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- PDB-6pi8: Crystal structure of Marinobacter subterrani acetylpolyamine amid... -

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Basic information

Entry
Database: PDB / ID: 6pi8
TitleCrystal structure of Marinobacter subterrani acetylpolyamine amidohydrolase (msAPAH) complexed with acetate
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
ACETATE ION / : / Acetoin utilization deacetylase AcuC
Similarity search - Component
Biological speciesMarinobacter subterrani (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.635 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: 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
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)76,56315
Polymers75,9612
Non-polymers60213
Water8,953497
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-125 kcal/mol
Surface area22500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.371, 121.060, 66.556
Angle α, β, γ (deg.)90.00, 109.53, 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 , 6 types, 510 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 39.098 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.62 Å3/Da / Density % sol: 53.11 % / Description: Thick cubic crystals
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/ml msAPAH Protein, 0.2 M calcium acetate hydrate, 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: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.635→28.081 Å / Num. obs: 95962 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rpim(I) all: 0.066 / Net I/σ(I): 10.2
Reflection shellResolution: 1.64→1.69 Å / Num. unique obs: 9560 / Rpim(I) all: 0.531

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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: 1.635→28.081 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.26
RfactorNum. reflection% reflection
Rfree0.1935 4864 5.07 %
Rwork0.1678 --
obs0.1691 95962 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.635→28.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5325 0 25 498 5848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065549
X-RAY DIFFRACTIONf_angle_d0.8537551
X-RAY DIFFRACTIONf_dihedral_angle_d4.6734417
X-RAY DIFFRACTIONf_chiral_restr0.054810
X-RAY DIFFRACTIONf_plane_restr0.0061007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.635-1.65360.37081510.29453022X-RAY DIFFRACTION100
1.6536-1.6730.35481590.28023015X-RAY DIFFRACTION100
1.673-1.69340.28131520.25763061X-RAY DIFFRACTION100
1.6934-1.71490.2651890.24282976X-RAY DIFFRACTION100
1.7149-1.73740.28331760.24443028X-RAY DIFFRACTION100
1.7374-1.76120.28151510.23583018X-RAY DIFFRACTION100
1.7612-1.78640.25441970.22273010X-RAY DIFFRACTION100
1.7864-1.8130.24581640.19133042X-RAY DIFFRACTION100
1.813-1.84140.23381670.17363009X-RAY DIFFRACTION100
1.8414-1.87160.21441480.17283059X-RAY DIFFRACTION100
1.8716-1.90380.22321620.19572984X-RAY DIFFRACTION99
1.9038-1.93840.29751560.22233037X-RAY DIFFRACTION98
1.9384-1.97570.21151570.18482987X-RAY DIFFRACTION100
1.9757-2.0160.20041700.18213060X-RAY DIFFRACTION100
2.016-2.05980.22751700.18072996X-RAY DIFFRACTION100
2.0598-2.10770.22331510.17173090X-RAY DIFFRACTION100
2.1077-2.16040.18871800.16453032X-RAY DIFFRACTION100
2.1604-2.21880.20821790.16333001X-RAY DIFFRACTION100
2.2188-2.28410.24041740.17372985X-RAY DIFFRACTION99
2.2841-2.35780.17881400.16353066X-RAY DIFFRACTION100
2.3578-2.4420.1831630.1613030X-RAY DIFFRACTION100
2.442-2.53970.22411650.1643047X-RAY DIFFRACTION100
2.5397-2.65520.20191120.16373107X-RAY DIFFRACTION100
2.6552-2.79510.18951560.16223053X-RAY DIFFRACTION100
2.7951-2.970.20161570.16753026X-RAY DIFFRACTION100
2.97-3.1990.19591660.16673075X-RAY DIFFRACTION100
3.199-3.52040.16081530.15773064X-RAY DIFFRACTION100
3.5204-4.02860.13891740.14663042X-RAY DIFFRACTION100
4.0286-5.07070.13031560.12183073X-RAY DIFFRACTION100
5.0707-28.08530.15061690.14633103X-RAY DIFFRACTION100

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