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- PDB-9r7o: DhhP of Borrelia burgdorferi in complex with AMP -

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Basic information

Entry
Database: PDB / ID: 9r7o
TitleDhhP of Borrelia burgdorferi in complex with AMP
ComponentsDHH family
KeywordsHYDROLASE / phosphodiesterase / c-di-AMP / cyclic di-AMP / heterobimetallic
Function / homology
Function and homology information


nucleic acid binding
Similarity search - Function
: / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / : / : / DHH family
Similarity search - Component
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsKlima, M. / Boura, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: DhhP of Borrelia burgdorferi in complex with AMP
Authors: Klima, M. / Boura, E.
History
DepositionMay 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DHH family
B: DHH family
C: DHH family
D: DHH family
E: DHH family
F: DHH family
G: DHH family
H: DHH family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,54828
Polymers293,2738
Non-polymers2,27520
Water18010
1
A: DHH family
B: DHH family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8877
Polymers73,3182
Non-polymers5695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-81 kcal/mol
Surface area27580 Å2
2
C: DHH family
D: DHH family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8877
Polymers73,3182
Non-polymers5695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-76 kcal/mol
Surface area27620 Å2
3
E: DHH family
F: DHH family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8877
Polymers73,3182
Non-polymers5695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-76 kcal/mol
Surface area27350 Å2
4
G: DHH family
H: DHH family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8877
Polymers73,3182
Non-polymers5695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-76 kcal/mol
Surface area27400 Å2
Unit cell
Length a, b, c (Å)74.745, 80.239, 132.703
Angle α, β, γ (deg.)91.240, 91.300, 92.710
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
DHH family


Mass: 36659.094 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Gene: BB_0619 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O51564
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% v/v PEG 500 MME; 10% w/v PEG 20.000; 100mM Gly-Gly/AMPD pH 8.5; 0.3% w/v CHAPS; 0.3% w/v CHAPSO; 0.3% w/v Sodium glycocholate hydrate; 0.3% w/v Taurocholic acid sodium salt hydrate; 3% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.05969 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05969 Å / Relative weight: 1
ReflectionResolution: 2.28→40.06 Å / Num. obs: 132861 / % possible obs: 94.61 % / Redundancy: 3.8 % / Biso Wilson estimate: 49.93 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.09486 / Rpim(I) all: 0.05681 / Rrim(I) all: 0.1108 / Net I/σ(I): 8.02
Reflection shellResolution: 2.28→2.361 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.205 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 13334 / CC1/2: 0.509 / CC star: 0.821 / Rpim(I) all: 0.7085 / Rrim(I) all: 1.399 / % possible all: 95.18

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Processing

Software
NameVersionClassification
XDSbuilt 20241002data reduction
XDSbuilt 20241002data scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
Coot0.9.8.7model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→40.06 Å / SU ML: 0.3784 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.5348
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2525 6640 5 %random selection
Rwork0.2263 126173 --
obs0.2276 132813 94.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.13 Å2
Refinement stepCycle: LAST / Resolution: 2.28→40.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20431 0 108 10 20549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00220952
X-RAY DIFFRACTIONf_angle_d0.452328225
X-RAY DIFFRACTIONf_chiral_restr0.04093121
X-RAY DIFFRACTIONf_plane_restr0.00273576
X-RAY DIFFRACTIONf_dihedral_angle_d9.48917788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.310.42112210.39544205X-RAY DIFFRACTION95.59
2.31-2.330.38942230.3694234X-RAY DIFFRACTION94.61
2.33-2.360.41422220.3654227X-RAY DIFFRACTION95.35
2.36-2.390.37182230.3634231X-RAY DIFFRACTION95.09
2.39-2.420.38012200.35334167X-RAY DIFFRACTION94.38
2.42-2.460.34462210.33794203X-RAY DIFFRACTION95.08
2.46-2.490.35052220.33844225X-RAY DIFFRACTION93.11
2.49-2.530.37462190.33884158X-RAY DIFFRACTION94.97
2.53-2.570.33732180.32454141X-RAY DIFFRACTION92.76
2.57-2.610.32442220.31524214X-RAY DIFFRACTION94.34
2.61-2.650.32492170.30284121X-RAY DIFFRACTION93.25
2.65-2.70.34072170.29344116X-RAY DIFFRACTION92.49
2.7-2.760.36342020.30513844X-RAY DIFFRACTION86.25
2.76-2.810.32542220.28384230X-RAY DIFFRACTION95.45
2.81-2.870.32252250.28824270X-RAY DIFFRACTION95.13
2.87-2.940.29742260.26644293X-RAY DIFFRACTION98.09
2.94-3.010.30752230.27114240X-RAY DIFFRACTION94.94
3.01-3.090.29262270.27574312X-RAY DIFFRACTION96.49
3.09-3.190.36452240.27854260X-RAY DIFFRACTION96.76
3.19-3.290.30682230.2734245X-RAY DIFFRACTION95.19
3.29-3.410.28282250.24894263X-RAY DIFFRACTION94.84
3.41-3.540.29692250.244270X-RAY DIFFRACTION96.11
3.54-3.70.23772200.23194197X-RAY DIFFRACTION94.79
3.7-3.90.23012160.2194101X-RAY DIFFRACTION92.64
3.9-4.140.22732110.1984000X-RAY DIFFRACTION89.56
4.14-4.460.18442270.17514324X-RAY DIFFRACTION97.16
4.46-4.910.17082290.16364334X-RAY DIFFRACTION98.07
4.91-5.620.22432280.17524331X-RAY DIFFRACTION97.44
5.62-7.070.2252210.19654209X-RAY DIFFRACTION94.92
7.07-40.060.15742210.13874208X-RAY DIFFRACTION94.31

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