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- PDB-4lmi: Crystal structure of putative ketosteroid isomerase from Kribbell... -

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Basic information

Entry
Database: PDB / ID: 4lmi
TitleCrystal structure of putative ketosteroid isomerase from Kribbella flavida DSM 17836
ComponentsUncharacterized protein
KeywordsStructural genomics / unknown function / PSI-BIOLOGY / MCSG / MIDWEST CENTER FOR STRUCTURAL GENOMICS
Function / homologySnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / SnoaL-like domain-containing protein
Function and homology information
Biological speciesKribbella flavida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsChang, C. / Chhor, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of putative ketosteroid isomerase from Kribbella flavida DSM 17836
Authors: Chang, C. / Chhor, G. / Endres, M. / Joachimiak, A.
History
DepositionJul 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references / Structure summary
Revision 1.2Oct 30, 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)32,0114
Polymers31,5352
Non-polymers4772
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-5 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.536, 69.873, 94.809
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: 15767.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kribbella flavida (bacteria) / Strain: DSM 17836 / JCM 10339 / NBRC 14399 / Gene: Kfla_6894 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D2Q2I7
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M di-Ammonium hydrogen Citrate, 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 30818 / Num. obs: 30387 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 35.7
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.98 / Num. unique all: 1453 / % possible all: 97.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
RESOLVEphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.168 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.114
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2098 1536 5.1 %RANDOM
Rwork0.1579 ---
all0.1606 30334 --
obs0.1606 30334 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.15 Å2 / Biso mean: 34.2618 Å2 / Biso min: 16.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.81 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2169 0 30 229 2428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192362
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.9753238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7385293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.64223.386127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87515363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3941527
X-RAY DIFFRACTIONr_chiral_restr0.0720.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211887
X-RAY DIFFRACTIONr_rigid_bond_restr1.94432362
X-RAY DIFFRACTIONr_sphericity_free28.917566
X-RAY DIFFRACTIONr_sphericity_bonded16.49452463
LS refinement shellResolution: 1.795→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 89 -
Rwork0.249 1860 -
all-1949 -
obs-1949 94.11 %

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