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- PDB-6uk3: Crystal Structure of S-adenosyl-L-homocysteine hydrolase from Aca... -

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Basic information

Entry
Database: PDB / ID: 6uk3
TitleCrystal Structure of S-adenosyl-L-homocysteine hydrolase from Acanthamoeba castellanii with bound NAD and Adenosine
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / SSGCID / GS-adenosyl-L-homocysteine hydrolase / NAD / AMP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


adenosylhomocysteinase / adenosylhomocysteinase activity / one-carbon metabolic process
Similarity search - Function
Adenosylhomocysteinase-like / Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain ...Adenosylhomocysteinase-like / Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE / FORMIC ACID / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / OXAMIC ACID / Adenosylhomocysteinase
Similarity search - Component
Biological speciesAcanthamoeba castellanii str. Neff (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of S-adenosyl-L-homocysteine hydrolase from Acanthamoeba castellanii with bound NAD and Adenosine
Authors: Romanaggi, C.T. / Dranow, D.M. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionOct 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
C: Adenosylhomocysteinase
D: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,37731
Polymers216,7004
Non-polymers4,67827
Water41,9572329
1
A: Adenosylhomocysteinase
C: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,57613
Polymers108,3502
Non-polymers2,22611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-48 kcal/mol
Surface area34450 Å2
MethodPISA
2
B: Adenosylhomocysteinase
D: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,80218
Polymers108,3502
Non-polymers2,45216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11310 Å2
ΔGint-52 kcal/mol
Surface area34340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.030, 112.730, 105.920
Angle α, β, γ (deg.)90.000, 114.725, 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
Adenosylhomocysteinase


Mass: 54174.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba castellanii str. Neff (eukaryote)
Gene: ACA1_054200 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L8H6B5, adenosylhomocysteinase

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Non-polymers , 7 types, 2356 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3NO3
#7: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2329 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: AccaA.00032.a.B1.PW38645 at 20.81 mg/ml, incubated with 2 mM NAD, SAH, mixed 1:1 with 12.5% (w/v) PEG-1000, 12.5% (w/v) PEG-3350, 12.5% (v/v) MPD, 0.1 M MOPS/HEPES-Na, pH=7.5, 0.02 M of ...Details: AccaA.00032.a.B1.PW38645 at 20.81 mg/ml, incubated with 2 mM NAD, SAH, mixed 1:1 with 12.5% (w/v) PEG-1000, 12.5% (w/v) PEG-3350, 12.5% (v/v) MPD, 0.1 M MOPS/HEPES-Na, pH=7.5, 0.02 M of sodium formate, ammonium acetate, trisodium citrate, sodium potassium L-tartrate, 0.2 M sodium oxamate. Tray: 311079g8, puck: ved0-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 1, 2019 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 400199 / % possible obs: 99.7 % / Redundancy: 4.142 % / Biso Wilson estimate: 22.399 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.05 / Χ2: 1.025 / Net I/σ(I): 16.63
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.444.1250.5842.2294950.8010.6799.5
1.44-1.484.1360.4672.8287780.8630.53599.6
1.48-1.524.1430.3643.59280080.9080.41799.7
1.52-1.574.1470.2744.72271830.9470.31499.8
1.57-1.624.1560.2265.77263770.9630.25899.8
1.62-1.674.1660.1887.02255320.9720.21599.8
1.67-1.744.1690.1518.74246700.9820.17399.8
1.74-1.814.170.11811.07236760.9890.13599.7
1.81-1.894.1660.09214.13227870.9920.10699.7
1.89-1.984.1610.07417.46217100.9950.08599.7
1.98-2.094.1440.05821.4206660.9970.06799.6
2.09-2.214.140.04825.53195550.9980.05499.6
2.21-2.374.1360.04128.95183350.9980.04799.7
2.37-2.564.1380.03632.26171900.9980.04199.7
2.56-2.84.140.03335.48157900.9990.03799.7
2.8-3.134.1270.02939.15142950.9990.03399.7
3.13-3.614.1180.02543.03126250.9990.02999.7
3.61-4.434.1110.02345.74106930.9990.02799.8
4.43-6.264.0970.02346.1583060.9990.02699.6
6.26-503.8870.02545.5845280.9980.0397.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.73 Å49.01 Å
Translation3.73 Å49.01 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
PHENIX1.17rc1_3602refinement
PDB_EXTRACT3.25data extraction
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5v96

5v96


Resolution: 1.4→50 Å / SU ML: 0.1168 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.9814
RfactorNum. reflection% reflection
Rfree0.1611 2000 0.5 %
Rwork0.1299 --
obs0.1301 400168 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.17 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14732 0 309 2329 17370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005115788
X-RAY DIFFRACTIONf_angle_d0.862221492
X-RAY DIFFRACTIONf_chiral_restr0.08242424
X-RAY DIFFRACTIONf_plane_restr0.00512894
X-RAY DIFFRACTIONf_dihedral_angle_d16.21285995
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.22831280.193228335X-RAY DIFFRACTION99.52
1.43-1.470.23011540.174128313X-RAY DIFFRACTION99.64
1.47-1.520.21211450.156528370X-RAY DIFFRACTION99.73
1.52-1.570.18341410.138328392X-RAY DIFFRACTION99.84
1.57-1.620.17881240.127128375X-RAY DIFFRACTION99.82
1.62-1.690.1421240.122528474X-RAY DIFFRACTION99.85
1.69-1.760.14531670.118128420X-RAY DIFFRACTION99.83
1.76-1.860.17371460.120628377X-RAY DIFFRACTION99.8
1.86-1.970.1471480.117728379X-RAY DIFFRACTION99.71
1.97-2.130.1441390.120428458X-RAY DIFFRACTION99.71
2.13-2.340.15231570.122628437X-RAY DIFFRACTION99.75
2.34-2.680.15571390.131528469X-RAY DIFFRACTION99.79
2.68-3.370.15581230.136628619X-RAY DIFFRACTION99.89
3.37-43.610.1611650.126228750X-RAY DIFFRACTION99.58

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