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- PDB-6f3p: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pse... -

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Basic information

Entry
Database: PDB / ID: 6f3p
TitleCrystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa in complex with 3'-deoxyadenosine and K+ cation
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / REGULATION OF SAM-DEPENDENT METHYLATION REACTIONS
Function / homology
Function and homology information


L-homocysteine biosynthetic process / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / cytosol
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
3'-DEOXYADENOSINE / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Adenosylhomocysteinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsCzyrko, J. / Brzezinski, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science Centre, PolandUMO-2013/09/B/NZ1/01880 Poland
CitationJournal: Sci Rep / Year: 2018
Title: Metal-cation regulation of enzyme dynamics is a key factor influencing the activity of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa.
Authors: Czyrko, J. / Sliwiak, J. / Imiolczyk, B. / Gdaniec, Z. / Jaskolski, M. / Brzezinski, K.
History
DepositionNov 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim
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.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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosylhomocysteinase
C: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,63812
Polymers103,4702
Non-polymers2,16810
Water20,3031127
1
A: Adenosylhomocysteinase
C: Adenosylhomocysteinase
hetero molecules

A: Adenosylhomocysteinase
C: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,27724
Polymers206,9404
Non-polymers4,33720
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area30970 Å2
ΔGint-191 kcal/mol
Surface area57220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.900, 85.740, 112.010
Angle α, β, γ (deg.)90.00, 122.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-978-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 10 - 469 / Label seq-ID: 13 - 472

Dom-IDAuth asym-IDLabel asym-ID
1AA
2CB

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase


Mass: 51735.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: ahcY, sahH, PA0432 / Plasmid: pMCSG57 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus RILP / References: UniProt: Q9I685, adenosylhomocysteinase

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Non-polymers , 6 types, 1137 molecules

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


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-3AD / 3'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1127 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.16 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 50 mM KH2PO4, 15% (W/V) PEG8000, 20% (V/V) GLYCEROL, 2 mM 3'-deoxyadenosine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 245319 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.1
Reflection shellResolution: 1.35→1.4 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LI4

1li4


Resolution: 1.35→30 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.981 / SU B: 1.337 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.033 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12701 1220 0.5 %RANDOM
Rwork0.10075 ---
obs0.10088 244097 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.554 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20.18 Å2
2--0.45 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7096 0 138 1127 8361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0197675
X-RAY DIFFRACTIONr_bond_other_d0.0020.027378
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.95210457
X-RAY DIFFRACTIONr_angle_other_deg1.04317034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35851001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61925.373335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.128151360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4921535
X-RAY DIFFRACTIONr_chiral_restr0.1260.21176
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029101
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021682
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7761.5973821
X-RAY DIFFRACTIONr_mcbond_other1.7761.5973820
X-RAY DIFFRACTIONr_mcangle_it2.2092.414805
X-RAY DIFFRACTIONr_mcangle_other2.2092.414806
X-RAY DIFFRACTIONr_scbond_it2.561.8313854
X-RAY DIFFRACTIONr_scbond_other2.5621.8313846
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0312.6675615
X-RAY DIFFRACTIONr_long_range_B_refined3.59920.8988831
X-RAY DIFFRACTIONr_long_range_B_other3.19119.8858551
X-RAY DIFFRACTIONr_rigid_bond_restr3.063315052
X-RAY DIFFRACTIONr_sphericity_free28.7925803
X-RAY DIFFRACTIONr_sphericity_bonded10.376515213
Refine LS restraints NCS

Ens-ID: 1 / Number: 31288 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2C
LS refinement shellResolution: 1.348→1.383 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 67 -
Rwork0.202 15414 -
obs--83.81 %

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