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- PDB-9mro: Crystal structures of a cyanobacterial DAP epimerase bound to eit... -

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Basic information

Entry
Database: PDB / ID: 9mro
TitleCrystal structures of a cyanobacterial DAP epimerase bound to either D,L-aziDAP or D,L-alpha-methyl DAP
ComponentsDiaminopimelate epimerase
KeywordsANTIBIOTIC / DAP epimerase / diaminopimelic acid / DapF / cofactor-independent / protein biochemistry / enzyme mechanism / inhibitor / lysine biosynthesis
Function / homology
Function and homology information


diaminopimelate epimerase / diaminopimelate epimerase activity / L-lysine biosynthetic process via diaminopimelate / cytosol
Similarity search - Function
Diaminopimelate epimerase, active site / Diaminopimelate epimerase signature. / Diaminopimelate epimerase, DapF / Diaminopimelate epimerase
Similarity search - Domain/homology
(2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID / Diaminopimelate epimerase
Similarity search - Component
Biological speciesAnabaena sp. YBS01 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsChen, P. / Lamer, T. / Vederas, J.C. / Lemieux, M.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To Be Published
Title: Crystal structures of a cyanobacterial DAP epimerase bound to either D,L-aziDAP or D,L-alpha-methyl DAP
Authors: Lamer, T. / Chen, P. / Lemieux, M.J. / Vederas, J.C.
History
DepositionJan 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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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
C: Diaminopimelate epimerase
D: Diaminopimelate epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,5318
Polymers124,7144
Non-polymers8174
Water28,2481568
1
A: Diaminopimelate epimerase
C: Diaminopimelate epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7654
Polymers62,3572
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-9 kcal/mol
Surface area21250 Å2
MethodPISA
2
B: Diaminopimelate epimerase
hetero molecules

D: Diaminopimelate epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7654
Polymers62,3572
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_664x+1,y+1,z-11
Buried area2820 Å2
ΔGint-10 kcal/mol
Surface area21240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.622, 103.771, 103.770
Angle α, β, γ (deg.)60.23, 78.53, 78.54
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Diaminopimelate epimerase / DAP epimerase / PLP-independent amino acid racemase


Mass: 31178.504 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena sp. YBS01 (bacteria) / Gene: dapF, EH233_12580 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5Q0GFR1, diaminopimelate epimerase
#2: Chemical
ChemComp-ZDR / (2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID


Mass: 204.224 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H16N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1568 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.48 Å3/Da / Density % sol: 64.72 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Succinic acid pH 7.0, 15% w/v Polyethylene glycol 3,350
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.59→39.3 Å / Num. obs: 420990 / % possible obs: 94.71 % / Redundancy: 3.6 % / CC1/2: 0.998 / Net I/σ(I): 9.69
Reflection shellResolution: 1.59→1.91 Å / Num. unique obs: 11893 / CC1/2: 0.566

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→38.29 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2136 10310 4.82 %
Rwork0.2093 --
obs0.2095 213806 94.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→38.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8508 0 56 1568 10132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098740
X-RAY DIFFRACTIONf_angle_d1.06211880
X-RAY DIFFRACTIONf_dihedral_angle_d14.0343196
X-RAY DIFFRACTIONf_chiral_restr0.0591348
X-RAY DIFFRACTIONf_plane_restr0.0111564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.610.34593310.32615848X-RAY DIFFRACTION84
1.61-1.630.30543710.30596589X-RAY DIFFRACTION92
1.63-1.650.3052990.29436745X-RAY DIFFRACTION93
1.65-1.670.29743670.29366546X-RAY DIFFRACTION93
1.67-1.690.29133230.28776605X-RAY DIFFRACTION93
1.69-1.710.30383290.30186707X-RAY DIFFRACTION93
1.71-1.740.31533560.29746673X-RAY DIFFRACTION93
1.74-1.760.28363350.28536801X-RAY DIFFRACTION93
1.76-1.790.28753260.28556599X-RAY DIFFRACTION93
1.79-1.820.27283490.27766749X-RAY DIFFRACTION94
1.82-1.850.28233540.27296695X-RAY DIFFRACTION94
1.85-1.880.27633220.25846776X-RAY DIFFRACTION94
1.88-1.920.2533550.26416704X-RAY DIFFRACTION94
1.92-1.960.24592940.24866814X-RAY DIFFRACTION94
1.96-20.24313010.24396849X-RAY DIFFRACTION95
2-2.050.25563310.2426752X-RAY DIFFRACTION95
2.05-2.10.23723320.23626821X-RAY DIFFRACTION95
2.1-2.160.25713610.23616856X-RAY DIFFRACTION95
2.16-2.220.2353450.22766792X-RAY DIFFRACTION95
2.22-2.290.24163550.22976868X-RAY DIFFRACTION95
2.29-2.370.22983460.22836898X-RAY DIFFRACTION96
2.37-2.470.22743510.23386885X-RAY DIFFRACTION96
2.47-2.580.24063650.22786896X-RAY DIFFRACTION97
2.58-2.720.22563620.22786939X-RAY DIFFRACTION97
2.72-2.890.2273610.21866944X-RAY DIFFRACTION97
2.89-3.110.19834590.20156865X-RAY DIFFRACTION98
3.11-3.420.20533380.17577066X-RAY DIFFRACTION98
3.42-3.920.14243100.14897105X-RAY DIFFRACTION98
3.92-4.940.12683690.12667042X-RAY DIFFRACTION99
4.94-38.290.18193130.18287067X-RAY DIFFRACTION98

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