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- PDB-1z6m: Structure of Conserved Protein of Unknown Function from Enterococ... -

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Basic information

Entry
Database: PDB / ID: 1z6m
TitleStructure of Conserved Protein of Unknown Function from Enterococcus faecalis V583
Componentsconserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / conserved hypothetical protein / MCSG / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


DsbA-like domain / Thioredoxin / Thioredoxin-like fold / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Thioredoxin-like_fold domain-containing protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsNocek, B.P. / Li, H. / Collart, F. / Joachimiak, A. / MCSG / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of a conserved hypothetical protein from Enterococcus faecalis V583
Authors: Nocek, B.P. / Li, H. / Collart, F. / Joachimiak, A. / MCSG
History
DepositionMar 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jan 24, 2018Group: Advisory / Structure summary / Category: audit_author / pdbx_unobs_or_zero_occ_atoms / Item: _audit_author.name
Remark 300Biomolecule Author states that biological molecule for the protein is not yet known

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0872
Polymers19,9921
Non-polymers951
Water4,774265
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.797, 69.236, 82.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-345-

HOH

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Components

#1: Protein conserved hypothetical protein


Mass: 19991.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q837R1
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 1.99 Å3/Da / Density % sol: 38.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 2.0 ammonium sulfate, phosphate-citrate buffer, pH 4.2, 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: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 8, 2005 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.297→43 Å / Num. all: 39917 / Num. obs: 38760 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 25.27

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
Omodel building
Cootmodel building
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→43.44 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18688 1951 5 %RANDOM
Rwork0.15537 ---
all0.15695 38855 --
obs0.15695 36904 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.434 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2--0.67 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.3→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 5 265 1660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221528
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.251.9572089
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3375208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.46125.54174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01815295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.452157
X-RAY DIFFRACTIONr_chiral_restr0.0980.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021159
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.2757
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21067
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2212
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.282
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.255
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9431.5958
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.43321527
X-RAY DIFFRACTIONr_scbond_it2.3183636
X-RAY DIFFRACTIONr_scangle_it3.1434.5547
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.297→1.331 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 137 -
Rwork0.227 2626 -
obs--94.3 %
Refinement TLS params.Method: refined / Origin x: 36.2408 Å / Origin y: 20.0441 Å / Origin z: 46.4461 Å
111213212223313233
T-0.002 Å20.0008 Å2-0.0007 Å2--0.0098 Å20.0023 Å2---0.0071 Å2
L0.2077 °20.0461 °2-0.0404 °2-0.0974 °20.0864 °2--0.2153 °2
S-0.0025 Å °-0.0038 Å °-0.017 Å °0.0036 Å °-0.0057 Å °-0.0019 Å °0.0019 Å °0.0043 Å °0.0082 Å °

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