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- PDB-6yp4: Putative adenylyl cyclase HpAC1 from Hippeastrum reveals a domina... -

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Basic information

Entry
Database: PDB / ID: 6yp4
TitlePutative adenylyl cyclase HpAC1 from Hippeastrum reveals a dominant triphophatase activity
ComponentsAdenylate cyclase
KeywordsHYDROLASE / Triphosphatase / plant / PPPase / GTP analog / substrate complex / substrate specificity
Function / homology
Function and homology information


inorganic triphosphate phosphatase activity / root development
Similarity search - Function
Triphosphate tunnel metalloenzyme 3 / CYTH / CYTH domain / CYTH domain / CYTH domain profile. / CYTH-like domain superfamily
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Adenylate cyclase
Similarity search - Component
Biological speciesHippeastrum hybrid cultivar (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94541097376 Å
AuthorsKleinboelting, S. / Steegborn, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)236401975 Germany
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Crystal structure and enzymatic characterization of the putative adenylyl cyclase HpAC1 from Hippeastrum reveal dominant triphosphatase activity.
Authors: Kleinboelting, S. / Miehling, J. / Steegborn, C.
History
DepositionApr 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9699
Polymers24,1681
Non-polymers8008
Water3,387188
1
A: Adenylate cyclase
hetero molecules

A: Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,93718
Polymers48,3372
Non-polymers1,60116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)59.808, 59.808, 146.982
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Adenylate cyclase


Mass: 24168.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hippeastrum hybrid cultivar (plant) / Gene: AC1 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / References: UniProt: E1AQY1

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Non-polymers , 5 types, 196 molecules

#2: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 200 mM sodium thiocyanate 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9117 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9117 Å / Relative weight: 1
ReflectionResolution: 1.945→46.39 Å / Num. obs: 20207 / % possible obs: 99 % / Redundancy: 5.9 % / Biso Wilson estimate: 31.0463927181 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.111 / Net I/σ(I): 9.8
Reflection shellResolution: 1.945→1.955 Å / Redundancy: 4.8 % / Num. unique obs: 3116 / CC1/2: 0.766 / Rrim(I) all: 0.696 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V85

3v85


Resolution: 1.94541097376→46.3879815329 Å / SU ML: 0.268747387773 / Cross valid method: FREE R-VALUE / σ(F): 1.32551139312 / Phase error: 27.3703181465
RfactorNum. reflection% reflection
Rfree0.252284005977 1009 5.00943302552 %
Rwork0.1954571396 --
obs0.198401496391 20142 98.7014259813 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.5068368143 Å2
Refinement stepCycle: LAST / Resolution: 1.94541097376→46.3879815329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1653 0 45 188 1886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007168824869291782
X-RAY DIFFRACTIONf_angle_d0.8690498539932420
X-RAY DIFFRACTIONf_chiral_restr0.0563344251314259
X-RAY DIFFRACTIONf_plane_restr0.00654706298373313
X-RAY DIFFRACTIONf_dihedral_angle_d19.90236041311069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94541097376-2.0480.3939957208921340.3263960497442532X-RAY DIFFRACTION94.2382467303
2.048-2.17630.314775489381420.2597957333292684X-RAY DIFFRACTION98.9149457473
2.1763-2.34430.2960547085641410.2521468918182678X-RAY DIFFRACTION98.5319818245
2.3443-2.58020.2764765027571440.2159089958412731X-RAY DIFFRACTION99.9652294854
2.5802-2.95350.2665869789891440.2241861975422743X-RAY DIFFRACTION99.6548153262
2.9535-3.72090.2553014969811470.1784562750462797X-RAY DIFFRACTION99.5940460081
3.7209-46.38798153290.2041220096341570.1538281152472968X-RAY DIFFRACTION99.8721636306
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.218856987560.6908082036480.509143631371.054862737120.05702629426481.842312813360.116216948417-0.100541362337-0.3126885575470.09795366689710.052145908369-0.06424508735340.504263085010.14195694196-0.1232763063340.2785165360650.0385534167187-0.03360539265120.216003635819-0.00563257528190.235257443048-8.32881591543.11486413719-24.7231747596
21.662260253350.0190710188309-1.417064415642.533430560930.1203385323721.51901058161-0.046866602946-0.125425567569-0.0779935099552-0.254334189028-0.1431064970220.5981132475240.360974353159-0.6028297476160.1383977926390.252743779246-0.113883329742-0.02662942073320.475269006502-0.02158443608690.324159101382-28.6078416044.12481585105-28.5601399559
30.17260590843-0.0123160865369-0.4360286148511.48827828161.490314790293.720540208970.128177742582-0.0491948356381-0.4889383581930.348420405751-0.2460077925450.32256158841.60726900835-1.049382896290.1330323456350.758180346398-0.208071827792-0.005516784534430.4984141539060.0159379272260.517935178489-25.7353428678-6.68250614633-25.2693611158
42.261560021070.361913074383-1.096567772560.55803079276-0.4763113476961.941207275980.0538968529325-0.0916230603465-0.128907995306-0.009608579410160.0332211434999-0.03266830911430.2960624694910.437931780479-0.1711626019120.2040487691520.0447673747378-0.03971660178440.338143470516-0.04503038196460.236114298686-2.56740676419.41206235272-26.0898957093
51.730085668780.0272119872451-0.634913762471.081589798440.4847700574640.6505714395970.118642408411-0.434099572177-0.3343829860730.2512248766260.112324244476-0.09009833520860.5501429534280.713252944907-0.1337480002510.3853680632950.218995160499-0.07655798944730.592057052669-0.06717990955830.340288981345.825820987923.12290413047-22.5069294938
60.832384360392-1.45430665301-0.4272339525242.91973715472-0.3961756896393.61484604831-0.0978513148148-1.21910233122-0.4112194483480.8467345262120.286910978445-0.7226485702250.1171976650810.315831930514-0.3281889473630.4853019744360.0145312052595-0.1530603750550.6009293961520.0582811430020.42931016891-5.070299504862.75859167442-10.5776447438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 85 )
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 108 )
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 130 )
4X-RAY DIFFRACTION4chain 'A' and (resid 131 through 155 )
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 194 )
6X-RAY DIFFRACTION6chain 'A' and (resid 195 through 210 )

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