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- PDB-3q9c: Crystal Structure of H159A APAH complexed with N8-acetylspermidine -

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Basic information

Entry
Database: PDB / ID: 3q9c
TitleCrystal Structure of H159A APAH complexed with N8-acetylspermidine
ComponentsAcetylpolyamine amidohydrolase
KeywordsHYDROLASE / HDAC / polyamine / Arginase Fold / Deacetylase
Function / homology
Function and homology information


acetylspermidine deacetylase / acetylspermidine deacetylase activity / acetylputrescine deacetylase / acetylputrescine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase activity / epigenetic regulation of gene expression / metal ion binding
Similarity search - Function
Histone deacetylase domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / N-{4-[(3-aminopropyl)amino]butyl}acetamide / Acetylpolyamine amidohydrolase
Similarity search - Component
Biological speciesMycoplana ramosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsLombardi, P.M. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2011
Title: Structure of prokaryotic polyamine deacetylase reveals evolutionary functional relationships with eukaryotic histone deacetylases .
Authors: Lombardi, P.M. / Angell, H.D. / Whittington, D.A. / Flynn, E.F. / Rajashankar, K.R. / Christianson, D.W.
History
DepositionJan 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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 / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylpolyamine amidohydrolase
B: Acetylpolyamine amidohydrolase
C: Acetylpolyamine amidohydrolase
D: Acetylpolyamine amidohydrolase
E: Acetylpolyamine amidohydrolase
F: Acetylpolyamine amidohydrolase
G: Acetylpolyamine amidohydrolase
H: Acetylpolyamine amidohydrolase
I: Acetylpolyamine amidohydrolase
J: Acetylpolyamine amidohydrolase
K: Acetylpolyamine amidohydrolase
L: Acetylpolyamine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)439,41260
Polymers435,63512
Non-polymers3,77748
Water31,5621752
1
A: Acetylpolyamine amidohydrolase
I: Acetylpolyamine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,23510
Polymers72,6062
Non-polymers6308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-46 kcal/mol
Surface area22210 Å2
MethodPISA
2
B: Acetylpolyamine amidohydrolase
F: Acetylpolyamine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,23510
Polymers72,6062
Non-polymers6308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-45 kcal/mol
Surface area22040 Å2
MethodPISA
3
C: Acetylpolyamine amidohydrolase
K: Acetylpolyamine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,23510
Polymers72,6062
Non-polymers6308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-46 kcal/mol
Surface area22040 Å2
MethodPISA
4
D: Acetylpolyamine amidohydrolase
J: Acetylpolyamine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,23510
Polymers72,6062
Non-polymers6308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-47 kcal/mol
Surface area22140 Å2
MethodPISA
5
E: Acetylpolyamine amidohydrolase
H: Acetylpolyamine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,23510
Polymers72,6062
Non-polymers6308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-47 kcal/mol
Surface area21980 Å2
MethodPISA
6
G: Acetylpolyamine amidohydrolase
L: Acetylpolyamine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,23510
Polymers72,6062
Non-polymers6308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-45 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.461, 120.154, 118.448
Angle α, β, γ (deg.)98.470, 94.410, 115.890
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Acetylpolyamine amidohydrolase


Mass: 36302.926 Da / Num. of mol.: 12 / Mutation: H159A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplana ramosa (bacteria) / Gene: aphA, aph / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / References: UniProt: Q48935

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Non-polymers , 5 types, 1800 molecules

#2: Chemical
ChemComp-Q9C / N-{4-[(3-aminopropyl)amino]butyl}acetamide / N8-acetylspermidine


Mass: 187.283 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C9H21N3O
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1752 / 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: 3.37 Å3/Da / Density % sol: 63.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 1.0 M sodium phosphate, 0.8 M potassium phosphate, 0.2 M lithium sulfate, 0.1 M CAPS pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2010 / Details: Kirpatrick Baez focusing mirrors
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 252823 / Num. obs: 219596 / % possible obs: 86.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 7.472
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 2.059 / Num. unique all: 21913 / Rsym value: 0.361 / % possible all: 96.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
APS-24IDCIn House Programdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3Q9F

3q9f


Resolution: 2.3→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 21958 8.7 %random
Rwork0.1859 ---
all0.1859 252823 --
obs0.1859 219596 86.9 %-
Solvent computationBsol: 47.0561 Å2
Displacement parametersBiso max: 105.52 Å2 / Biso mean: 25.677 Å2 / Biso min: 4.33 Å2
Baniso -1Baniso -2Baniso -3
1-3.189 Å20.925 Å2-3.878 Å2
2--0.083 Å22.709 Å2
3----3.272 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30756 0 192 1752 32700
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.217
X-RAY DIFFRACTIONc_mcbond_it1.1091.5
X-RAY DIFFRACTIONc_scbond_it1.9752
X-RAY DIFFRACTIONc_mcangle_it1.7482
X-RAY DIFFRACTIONc_scangle_it2.9182.5
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection% reflection
Rfree0.285 1375 -
Rwork0.2455 --
obs-12714 56 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5unkedit.parunkedit.top

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