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- PDB-1j2r: Crystal structure of Escherichia coli gene product Yecd at 1.3 A ... -

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Basic information

Entry
Database: PDB / ID: 1j2r
TitleCrystal structure of Escherichia coli gene product Yecd at 1.3 A resolution
ComponentsHypothetical isochorismatase family protein yecD
KeywordsStructural genomics / unknown function / parallel beta-sheet 3-2-1-4-5-6 / alpha-beta-alpha motif / tetramere / Bacterial targets at IGS-CNRS / France / BIGS
Function / homology
Function and homology information


Hydrolases / hydrolase activity / cytosol
Similarity search - Function
: / Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Isochorismatase family protein YecD / Uncharacterized isochorismatase family protein YecD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSuhre, K. / Claverie, J.-M. / Abergel, C. / Bacterial targets at IGS-CNRS, France (BIGS)
CitationJournal: To be published
Title: Crystal structure of escherichia coli gene product Yecd at 1.3 A resolution
Authors: Suhre, K. / Claverie, J.-M. / Abergel, C.
History
DepositionJan 9, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical isochorismatase family protein yecD
B: Hypothetical isochorismatase family protein yecD
C: Hypothetical isochorismatase family protein yecD
D: Hypothetical isochorismatase family protein yecD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,59716
Polymers87,1794
Non-polymers1,41812
Water16,646924
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Hypothetical isochorismatase family protein yecD
B: Hypothetical isochorismatase family protein yecD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2988
Polymers43,5892
Non-polymers7096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-84 kcal/mol
Surface area14510 Å2
MethodPISA
3
C: Hypothetical isochorismatase family protein yecD
D: Hypothetical isochorismatase family protein yecD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2988
Polymers43,5892
Non-polymers7096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-81 kcal/mol
Surface area14620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.502, 108.886, 50.419
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Hypothetical isochorismatase family protein yecD / Yecd gene product


Mass: 21794.713 Da / Num. of mol.: 4 / Mutation: A103T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yecD / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: P37347, UniProt: P0ADI7*PLUS
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 924 / 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: 2.03 Å3/Da / Density % sol: 39.06 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.5
Details: MPD, TRIS, acetate, NaCl, Lysine, pH 5.5, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.3→50.77 Å / Num. all: 190258 / Num. obs: 163406 / % possible obs: 85.9 % / Observed criterion σ(I): 3 / Redundancy: 5.5 % / Biso Wilson estimate: 18.62 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 6.4
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.064 / Num. unique all: 13256 / % possible all: 72.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALAdata scaling
TRUNCATEdata scaling
T-COFFEEphasing
MODELLERphasing
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1NBA and 1IM5

1nba

1im5


Resolution: 1.3→50.77 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.686 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Hydrogens have been added in the riding positions. The structure was refined also with BUSTER, CNS and ARPWARP.
RfactorNum. reflection% reflectionSelection details
Rfree0.16494 8200 5 %RANDOM
Rwork0.14499 ---
obs0.14596 155206 85.89 %-
all-162173 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.354 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.3→50.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5751 0 96 924 6771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215955
X-RAY DIFFRACTIONr_bond_other_d0.0020.025537
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9538125
X-RAY DIFFRACTIONr_angle_other_deg0.83312794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6115744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2927
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026632
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021164
X-RAY DIFFRACTIONr_nbd_refined0.2240.21162
X-RAY DIFFRACTIONr_nbd_other0.2530.26697
X-RAY DIFFRACTIONr_nbtor_other0.0830.23533
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2676
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2710.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.249
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6911.53724
X-RAY DIFFRACTIONr_mcangle_it1.26325976
X-RAY DIFFRACTIONr_scbond_it1.92632231
X-RAY DIFFRACTIONr_scangle_it3.0924.52149
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.228 532
Rwork0.216 9366

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