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- PDB-4ik0: Crystal structure of diaminopimelate epimerase Y268A mutant from ... -

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Basic information

Entry
Database: PDB / ID: 4ik0
TitleCrystal structure of diaminopimelate epimerase Y268A mutant from Escherichia coli
ComponentsDiaminopimelate epimerase
KeywordsISOMERASE / DAP epimerase-like / Cytosol
Function / homology
Function and homology information


diaminopimelate epimerase / diaminopimelate epimerase activity / lysine biosynthetic process via diaminopimelate / enzyme activator activity / protein homodimerization activity / cytosol
Similarity search - Function
Diaminopimelate epimerase, active site / Diaminopimelate epimerase signature. / Diaminopimelate epimerase, DapF / Diaminopimelate epimerase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Diaminopimelate epimerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsHor, L. / Dobson, R.C.J. / Hutton, C.A. / Perugini, M.A.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Dimerization of bacterial diaminopimelate epimerase is essential for catalysis
Authors: Hor, L. / Dobson, R.C.J. / Downton, M.T. / Wagner, J. / Hutton, C.A. / Perugini, M.A.
History
DepositionDec 24, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Apr 17, 2013Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diaminopimelate epimerase
B: Diaminopimelate epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,61415
Polymers61,9652
Non-polymers1,65013
Water7,116395
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.180, 89.180, 179.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Diaminopimelate epimerase / DAP epimerase


Mass: 30982.326 Da / Num. of mol.: 2 / Mutation: Y268A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dapF / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6K1, diaminopimelate epimerase
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.88 Å3/Da / Density % sol: 57.28 % / Mosaicity: 0.19 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Sodium iodide, 18% PEG 3350, 0.1M Bis-Tris propane, 5mM diaminopimelic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→49.677 Å / Num. all: 46324 / Num. obs: 46324 / % possible obs: 100 % / Redundancy: 6.3 % / Rsym value: 0.126 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.05-2.166.40.6280.5771.34270066350.2460.6280.5773.2100
2.16-2.296.40.4590.4211.84044563080.180.4590.4214.4100
2.29-2.456.40.3260.2992.53775858970.1280.3260.2995.9100
2.45-2.656.40.2340.2153.53539055540.0920.2340.2158100
2.65-2.96.30.1690.1554.83247651200.0670.1690.15510.3100
2.9-3.246.30.1080.0997.22933946500.0430.1080.09913.9100
3.24-3.746.20.090.0827.52567941490.0360.090.08217.8100
3.74-4.586.10.0940.08672140335370.0380.0940.08620.3100
4.58-6.485.70.0730.0677.91609728000.030.0730.06719.799.8
6.48-49.6775.80.0590.0539963916740.0240.0590.05320.599.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→49.677 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2163 / WRfactor Rwork: 0.1773 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8854 / SU B: 5.494 / SU ML: 0.088 / SU R Cruickshank DPI: 0.1556 / SU Rfree: 0.1457 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 1863 4 %RANDOM
Rwork0.1764 ---
obs0.178 46242 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.81 Å2 / Biso mean: 26.1802 Å2 / Biso min: 8.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.05→49.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4224 0 13 395 4632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194329
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.955866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8345551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13123210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09415701
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5391544
X-RAY DIFFRACTIONr_chiral_restr0.1210.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213366
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 133 -
Rwork0.21 2942 -
all-3075 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9391-0.72790.64821.0443-0.63091.45060.07990.1165-0.0453-0.067-0.06530.0230.03680.0751-0.01470.06330.02470.00420.0315-0.0090.03019.2657-9.0428-9.8987
22.4351-1.7018-0.94262.90280.84831.2480.08610.0730.0341-0.2208-0.1504-0.03160.00540.02950.06430.08980.0281-0.0020.0160.00130.052115.0948-34.1222-16.1675
32.85321.40980.05111.23469.32989.53250.0846-0.20940.0141-0.5167-0.02060.0262-0.54440.0644-0.06390.12360.02670.00110.0680.01550.01285.7826-8.43051.2698
41.084-0.02310.38771.49920.03280.98360.0307-0.08840.00780.1058-0.0041-0.0731-0.0013-0.0487-0.02650.04670.0036-0.00220.05530.00730.03059.3088-7.675721.4741
52.939-1.36340.44161.7676-0.47771.62020.0590.0465-0.2376-0.0836-0.01250.0550.18630.146-0.04650.0512-0.0015-0.0360.030.01230.055934.395-13.969127.3996
63.885-0.14434.04460.2375-0.00785.18970.1017-0.18640.00290.0294-0.0238-0.00710.1117-0.2045-0.07790.079-0.01-0.01330.03920.0130.031116.7467-4.694222.5165
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 111
2X-RAY DIFFRACTION2A112 - 262
3X-RAY DIFFRACTION3A263 - 273
4X-RAY DIFFRACTION4B1 - 111
5X-RAY DIFFRACTION5B112 - 250
6X-RAY DIFFRACTION6B251 - 275

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