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- PDB-9r97: DhhP of Borrelia burgdorferi in complex with AMP (SAD/Mn) -

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Basic information

Entry
Database: PDB / ID: 9r97
TitleDhhP of Borrelia burgdorferi in complex with AMP (SAD/Mn)
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: 3.3 Å
AuthorsKlima, M. / Boura, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: DhhP of Borrelia burgdorferi in complex with AMP (SAD/Mn)
Authors: Klima, M. / Boura, E.
History
DepositionMay 19, 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 area5280 Å2
ΔGint-78 kcal/mol
Surface area27600 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 area5180 Å2
ΔGint-74 kcal/mol
Surface area27630 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-74 kcal/mol
Surface area27340 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 area27410 Å2
Unit cell
Length a, b, c (Å)74.760, 80.350, 132.860
Angle α, β, γ (deg.)91.150, 91.280, 92.700
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: 2.72 Å3/Da / Density % sol: 54.73 %
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: P14 (MX2) / Wavelength: 1.77 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Apr 5, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 3.3→49.05 Å / Num. obs: 90557 / % possible obs: 98.52 % / Redundancy: 3.6 % / Biso Wilson estimate: 49.93 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.08148 / Rpim(I) all: 0.05017 / Rrim(I) all: 0.09597 / Net I/σ(I): 13.75
Reflection shellResolution: 3.3→3.418 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.3503 / Mean I/σ(I) obs: 4.97 / Num. unique obs: 9126 / CC1/2: 0.917 / CC star: 0.978 / Rpim(I) all: 0.2146 / Rrim(I) all: 0.412 / % possible all: 97.23

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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: 3.3→49.05 Å / SU ML: 0.3568 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 22.7911
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 4516 4.99 %random selection
Rwork0.1671 86012 --
obs0.169 90528 97.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.45 Å2
Refinement stepCycle: LAST / Resolution: 3.3→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20431 0 108 10 20549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002920952
X-RAY DIFFRACTIONf_angle_d0.557928225
X-RAY DIFFRACTIONf_chiral_restr0.04323121
X-RAY DIFFRACTIONf_plane_restr0.00383576
X-RAY DIFFRACTIONf_dihedral_angle_d10.1037788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.340.29291560.25262959X-RAY DIFFRACTION97.65
3.34-3.380.30881450.23672796X-RAY DIFFRACTION96.74
3.38-3.420.30051540.23092916X-RAY DIFFRACTION97.28
3.42-3.460.27931500.22412839X-RAY DIFFRACTION98.58
3.46-3.510.26371540.22582898X-RAY DIFFRACTION96.95
3.51-3.550.26461480.22212804X-RAY DIFFRACTION95.97
3.55-3.610.24531530.21882913X-RAY DIFFRACTION98.02
3.61-3.660.23971480.21212835X-RAY DIFFRACTION97.29
3.66-3.720.24471470.19512810X-RAY DIFFRACTION96.32
3.72-3.780.24171520.1992856X-RAY DIFFRACTION97.03
3.78-3.840.2431520.19432914X-RAY DIFFRACTION97.64
3.84-3.910.24571420.1882728X-RAY DIFFRACTION93.98
3.91-3.990.24811470.18192828X-RAY DIFFRACTION96.91
3.99-4.070.25521510.18142864X-RAY DIFFRACTION97.57
4.07-4.160.25621520.17882915X-RAY DIFFRACTION96.45
4.16-4.250.19181510.17012840X-RAY DIFFRACTION98.91
4.25-4.360.2111510.15072858X-RAY DIFFRACTION97.63
4.36-4.480.15351540.14442926X-RAY DIFFRACTION97.96
4.48-4.610.15481510.14152857X-RAY DIFFRACTION98.3
4.61-4.760.21181500.14392871X-RAY DIFFRACTION97.96
4.76-4.930.19691550.14562944X-RAY DIFFRACTION98.76
4.93-5.130.14991510.14782869X-RAY DIFFRACTION97.92
5.13-5.360.17061500.1492908X-RAY DIFFRACTION97.45
5.36-5.640.20231480.17472820X-RAY DIFFRACTION97.44
5.64-5.990.27571520.17892866X-RAY DIFFRACTION97.35
5.99-6.460.21261540.17722884X-RAY DIFFRACTION98.83
6.46-7.10.21111500.18252911X-RAY DIFFRACTION98.93
7.1-8.130.18431510.15592925X-RAY DIFFRACTION98.84
8.13-10.220.12831480.11412872X-RAY DIFFRACTION97.23
10.22-49.050.13771490.11642786X-RAY DIFFRACTION95.35

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