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- PDB-4ijz: Crystal structure of diaminopimelate epimerase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 4ijz
TitleCrystal structure of diaminopimelate epimerase from Escherichia coli
ComponentsDiaminopimelate epimerase
KeywordsISOMERASE / DAP epimerase-like
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
NITRATE ION / Diaminopimelate epimerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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)62,3355
Polymers62,1492
Non-polymers1863
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-4 kcal/mol
Surface area24010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.380, 89.380, 179.618
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: 31074.420 Da / Num. of mol.: 2
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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.89 Å3/Da / Density % sol: 57.38 % / Mosaicity: 0.18 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Sodium nitrate, PEG 3350, Bis-Tris propane, pH 8.5, 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 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→179.618 Å / Num. all: 47663 / Num. obs: 47663 / % possible obs: 96.1 % / Redundancy: 4.5 % / Rsym value: 0.077 / Net I/σ(I): 13
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
2-2.114.30.3850.3392.22901266830.1780.3850.3394.293.7
2.11-2.244.60.2730.2423.13042766210.1230.2730.2425.997.6
2.24-2.394.60.1960.1744.32843261860.0880.1960.1747.897.1
2.39-2.584.60.1480.1315.62658857990.0660.1480.1319.997.4
2.58-2.834.60.1160.1037.12445853590.0520.1160.10312.397.6
2.83-3.164.50.0810.0729.72207848570.0360.0810.07216.597.4
3.16-3.654.50.0590.05211.91933042860.0260.0590.0522297
3.65-4.474.50.0540.04812.61623636050.0240.0540.04825.395.3
4.47-6.324.40.0490.04312.61196627260.0220.0490.04326.992.5
6.32-44.694.70.0460.04112.1723315410.020.0460.04128.789.9

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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→43.37 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.1989 / WRfactor Rwork: 0.1598 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8826 / SU B: 5.897 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1434 / SU Rfree: 0.1358 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2029 1949 4.1 %RANDOM
Rwork0.163 ---
obs0.1646 47638 95.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.29 Å2 / Biso mean: 25.5703 Å2 / Biso min: 10.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0 Å2-0 Å2
2---0.16 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2→43.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4244 0 12 516 4772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194394
X-RAY DIFFRACTIONr_angle_refined_deg1.641.955960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5185561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11823.196219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09615711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6011544
X-RAY DIFFRACTIONr_chiral_restr0.1240.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213446
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 145 -
Rwork0.215 2889 -
all-3034 -
obs--88.15 %
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)
10.6149-0.3876-0.22811.06570.71010.7388-0.0521-0.05820.02940.05090.0669-0.03950.08040.029-0.01480.050.0273-0.00480.05030.00020.05279.028-9.653310.153
21.8036-1.31820.61981.8121-0.79340.4084-0.0935-0.0968-0.074-0.04830.04840.0485-0.0023-0.0180.04510.02870.0184-0.01510.06310.00590.077634.1466-15.706316.2901
32.4766-1.62022.30452.8168-2.43452.6354-0.2073-0.04370.2443-0.23370.17820.22090.0017-0.1030.02910.1098-0.0075-0.09620.10660.00770.12148.2921-6.796-1.0399
40.7209-0.0724-0.00960.38160.40420.4652-0.01020.0122-0.0658-0.08310.015-0.0199-0.08-0.0138-0.00470.08410.01050.01370.0462-0.00930.04847.2161-9.4398-21.4323
51.366-1.2535-1.04411.60060.92410.8691-0.0673-0.11570.14780.17410.1408-0.17290.10220.1066-0.07360.07910.03020.00840.0515-0.03270.062115.8216-34.5036-27.5011
60.4406-0.1943-0.05981.63891.42931.2974-0.01390.0126-0.04630.067-0.07460.09270.0484-0.06860.08850.05750.00560.02190.0329-0.01580.03663.8611-24.7342-24.1872
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 111
2X-RAY DIFFRACTION2A112 - 261
3X-RAY DIFFRACTION3A262 - 274
4X-RAY DIFFRACTION4B1 - 112
5X-RAY DIFFRACTION5B113 - 228
6X-RAY DIFFRACTION6B229 - 275

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