6X-RAY DIFFRACTION3A101 - 113
7X-RAY DIFFRACTION4B14 - 21
8X-RAY DIFFRACTION4B61 - 78
9X-RAY DIFFRACTION5B22 - 41
10X-RAY DIFFRACTION5B79 - 110
11X-RAY DIFFRACTION6B42 - 60
12X-RAY DIFFRACTION6B111 - 113

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