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

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Basic information

Entry
Database: PDB / ID: 6pic
TitleCrystal structure of Marinobacter subterrani acetylpolyamine amidohydrolase (msAPAH) complexed with 6-amino-N-hydroxyhexanamide
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
6-amino-N-hydroxyhexanamide / : / Acetoin utilization deacetylase AcuC
Similarity search - Component
Biological speciesMarinobacter subterrani (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.031 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,35748
Polymers303,8448
Non-polymers2,51340
Water11,602644
1
A: Acetylpolyamine Amidohydrolase
hetero molecules

C: Acetylpolyamine Amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,58912
Polymers75,9612
Non-polymers62810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area5470 Å2
ΔGint-47 kcal/mol
Surface area21800 Å2
MethodPISA
2
B: Acetylpolyamine Amidohydrolase
hetero molecules

H: Acetylpolyamine Amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,58912
Polymers75,9612
Non-polymers62810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area5430 Å2
ΔGint-47 kcal/mol
Surface area21630 Å2
MethodPISA
3
D: Acetylpolyamine Amidohydrolase
hetero molecules

F: Acetylpolyamine Amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,58912
Polymers75,9612
Non-polymers62810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area5410 Å2
ΔGint-47 kcal/mol
Surface area22050 Å2
MethodPISA
4
E: Acetylpolyamine Amidohydrolase
hetero molecules

G: Acetylpolyamine Amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,58912
Polymers75,9612
Non-polymers62810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_465x-1,y+1,z1
Buried area5380 Å2
ΔGint-47 kcal/mol
Surface area21760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.340, 67.040, 167.531
Angle α, β, γ (deg.)90.00, 90.00, 92.60
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Acetylpolyamine Amidohydrolase


Mass: 37980.547 Da / Num. of mol.: 8
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, 684 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-6XA / 6-amino-N-hydroxyhexanamide


Mass: 146.188 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 2.45 Å3/Da / Density % sol: 49.79 % / Description: 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: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.03→66.97 Å / Num. obs: 154543 / % possible obs: 85.91 % / Redundancy: 1.9 % / Rpim(I) all: 0.158 / Net I/σ(I): 4.4
Reflection shellResolution: 2.03→2.07 Å / Num. unique obs: 15944 / Rpim(I) all: 0.403

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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: 2.031→51.973 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.51
RfactorNum. reflection% reflection
Rfree0.2471 7623 4.93 %
Rwork0.2195 --
obs0.2209 154540 83.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.031→51.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21097 0 112 645 21854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00321746
X-RAY DIFFRACTIONf_angle_d0.73729530
X-RAY DIFFRACTIONf_dihedral_angle_d5.90114921
X-RAY DIFFRACTIONf_chiral_restr0.0543163
X-RAY DIFFRACTIONf_plane_restr0.0053929
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.031-2.05410.29113330.26135043X-RAY DIFFRACTION87
2.0541-2.07830.34392740.30645009X-RAY DIFFRACTION85
2.0783-2.10360.30472670.26295017X-RAY DIFFRACTION86
2.1036-2.13020.29452830.24414982X-RAY DIFFRACTION85
2.1302-2.15830.27312250.24115032X-RAY DIFFRACTION84
2.1583-2.18780.27252770.23254864X-RAY DIFFRACTION84
2.1878-2.21910.27442650.2314934X-RAY DIFFRACTION83
2.2191-2.25220.30332420.284690X-RAY DIFFRACTION80
2.2522-2.28740.32832850.30614517X-RAY DIFFRACTION77
2.2874-2.32490.25642220.23134053X-RAY DIFFRACTION69
2.3249-2.3650.23632790.22074817X-RAY DIFFRACTION82
2.365-2.4080.24862540.2175171X-RAY DIFFRACTION87
2.408-2.45430.26912390.21985131X-RAY DIFFRACTION87
2.4543-2.50440.25122490.22295102X-RAY DIFFRACTION87
2.5044-2.55890.25292170.22255137X-RAY DIFFRACTION86
2.5589-2.61840.24392420.22084927X-RAY DIFFRACTION83
2.6184-2.68390.26012870.22484846X-RAY DIFFRACTION83
2.6839-2.75640.23042680.22384735X-RAY DIFFRACTION80
2.7564-2.83750.23312280.22224097X-RAY DIFFRACTION71
2.8375-2.92910.23812590.21584977X-RAY DIFFRACTION84
2.9291-3.03380.24813070.21985089X-RAY DIFFRACTION87
3.0338-3.15520.25232710.22795119X-RAY DIFFRACTION87
3.1552-3.29880.20812260.21875057X-RAY DIFFRACTION85
3.2988-3.47270.27071900.22775070X-RAY DIFFRACTION85
3.4727-3.69020.26852460.22024444X-RAY DIFFRACTION75
3.6902-3.97510.20572410.20065026X-RAY DIFFRACTION85
3.9751-4.37490.18372180.17295278X-RAY DIFFRACTION88
4.3749-5.00750.17372320.15725058X-RAY DIFFRACTION86
5.0075-6.30720.20582680.18164623X-RAY DIFFRACTION79
6.3072-51.970.17842290.17755072X-RAY DIFFRACTION85
Refinement TLS params.Method: refined / Origin x: 55.138 Å / Origin y: -21.0913 Å / Origin z: 20.6044 Å
111213212223313233
T0.0558 Å2-0.0114 Å20.0015 Å2-0.0649 Å2-0.018 Å2--0.077 Å2
L0.0079 °2-0.0048 °2-0.0064 °2-0.0044 °2-0.003 °2---0.0027 °2
S0.006 Å °-0.0047 Å °-0.0063 Å °0.001 Å °-0.0002 Å °-0.0097 Å °0.0019 Å °-0.0053 Å °-0.0073 Å °
Refinement TLS groupSelection details: all

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