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- PDB-9ntf: Helix pomatia AMP deaminase (HPAMPD) with unknown density in the ... -

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Basic information

Entry
Database: PDB / ID: 9ntf
TitleHelix pomatia AMP deaminase (HPAMPD) with unknown density in the active site
ComponentsAMP deaminase
KeywordsHYDROLASE / Helix pomatia AMP deaminase (HPAMPD) / Inosine 5'-monophosphate
Function / homologyACETATE ION / PHOSPHATE ION
Function and homology information
Biological speciesHelix pomatia (Roman snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsKaur, G. / Horton, J.R. / Cheng, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM134744 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR160029 United States
CitationJournal: To Be Published
Title: Structural basis of substrate specificity of Helix pomatia AMP deaminase and a chimeric ADGF adenosine deaminase
Authors: Kaur, G. / Horton, J.R. / Cheng, X.
History
DepositionMar 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 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: AMP deaminase
B: AMP deaminase
C: AMP deaminase
D: AMP deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,874104
Polymers245,0064
Non-polymers9,867100
Water33,1301839
1
A: AMP deaminase
D: AMP deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,75840
Polymers122,5032
Non-polymers4,25538
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AMP deaminase
C: AMP deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,11664
Polymers122,5032
Non-polymers5,61262
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.344, 82.351, 211.495
Angle α, β, γ (deg.)90.000, 92.287, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
AMP deaminase


Mass: 61251.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helix pomatia (Roman snail) / Production host: Komagataella pastoris (fungus)

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Sugars , 2 types, 15 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 7 types, 1924 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 73 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#9: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1839 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M BIS-TRIS pH 6.5, 28% w/v Polyethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.56→70.85 Å / Num. obs: 372245 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 21.04 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.065 / Net I/σ(I): 6
Reflection shellResolution: 1.56→1.585 Å / Num. unique obs: 18514 / CC1/2: 0.32 / Rpim(I) all: 1.013

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→70.85 Å / SU ML: 0.2029 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.4218
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1879 18895 5.09 %
Rwork0.1607 352405 -
obs0.162 371300 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.81 Å2
Refinement stepCycle: LAST / Resolution: 1.56→70.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16004 0 622 1839 18465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014417110
X-RAY DIFFRACTIONf_angle_d1.252123131
X-RAY DIFFRACTIONf_chiral_restr0.0842588
X-RAY DIFFRACTIONf_plane_restr0.01272930
X-RAY DIFFRACTIONf_dihedral_angle_d13.07116637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.580.36416130.347511238X-RAY DIFFRACTION96.66
1.58-1.590.33266500.331111495X-RAY DIFFRACTION97.98
1.59-1.610.32015850.310211690X-RAY DIFFRACTION98.94
1.61-1.630.33116630.297311658X-RAY DIFFRACTION99.53
1.63-1.660.29916120.278711786X-RAY DIFFRACTION99.73
1.66-1.680.28947050.265111652X-RAY DIFFRACTION99.77
1.68-1.70.29755970.254211790X-RAY DIFFRACTION99.87
