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- PDB-6pht: Crystal structure of Marinobacter subterrani acetylpolyamine amid... -

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Basic information

Entry
Database: PDB / ID: 6pht
TitleCrystal structure of Marinobacter subterrani acetylpolyamine amidohydrolase (msAPAH) complexed with 5-[(3-aminopropyl)amino]pentylboronic acid
ComponentsAcetylpolyamine amidohydrolase
KeywordsHYDROLASE/INHIBITOR / acetylpolyamine amidohydrolase / polyamine deacetylase / hydrolase / hydrolase inhibitor / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


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
: / {5-[(3-aminopropyl)amino]pentyl}boronic acid / Acetoin utilization deacetylase AcuC
Similarity search - Component
Biological speciesMarinobacter subterrani (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOsko, J.D. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM49758 United States
CitationJournal: Biochemistry / Year: 2019
Title: Structure and Function of the Acetylpolyamine Amidohydrolase from the Deep Earth HalophileMarinobacter subterrani.
Authors: Osko, J.D. / Roose, B.W. / Shinsky, S.A. / Christianson, D.W.
History
DepositionJun 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,37025
Polymers151,9224
Non-polymers1,44821
Water10,755597
1
A: Acetylpolyamine amidohydrolase
hetero molecules

C: Acetylpolyamine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,69713
Polymers75,9612
Non-polymers73611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area5660 Å2
ΔGint-53 kcal/mol
Surface area21680 Å2
MethodPISA
2
B: Acetylpolyamine amidohydrolase
D: Acetylpolyamine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,67312
Polymers75,9612
Non-polymers71210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-48 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.630, 163.480, 65.720
Angle α, β, γ (deg.)90.00, 94.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Acetylpolyamine amidohydrolase


Mass: 37980.547 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinobacter subterrani (bacteria) / Gene: Msub_13096 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J7JFD7

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Non-polymers , 5 types, 618 molecules

#2: Chemical
ChemComp-OKP / {5-[(3-aminopropyl)amino]pentyl}boronic acid


Mass: 188.076 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H21BN2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 597 / 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: 2.31 Å3/Da / Density % sol: 46.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/ml msAPAH protein, 0.2 M magnesium chloride hexahydrate, 0.1 M HEPES (pH 7.5), 25% w/v PEG 3350, 1:1 ratio protein to precipitant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→65.44 Å / Num. obs: 125734 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rpim(I) all: 0.102 / Net I/σ(I): 4.7
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 12518 / Rpim(I) all: 0.312

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB: 4ZUM

4zum


Resolution: 1.8→65.44 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.04
RfactorNum. reflection% reflection
Rfree0.2257 6545 5.21 %
Rwork0.1935 --
obs0.1952 125734 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→65.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10571 0 69 597 11237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810903
X-RAY DIFFRACTIONf_angle_d0.89114795
X-RAY DIFFRACTIONf_dihedral_angle_d7.0647523
X-RAY DIFFRACTIONf_chiral_restr0.0531581
X-RAY DIFFRACTIONf_plane_restr0.0061960
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.28142130.22814035X-RAY DIFFRACTION99
1.8205-1.84190.27371920.23263903X-RAY DIFFRACTION98
1.8419-1.86430.27922230.22493952X-RAY DIFFRACTION98
1.8643-1.88790.2932210.21933922X-RAY DIFFRACTION97
1.8879-1.91280.28722440.21743805X-RAY DIFFRACTION96
1.9128-1.9390.26342280.21153856X-RAY DIFFRACTION95
1.939-1.96670.27191840.20933654X-RAY DIFFRACTION92
1.9667-1.9960.25852200.2083757X-RAY DIFFRACTION94
1.996-2.02720.25081850.20444004X-RAY DIFFRACTION99
2.0272-2.06050.2492210.20544053X-RAY DIFFRACTION100
2.0605-2.0960.23972080.19254048X-RAY DIFFRACTION100
2.096-2.13410.23242140.19453990X-RAY DIFFRACTION100
2.1341-2.17520.23192180.19334015X-RAY DIFFRACTION100
2.1752-2.21960.20612530.18983948X-RAY DIFFRACTION100
2.2196-2.26780.24922230.1954053X-RAY DIFFRACTION100
2.2678-2.32060.24242310.19313968X-RAY DIFFRACTION100
2.3206-2.37860.23762190.19524021X-RAY DIFFRACTION100
2.3786-2.4430.2282550.19523997X-RAY DIFFRACTION100
2.443-2.51480.21172400.18664006X-RAY DIFFRACTION100
2.5148-2.5960.23382210.18983988X-RAY DIFFRACTION100
2.596-2.68880.23342340.19364019X-RAY DIFFRACTION100
2.6888-2.79650.23762500.19693974X-RAY DIFFRACTION100
2.7965-2.92370.21812170.20354019X-RAY DIFFRACTION100
2.9237-3.07790.23421710.2024048X-RAY DIFFRACTION99
3.0779-3.27070.21671910.20784086X-RAY DIFFRACTION100
3.2707-3.52320.2112140.19993934X-RAY DIFFRACTION98
3.5232-3.87770.22522150.193967X-RAY DIFFRACTION97
3.8777-4.43880.17492240.16214013X-RAY DIFFRACTION100
4.4388-5.59190.1552140.16134042X-RAY DIFFRACTION100
5.5919-65.4860.20282020.16964112X-RAY DIFFRACTION100

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