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- PDB-9mrp: Crystal structures of a cyanobacterial DAP epimerase bound to L,L... -

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Basic information

Entry
Database: PDB / ID: 9mrp
TitleCrystal structures of a cyanobacterial DAP epimerase bound to L,L-aziDAP
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 / 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
(2S,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID / Diaminopimelate epimerase
Similarity search - Component
Biological speciesAnabaena sp. YBS01 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 L,L-aziDAP
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
Water17,853991
1
A: 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_556x,y,z+11
Buried area2840 Å2
ΔGint-10 kcal/mol
Surface area21240 Å2
MethodPISA
2
B: Diaminopimelate epimerase
hetero molecules

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
crystal symmetry operation1_545x,y-1,z1
Buried area2830 Å2
ΔGint-10 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.460, 102.596, 47.674
Angle α, β, γ (deg.)90.00, 103.13, 90.00
Int Tables number3
Space group name H-MP121

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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-ZDP / (2S,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.: 991 / 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: 3.44 Å3/Da / Density % sol: 64.24 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 0.1M Phosphate/citrate 4.2, 40% v/v PEG 300

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→45.51 Å / Num. obs: 264860 / % possible obs: 98.32 % / Redundancy: 6.9 % / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 7.53
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 7 % / Num. unique obs: 26460 / CC1/2: 0.846 / CC star: 0.957 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALAdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→45.51 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 41.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2415 13408 5.08 %
Rwork0.2298 --
obs0.2303 263782 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→45.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8508 0 56 991 9555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0148740
X-RAY DIFFRACTIONf_angle_d1.38111880
X-RAY DIFFRACTIONf_dihedral_angle_d13.9613196
X-RAY DIFFRACTIONf_chiral_restr0.1051348
X-RAY DIFFRACTIONf_plane_restr0.0131564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.39144150.3868075X-RAY DIFFRACTION96
1.52-1.530.35564560.34558487X-RAY DIFFRACTION99
1.53-1.550.35314510.34168303X-RAY DIFFRACTION99
1.55-1.570.33584870.32958308X-RAY DIFFRACTION99
1.57-1.590.31634700.31828445X-RAY DIFFRACTION99
1.59-1.620.30074740.30978290X-RAY DIFFRACTION99
1.62-1.640.3274650.29798403X-RAY DIFFRACTION99
1.64-1.660.30324390.29538355X-RAY DIFFRACTION99
1.66-1.690.31374630.29178380X-RAY DIFFRACTION99
1.69-1.720.29814390.28658336X-RAY DIFFRACTION99
1.72-1.750.28554380.27888331X-RAY DIFFRACTION98
1.75-1.780.30614440.28938182X-RAY DIFFRACTION96
1.78-1.810.28334560.27858196X-RAY DIFFRACTION97
1.81-1.850.30974130.26948449X-RAY DIFFRACTION99
1.85-1.890.29744070.26328432X-RAY DIFFRACTION99
1.89-1.930.26154320.25258388X-RAY DIFFRACTION99
1.93-1.980.26244960.23948399X-RAY DIFFRACTION99
1.98-2.040.25424600.24138305X-RAY DIFFRACTION99
2.04-2.090.2264470.23388430X-RAY DIFFRACTION99
2.09-2.160.24554250.23438431X-RAY DIFFRACTION99
2.16-2.240.23874550.23158380X-RAY DIFFRACTION99
2.24-2.330.24454450.23118381X-RAY DIFFRACTION99
2.33-2.440.27594070.2358287X-RAY DIFFRACTION97
2.44-2.560.25014280.22848194X-RAY DIFFRACTION96
2.56-2.720.2454280.2318460X-RAY DIFFRACTION99
2.72-2.930.22634320.23658503X-RAY DIFFRACTION99
2.94-3.230.24974820.21918387X-RAY DIFFRACTION99
3.23-3.70.19954810.2018376X-RAY DIFFRACTION98
3.7-4.660.16524350.15738400X-RAY DIFFRACTION98
4.66-45.510.18254380.17918081X-RAY DIFFRACTION93

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