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

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Basic information

Entry
Database: PDB / ID: 6pid
TitleCrystal structure of Marinobacter subterrani acetylpolyamine amidohydrolase (msAPAH) complexed with 8-amino-N-hydroxyoctanamide
ComponentsAcetylpolyamine amidohydrolase
KeywordsHYDROLASE/INHIBITOR / acetylpolyamine amidohydrolase / polyamine deacetylase / hydrolase / hydrolase inhibitor / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


histone deacetylase activity / 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
: / 8-amino-N-hydroxyoctanamide / Acetoin utilization deacetylase AcuC
Similarity search - Component
Biological speciesMarinobacter subterrani (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.546 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 26, 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.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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetylpolyamine amidohydrolase
B: Acetylpolyamine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,67013
Polymers75,9612
Non-polymers70911
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-52 kcal/mol
Surface area21920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.330, 119.060, 66.220
Angle α, β, γ (deg.)90.00, 109.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acetylpolyamine amidohydrolase


Mass: 37980.547 Da / Num. of mol.: 2
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, 262 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-OKS / 8-amino-N-hydroxyoctanamide


Mass: 174.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.56 Å3/Da / Density % sol: 52.03 % / Description: Thick plate-like crystals
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/ml msAPAH Protein, 0.2 M magnesium acetate tetrahydrate, 20% 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-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.54→59.53 Å / Num. obs: 95821 / % possible obs: 88.7 % / Redundancy: 3.4 % / Rpim(I) all: 0.172 / Net I/σ(I): 5.6
Reflection shellResolution: 1.55→1.6 Å / Num. unique obs: 7699 / Rpim(I) all: 0.742

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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: 1.546→59.53 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.09
RfactorNum. reflection% reflection
Rfree0.2805 1833 1.91 %
Rwork0.244 --
obs0.2447 95821 85.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.546→59.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5325 0 33 251 5609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065503
X-RAY DIFFRACTIONf_angle_d0.857467
X-RAY DIFFRACTIONf_dihedral_angle_d5.3174387
X-RAY DIFFRACTIONf_chiral_restr0.049796
X-RAY DIFFRACTIONf_plane_restr0.006994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.546-1.58780.42571080.42115606X-RAY DIFFRACTION67
1.5878-1.63460.42421360.39276667X-RAY DIFFRACTION80
1.6346-1.68730.46171330.37536806X-RAY DIFFRACTION81
1.6873-1.74760.41691420.356932X-RAY DIFFRACTION83
1.7476-1.81760.35271310.33096760X-RAY DIFFRACTION81
1.8176-1.90030.3321290.29097103X-RAY DIFFRACTION85
1.9003-2.00050.28391490.27547269X-RAY DIFFRACTION86
2.0005-2.12590.32931340.25337431X-RAY DIFFRACTION88
2.1259-2.290.31441510.22677468X-RAY DIFFRACTION89
2.29-2.52050.23181510.21537895X-RAY DIFFRACTION94
2.5205-2.88520.24061550.20977817X-RAY DIFFRACTION93
2.8852-3.6350.24571610.19888138X-RAY DIFFRACTION97
3.635-59.530.18021530.16848097X-RAY DIFFRACTION95

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