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

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Basic information

Entry
Database: PDB / ID: 6phr
TitleCrystal structure of Marinobacter subterrani acetylpolyamine amidohydrolase (msAPAH) complexed with 5-[(3-aminopropyl)amino]pentane-1-thiol
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]pentane-1-thiol / Acetoin utilization deacetylase AcuC
Similarity search - Component
Biological speciesMarinobacter subterrani (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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.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

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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)77,04014
Polymers75,9612
Non-polymers1,07912
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-40 kcal/mol
Surface area21790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.874, 120.680, 65.360
Angle α, β, γ (deg.)90.00, 109.09, 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, 305 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SS9 / 5-[(3-aminopropyl)amino]pentane-1-thiol


Mass: 176.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H20N2S / Feature type: SUBJECT OF INVESTIGATION
#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.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.25 Å3/Da / Density % sol: 45.35 % / Description: Rod-like crystals
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 10 mg/ml protein, 20% v/v-propanol, 0.1 MES monohydrate (pH 6.0), 20% w/v polyethylene glycol monomethyl ether 2000, 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→61.77 Å / Num. obs: 79658 / % possible obs: 99.2 % / Redundancy: 6.1 % / Rpim(I) all: 0.106 / Net I/σ(I): 2.2
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 7965 / Rpim(I) all: 0.675

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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: 1.65→61.765 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.15
RfactorNum. reflection% reflection
Rfree0.2082 4037 5.07 %
Rwork0.1792 --
obs0.1807 79658 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→61.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5314 0 54 293 5661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0175549
X-RAY DIFFRACTIONf_angle_d0.9467478
X-RAY DIFFRACTIONf_dihedral_angle_d6.4224404
X-RAY DIFFRACTIONf_chiral_restr0.055797
X-RAY DIFFRACTIONf_plane_restr0.007988
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.66940.29331280.26132628X-RAY DIFFRACTION99
1.6694-1.68980.28121250.25532601X-RAY DIFFRACTION99
1.6898-1.71120.29321570.24292575X-RAY DIFFRACTION99
1.7112-1.73370.26821300.2382585X-RAY DIFFRACTION99
1.7337-1.75740.26581360.22092650X-RAY DIFFRACTION99
1.7574-1.78260.24411330.22392565X-RAY DIFFRACTION99
1.7826-1.80920.25111330.21422595X-RAY DIFFRACTION99
1.8092-1.83740.25631150.20522658X-RAY DIFFRACTION99
1.8374-1.86760.27691590.19722552X-RAY DIFFRACTION99
1.8676-1.89980.23671610.19682579X-RAY DIFFRACTION99
1.8998-1.93430.19181350.19262537X-RAY DIFFRACTION97
1.9343-1.97150.21541380.18922481X-RAY DIFFRACTION94
1.9715-2.01180.22631270.19012607X-RAY DIFFRACTION98
2.0118-2.05550.22081440.19362601X-RAY DIFFRACTION99
2.0555-2.10330.21051480.18722606X-RAY DIFFRACTION99
2.1033-2.15590.21581630.18282598X-RAY DIFFRACTION99
2.1559-2.21420.23711500.17532600X-RAY DIFFRACTION99
2.2142-2.27940.20151480.17262619X-RAY DIFFRACTION99
2.2794-2.3530.23841560.18172583X-RAY DIFFRACTION100
2.353-2.43710.21221530.1732624X-RAY DIFFRACTION99
2.4371-2.53460.19151570.17472610X-RAY DIFFRACTION99
2.5346-2.650.1881290.17632613X-RAY DIFFRACTION100
2.65-2.78970.20591280.17332646X-RAY DIFFRACTION100
2.7897-2.96450.17951440.17372623X-RAY DIFFRACTION100
2.9645-3.19340.19441460.17462645X-RAY DIFFRACTION100
3.1934-3.51470.19691200.16832662X-RAY DIFFRACTION99
3.5147-4.02320.19891230.15672591X-RAY DIFFRACTION98
4.0232-5.06850.1621050.14682715X-RAY DIFFRACTION100
5.0685-61.80860.14451460.15132673X-RAY DIFFRACTION100

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