1.7-1.730.28716570.24311750X-RAY DIFFRACTION99.94
1.73-1.750.25826700.232211677X-RAY DIFFRACTION99.89
1.75-1.780.24726380.216311720X-RAY DIFFRACTION99.96
1.78-1.810.22976160.20711776X-RAY DIFFRACTION99.96
1.81-1.850.23426260.198411729X-RAY DIFFRACTION99.98
1.85-1.880.22996240.192511765X-RAY DIFFRACTION99.95
1.88-1.920.22526280.1911801X-RAY DIFFRACTION99.93
1.92-1.960.21076620.179911767X-RAY DIFFRACTION99.87
1.96-2.010.19476330.166211781X-RAY DIFFRACTION99.92
2.01-2.060.1867040.151311699X-RAY DIFFRACTION99.92
2.06-2.110.17595920.149211832X-RAY DIFFRACTION99.94
2.11-2.180.1785730.14211775X-RAY DIFFRACTION99.88
2.18-2.250.17266020.147511849X-RAY DIFFRACTION99.79
2.25-2.330.18086310.149711714X-RAY DIFFRACTION99.77
2.33-2.420.18136430.145811780X-RAY DIFFRACTION99.77
2.42-2.530.19376270.151411786X-RAY DIFFRACTION99.76
2.53-2.660.17675920.14711848X-RAY DIFFRACTION99.72
2.66-2.830.1685800.148911812X-RAY DIFFRACTION99.49
2.83-3.050.18266770.152411666X-RAY DIFFRACTION98.69
3.05-3.360.17536600.150811696X-RAY DIFFRACTION99.04
3.36-3.840.17076200.14111811X-RAY DIFFRACTION99.23
3.84-4.840.13695890.116311969X-RAY DIFFRACTION99.64
4.84-70.850.15156260.144612093X-RAY DIFFRACTION99.5
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.96577970167-0.6289630031840.8467736272333.93384792546-2.801759206833.96448482319-0.15753660487-0.39290437506-0.1474456249690.8968449828860.1556907862930.234484010736-0.478586890936-0.348019797341-0.02537096681220.3781291400080.05513512436290.06590596515640.407633430979-0.08037837971760.221670991078.83964813549-0.771041608393102.537347192
23.66267375145-3.36896398571-0.3107288875253.118269138750.4039445221540.290716862513-0.0729247850225-0.330282759702-0.172668388820.5287725970060.09431562450870.697843772557-0.0127565852607-0.271509075151-0.00793289165530.216011230554-0.004482610204790.04463276345160.429743331649-0.005203090914160.21904291888-2.05450742188-5.671170679887.9970442059
31.942734281750.04825347046790.049702493692.511173934390.4991923377310.550193086220.0160578786901-0.114243797596-0.104391870445-0.03567107190440.0113981181650.2490120250360.0410799225016-0.174251253741-0.03380741068050.13019001589-0.00801253148999-0.000872820241190.227808525165-0.003623151702370.1273064953243.258767926-8.2481542110174.6949491048
43.689113395862.457946812914.298232669922.271955775753.339892491866.00159101192-0.0250737841979-0.1276738715020.148264808750.0258638445808-0.1088396532880.195031231185-0.067033127586-0.3095263656210.1387298379660.1104232414350.03437920243-0.002294235402270.1575048961340.00407139302290.15964667144511.5356933662-0.89390704446653.0656980633
54.78810267828-0.3115342962870.4106934763925.97977183927-0.3926714561764.250223702680.02798551374250.42537138518-0.11414163605-0.204102595758-0.015562279747-0.256735778410.195458746930.227495776454-0.006455123121040.1583997188010.01349943316310.006259722674720.191664352919-0.02345552095940.10463652153114.2325153246-12.046053214843.0914337841
60.6602521949080.396526599236-0.2557177910760.625895928939-0.1283467731460.9886373505910.02466105684370.03331208552980.0783768080216-0.03325796576890.0181983473790.0138666901423-0.0510010514576-0.079509533909-0.04400040458460.1479775107120.0124050714576-0.01422494278560.1964041466210.003020796094380.1571456842816.42481533332.1804042722456.5115472723
75.77283836575-2.79525506189-0.1369221703182.45169231446-0.36132057731.039722920040.07523842103420.160922418969-0.0241488023039-0.111123415534-0.119139631437-0.0582561966578-0.06147995398810.08272675640820.04255395218740.224792708345-0.00800393227993-0.01082937775860.177407966435-0.01934111995730.11889648240428.214078733110.604620473361.2586306161
