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- PDB-1k4n: Structural Genomics, Protein EC4020 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1k4n
TitleStructural Genomics, Protein EC4020
ComponentsProtein EC4020
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / A new fold of protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyProtein of unknown function DUF991, YecM-like / YecM protein / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / cytosol / Alpha Beta / Protein YecM
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsZhang, R.G. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Skarina, T. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2003
Title: Conserved protein YecM from Escherichia coli shows structural homology to metal-binding isomerases and oxygenases.
Authors: Zhang, R.G. / Duke, N. / Laskowski, R. / Evdokimova, E. / Skarina, T. / Edwards, A. / Joachimiak, A. / Savchenko, A.
History
DepositionOct 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / software / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein EC4020


Theoretical massNumber of molelcules
Total (without water)21,8111
Polymers21,8111
Non-polymers00
Water4,558253
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.661, 41.783, 105.748
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 Protein EC4020 / protein yecM


Mass: 21811.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P52007
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 1.96 Å3/Da / Density % sol: 37.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
22 %PEG4001reservoir
32.2 Mammonium sulfate1reservoir
40.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795, 0.9798, 0.94656
DetectorType: SBC-2 / Detector: CCD / Date: Aug 8, 2001 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97981
30.946561
ReflectionResolution: 1.6→50 Å / Num. all: 24450 / Num. obs: 24275 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 7.9 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 25.1
Reflection shellResolution: 1.58→1.66 Å / Redundancy: 5 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 5.3 / Num. unique all: 3402 / % possible all: 99.4
Reflection
*PLUS
Redundancy: 6.9 %

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Processing

Software
NameClassification
d*TREKdata scaling
HKL-2000data reduction
CNSrefinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementResolution: 1.6→38.86 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 405396.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1928 4.9 %RANDOM
Rwork0.199 ---
obs0.21 39219 89.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.6398 Å2 / ksol: 0.372806 e/Å3
Displacement parametersBiso mean: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---2.11 Å20 Å2
3---2.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.6→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1460 0 0 253 1713
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.195 280 5.2 %
Rwork0.186 5135 -
obs--74.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Lowest resolution: 50 Å / Num. reflection all: 24450 / Num. reflection obs: 23643
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87

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