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- PDB-4lqb: Crystal structure of uncharacterized protein Kfla3161 -

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Basic information

Entry
Database: PDB / ID: 4lqb
TitleCrystal structure of uncharacterized protein Kfla3161
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / MCSG / STRUCTURAL GENOMICS / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / UNKOWN FUNCTION
Function / homologyGlyoxalase-like domain, group 6 / Glyoxalase-like domain / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta / CITRIC ACID / Glyoxalase_6 domain-containing protein
Function and homology information
Biological speciesKribbella flavida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.72 Å
AuthorsChang, C. / Chhor, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized protein Kfla3161
Authors: Chang, C. / Chhor, G. / Endres, M. / Joachimiak, A.
History
DepositionJul 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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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)28,5896
Polymers28,1212
Non-polymers4684
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-30 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.610, 56.053, 80.436
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 14060.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kribbella flavida (bacteria) / Strain: DSM 17836 / Gene: Kfla_3161 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D2Q399
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


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


Mass: 18.015 Da / Num. of mol.: 232 / 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: 38.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M di-Ammonium hydrogen citrate, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935, 0.97948
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2012
RadiationMonochromator: SI(111) double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979351
20.979481
ReflectionResolution: 1.72→50 Å / Num. all: 24505 / Num. obs: 24257 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 17.8
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2.15 / Num. unique all: 1200 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SBC-CollectCOLLECTdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
ARP/wARPmodel building
RESOLVEphasing
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.72→37.18 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.309 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.26 / ESU R Free: 0.104
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1834 1182 5.1 %RANDOM
Rwork0.1395 ---
all0.1416 23281 --
obs0.1416 23281 95.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.7 Å2 / Biso mean: 21.1146 Å2 / Biso min: 11.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å20 Å2
2--0.22 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.72→37.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 31 232 2219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192039
X-RAY DIFFRACTIONr_bond_other_d0.0010.021894
X-RAY DIFFRACTIONr_angle_refined_deg1.1451.9712783
X-RAY DIFFRACTIONr_angle_other_deg0.70834350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3685258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.28823.19194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.81115292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7221521
X-RAY DIFFRACTIONr_chiral_restr0.0620.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212343
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02454
X-RAY DIFFRACTIONr_rigid_bond_restr1.21733933
X-RAY DIFFRACTIONr_sphericity_free18.287556
X-RAY DIFFRACTIONr_sphericity_bonded4.52154068
LS refinement shellResolution: 1.721→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 60 -
Rwork0.19 1126 -
all-1186 -
obs-1186 67.12 %

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