80.7748451671860.0387337155974-0.2973937427810.367283183847-0.1215288091380.8107633367810.0296345350151-0.105726087130.0670124089380.0379868503342-0.02975933129790.0049030154107-0.0857539821326-0.0164826503822-0.00101516613650.1693288785420.00449774652611-0.004378936097910.190994949775-0.01351298165230.16866271590623.5362171481.3542876606975.3947453897
98.458630922214.93145902468-1.897301973685.78139558696-1.851913941562.060363247260.324978995245-0.06011736851410.6332917190470.379765227461-0.05730401121810.735094800245-0.328993815266-0.515015844371-0.3106706635390.2072765453420.08776648035460.0487295424860.329822957135-0.05114476454350.220014005657-1.5051523724611.611839419778.3727911753
100.6470126273960.1246149824850.3358825888460.9865923865330.2712934196870.841982146573-0.01744634202210.1361168111980.0625349425944-0.147464561850.0481981837489-0.0928589250999-0.1080089820570.162531539781-0.02572346634430.131776205163-0.02832603648190.03203770016220.17244977850.01895965468580.163254855588-3.983605091493.4379003692819.2071147967
111.09716767844-1.06526613171.225203452152.62375843874-1.089064310782.050393225630.0126862299036-0.251572830598-0.08030292144630.1340041097910.03787821554330.05325123414950.180190580155-0.130645694293-0.02595403735390.128606039435-0.02926773581870.008510143477710.2150622185360.02374308571330.139167333252-13.7739043122-9.8841350922458.7596839771
120.61463501163-0.268383554343-0.1002127016210.5062519748960.1697290714460.7425410640520.0115403333228-0.1147148035020.06530352452010.05629989574850.0113459803574-0.021118335575-0.0709754591610.0520428047723-0.021284291930.153596971032-0.0220061035824-0.0008172954253920.1753760623020.00261918286140.146730007263-20.11414547385.2262401173450.5859588277
130.8618791541740.0420606917764-0.2157918109410.1255034192240.0294589981240.5341976874540.0281826685753-0.005631287655730.1140106391860.000747963296134-0.00953760016126-0.00437819750255-0.0987913621939-0.011504391684-0.02231178755370.158548529606-0.005936298212610.001544169025380.1220882402560.007159836407220.171178531573-24.0704468336.4363372885832.7137320542
148.00868201105-3.89115857546-5.552802223582.23022040882.76478926954.409699282790.357308723428-0.4934030133490.465829242847-0.2079641777240.0103871352307-0.220678858084-0.3132216688730.455399967617-0.4090492323660.181405868233-0.07330455571270.008488845524710.2023997670060.01080792304350.2166145173526.8682483286214.881306023329.1426696617
150.388613236643-0.135145587882-0.1066510646280.576230179090.3372479370040.862924679807-0.0220552687494-0.0346871746959-0.02844870134890.0445619217264-0.01253299417980.0882629828562-0.0139310492848-0.1299912568510.03793703408960.143052985065-0.004263673207730.01234465119660.1824112293720.01937330077280.191186209601-41.3284014811-8.2084387404521.31214453
161.6657618023-0.8215808637070.8793159948274.53379781704-0.5923876489351.881851908220.07690308708150.06244497771-0.4032013682890.1655687624350.0622554085259-0.1595720555710.3029421292740.184157937321-0.1265241790110.1452585990190.0174207710433-0.02384527631190.154657012542-0.0307168908850.249230566498-15.3869681175-39.40401428864.74056495845
170.628253273385-0.298573779294-0.05088631862540.6262748931680.1008819014111.289331043910.0193751958470.113221287977-0.106630198489-0.0302672446389-0.014873450714-0.008900334551140.03603244106210.0437049311783-0.006262380447970.134706691137-0.01605048362240.008756669804750.137615806656-0.01654383007960.188229310215-20.8429293133-26.7489440306-1.03976414615
181.0377591647-0.0384508233275-0.1369950386950.4524073315390.1301328153140.740212588329-0.001577973889660.136535864937-0.00753142201998-0.05882982163320.000649295284937-0.00323096657844-0.0406426155292-0.0144232447659-0.002801586117640.1431914656030.0009186957530920.0005096264035970.1299818217520.008899599361570.149463978265-24.9080189497-9.856087688752.77861913418
