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- PDB-3mqz: Crystal Structure of Conserved Protein DUF1054 from Pink Subaeria... -

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Basic information

Entry
Database: PDB / ID: 3mqz
TitleCrystal Structure of Conserved Protein DUF1054 from Pink Subaerial Biofilm Microbial Leptospirillum sp. Group II UBA.
Componentsuncharacterized Conserved Protein DUF1054
Keywordsstructural genomics / unknown function / alpha-beta fold / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyProtein of unknown function DUF1054 / BirA Bifunctional Protein; domain 2 / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesLeptospirillum rubarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsKim, Y. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Conserved Protein DUF1054 from Pink Subaerial Biofilm Microbial Leptospirillum sp. Group II UBA.
Authors: Kim, Y. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionApr 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 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_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_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 Conserved Protein DUF1054
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8254
Polymers24,6621
Non-polymers1633
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.967, 62.862, 81.839
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein uncharacterized Conserved Protein DUF1054


Mass: 24662.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospirillum rubarum (bacteria) / Gene: UBAL2_82410687 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: A3ER16
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 1.88 Å3/Da / Density % sol: 34.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2M Sodium Formate, 20%PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 4, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 44135 / Num. obs: 44135 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rsym value: 0.056 / Net I/σ(I): 17.1
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.287 / % possible all: 59.2

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→27.015 Å / SU ML: 0.16 / Isotropic thermal model: anisotropic / σ(F): 1.35 / Phase error: 14.72 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1739 2207 5.01 %
Rwork0.1483 --
obs0.1496 44069 94.53 %
all-44070 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.3→27.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1657 0 8 309 1974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081972
X-RAY DIFFRACTIONf_angle_d1.2442700
X-RAY DIFFRACTIONf_dihedral_angle_d14.604777
X-RAY DIFFRACTIONf_chiral_restr0.079269
X-RAY DIFFRACTIONf_plane_restr0.007369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2985-1.3450.2021600.13952773X-RAY DIFFRACTION64
1.345-1.39880.20682130.13193645X-RAY DIFFRACTION84
1.3988-1.46250.17892270.12244228X-RAY DIFFRACTION97
1.4625-1.53960.15372300.11354421X-RAY DIFFRACTION100
1.5396-1.6360.1642420.11174360X-RAY DIFFRACTION100
1.636-1.76230.17632530.12384347X-RAY DIFFRACTION100
1.7623-1.93960.15532040.12894455X-RAY DIFFRACTION100
1.9396-2.22020.15662220.12724451X-RAY DIFFRACTION100
2.2202-2.79670.17932240.15444524X-RAY DIFFRACTION100
2.7967-27.02050.16062320.15574658X-RAY DIFFRACTION100

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