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- PDB-3fve: Crystal structure of diaminopimelate epimerase Mycobacterium tube... -

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Basic information

Entry
Database: PDB / ID: 3fve
TitleCrystal structure of diaminopimelate epimerase Mycobacterium tuberculosis DapF
ComponentsDiaminopimelate epimerase
KeywordsISOMERASE / alpha/beta / Amino-acid biosynthesis / Lysine biosynthesis
Function / homology
Function and homology information


diaminopimelate epimerase / diaminopimelate epimerase activity / lysine biosynthetic process via diaminopimelate / plasma membrane / 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Diaminopimelate epimerase / Diaminopimelate epimerase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsUsha, V. / Dover, L.G. / Roper, D.I. / Futterer, K. / Besra, G.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the diaminopimelate epimerase DapF from Mycobacterium tuberculosis
Authors: Usha, V. / Dover, L.G. / Roper, D.I. / Futterer, K. / Besra, G.S.
History
DepositionJan 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2034
Polymers29,8651
Non-polymers3383
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Diaminopimelate epimerase
hetero molecules

A: Diaminopimelate epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4068
Polymers59,7292
Non-polymers6776
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
Buried area3400 Å2
ΔGint-11 kcal/mol
Surface area22510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.640, 183.640, 45.210
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
DetailsBIOLOGICAL UNIT IS THE SAME AS ASYM.

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Components

#1: Protein Diaminopimelate epimerase / DAP epimerase


Mass: 29864.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: dapF, MT2798, MTCY154.06c, Rv2726c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: P63897, UniProt: P9WP19*PLUS, diaminopimelate epimerase
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.68 Å3/Da / Density % sol: 66.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 9.5
Details: 1.9 M (NH4)H2PO4, 0.1 M bis-tris propane, pH 9.5, 2.5% glycerol, vapor diffusion, temperature 291K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Sep 27, 2008
RadiationMonochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.59→45.22 Å / Num. all: 14430 / Num. obs: 14430 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.2 % / Biso Wilson estimate: 64.8 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086
Reflection shellResolution: 2.59→2.73 Å / Redundancy: 13 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2020 / Rsym value: 0.758 / % possible all: 98.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å9.99 Å
Translation3.5 Å9.99 Å

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BWZ

1bwz


Resolution: 2.6→45 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.229 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.807 / SU B: 20.884 / SU ML: 0.213 / SU R Cruickshank DPI: 0.416 / SU Rfree: 0.291 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.367 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 722 5 %RANDOM
Rwork0.224 ---
all0.226 14341 --
obs0.226 14341 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.85 Å2 / Biso mean: 38.103 Å2 / Biso min: 27.12 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å2-0.53 Å2-0 Å2
2---1.06 Å20 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 20 38 2061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212055
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.9452799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6395280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89623.16579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.315270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.411515
X-RAY DIFFRACTIONr_chiral_restr0.070.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021571
X-RAY DIFFRACTIONr_nbd_refined0.2110.2820
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21363
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.273
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.26
X-RAY DIFFRACTIONr_mcbond_it0.4581.51407
X-RAY DIFFRACTIONr_mcangle_it0.81722184
X-RAY DIFFRACTIONr_scbond_it0.9663718
X-RAY DIFFRACTIONr_scangle_it1.6094.5615
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 45 -
Rwork0.341 994 -
all-1039 -
obs--99.81 %
Refinement TLS params.Method: refined / Origin x: -17.389 Å / Origin y: 73.299 Å / Origin z: -3.47 Å
111213212223313233
T0.0183 Å2-0.022 Å20.0786 Å2-0.0388 Å2-0.0327 Å2--0.1083 Å2
L4.0218 °20.6657 °2-1.4457 °2-1.8749 °2-1.1234 °2--1.7028 °2
S-0.2642 Å °-0.0106 Å °-0.8263 Å °-0.2333 Å °-0.0463 Å °-0.1792 Å °0.3722 Å °0.0664 Å °0.3105 Å °

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