190.619914142353-1.519330314251.795340289024.0876498129-5.273288899857.17652134367-0.03712556874460.1146260861470.0233485448080.380368864462-0.0788947939868-0.256756855259-0.4930076779290.1254957423660.123641466590.213013581241-0.0377997724892-0.01517246218470.268151424999-0.03091063762830.17574792047644.07055126830.028931364967485.4853785945
202.86225148912-2.647396601632.526479632032.44815309004-2.406197560632.40062421784-0.07708442326220.7671135161850.253287697503-0.0141451505085-0.216904561438-0.161189529379-0.1471557331430.7782580999610.3113879829980.166737414286-0.0007121265774220.0359458342920.2867372851220.04725844625180.20025259800445.427006258-18.515569099780.2069409361
211.079850385430.621431637309-0.138292760721.43778514397-0.4120331271260.618027989180.0868134999575-0.0169642271807-0.111821990975-0.14044291890.00114736641013-0.02017622527220.28991857735-0.0856217270653-0.08414308793250.216509016934-0.0162669665084-0.03662969170360.1844268193620.01009041607360.14480992913330.0124825763-34.994257762288.5436488244
221.6005470161-0.6638803703091.355134748585.09570290059-0.1889716132782.631534705020.144114850098-0.151108129535-0.393137969767-0.4628963876160.2297274943720.5729659406290.570202665274-0.637991660112-0.3022902470050.453711701484-0.179050257001-0.1805288071650.3525263920980.1201889828290.34385193391112.4452039458-52.462312390189.7369504925
230.437245476451-0.1368316725770.3045835209120.688710015377-0.3140535499540.6696697523230.0548065895986-0.182057048715-0.06671852868670.09222243473980.01252523710450.08923678024370.0780600489279-0.193030529279-0.06355309027030.185918197302-0.0494229274789-0.00486490664370.26265679860.02435395094290.1349682412720.4720077545-27.0032658576100.7971176
242.95448327867-1.64373226522-1.935096097793.083129211551.621936078557.86703282560.00661496836889-0.291290739890.03758857147070.146853252637-0.0219651344618-0.2317655822230.1630057056350.225105798220.003293411055070.123623730883-0.0595705319137-0.0479158973780.1462362834120.02430428538480.16472218128944.0629291958-23.937209768699.8683620199
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 31 through 61 )AC31 - 613 - 33
22chain 'A' and (resid 62 through 85 )AC62 - 8534 - 57
33chain 'A' and (resid 86 through 119 )AC86 - 11958 - 91
44chain 'A' and (resid 120 through 142 )AC120 - 14292 - 114
55chain 'A' and (resid 143 through 194 )AC143 - 194115 - 166
66chain 'A' and (resid 195 through 287 )AC195 - 287167 - 259
77chain 'A' and (resid 288 through 322 )AC288 - 322260 - 294
88chain 'A' and (resid 323 through 496 )AC323 - 496295 - 468
99chain 'A' and (resid 497 through 527 )AC497 - 527469 - 499
1010chain 'B' and (resid 31 through 119 )BI31 - 1193 - 91
1111chain 'B' and (resid 120 through 194 )BI120 - 19492 - 166
1212chain 'B' and (resid 195 through 322 )BI195 - 322167 - 294
1313chain 'B' and (resid 323 through 496 )BI323 - 496295 - 468
1414chain 'B' and (resid 497 through 535 )BI497 - 535469 - 507
1515chain 'C' and (resid 30 through 119 )CO30 - 1193 - 92
1616chain 'C' and (resid 120 through 194 )CO120 - 19493 - 167
1717chain 'C' and (resid 195 through 287 )CO195 - 287168 - 260
1818chain 'C' and (resid 288 through 525 )CO288 - 525261 - 498
1919chain 'D' and (resid 30 through 61 )DT30 - 613 - 34
2020chain 'D' and (resid 62 through 85 )DT62 - 8535 - 58
2121chain 'D' and (resid 86 through 142 )DT86 - 14259 - 115
2222chain 'D' and (resid 143 through 194 )DT143 - 194116 - 167
2323chain 'D' and (resid 195 through 478 )DT195 - 478168 - 451
2424chain 'D' and (resid 479 through 526 )DT479 - 526452 - 499

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