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- PDB-3nat: Crystal Structure of Conserved Protein of Unknown Function EF_197... -

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Basic information

Entry
Database: PDB / ID: 3nat
TitleCrystal Structure of Conserved Protein of Unknown Function EF_1977 from Enterococcus faecalis
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / alpha-beta half sandwich / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyProtein of unknown function DUF3013 / Protein of unknown function DUF3013 / Protein of unknown function (DUF3013) / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / CITRIC ACID / DUF3013 family protein
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.925 Å
AuthorsKim, Y. / Mulligan, R. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Conserved Protein of Unknown Function EF_1977 from Enterococcus faecalis
Authors: Kim, Y. / Mulligan, R. / Moy, S. / Joachimiak, A.
History
DepositionJun 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 27, 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

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7314
Polymers38,4742
Non-polymers2582
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-39 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.381, 81.381, 164.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Uncharacterized protein


Mass: 19236.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_1977 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q833H6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.53 Å3/Da / Density % sol: 65.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.0 M Sodium Citrate, 0.1 M Imidazole pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2007 / Details: mirrors
RadiationMonochromator: single crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.93→50 Å / Num. all: 12505 / Num. obs: 12505 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 16.3 % / Biso Wilson estimate: 92.3 Å2 / Rsym value: 0.105 / Net I/σ(I): 8.5
Reflection shellResolution: 2.93→3.03 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 1180 / Rsym value: 0.676 / % possible all: 95.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
PHENIXmodel building
PHENIX(phenix.refine: 1.6_289)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.925→40.691 Å / SU ML: 0.41 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.88 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.253 623 5.01 %random
Rwork0.203 ---
all0.206 12442 --
obs0.206 12442 99.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 124.405 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso mean: 129.7 Å2
Baniso -1Baniso -2Baniso -3
1-8.3981 Å20 Å2-0 Å2
2--8.3981 Å20 Å2
3----16.7961 Å2
Refinement stepCycle: LAST / Resolution: 2.925→40.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2443 0 14 53 2510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062518
X-RAY DIFFRACTIONf_angle_d0.9133408
X-RAY DIFFRACTIONf_dihedral_angle_d18.202915
X-RAY DIFFRACTIONf_chiral_restr0.057367
X-RAY DIFFRACTIONf_plane_restr0.003439
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.9248-3.2190.35191480.26482818296697
3.219-3.68450.25011540.201729143068100
3.6845-4.64110.23311550.158629573112100
4.6411-40.69440.24221660.206231303296100
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)
13.52990.1283-0.08714.4540.81882.14170.16640.30180.049-0.02880.00760.27550.137-0.3599-0.10170.51520.0484-0.03030.66780.01880.376253.800977.021581.6416
22.29571.61662.53313.75610.83452.96990.12890.05270.95330.3720.1057-0.5397-0.58960.8415-0.30710.5734-0.2210.20960.8207-0.58041.202568.9624101.991895.4583
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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