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- PDB-3men: Crystal structure of acetylpolyamine aminohydrolase from Burkhold... -

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Basic information

Entry
Database: PDB / ID: 3men
TitleCrystal structure of acetylpolyamine aminohydrolase from Burkholderia pseudomallei, iodide soak
ComponentsAcetylpolyamine aminohydrolase
KeywordsHYDROLASE / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / ACETYLPOLYAMINE AMINOHYDROLASE / HISTONE DEACETYLASE
Function / homology
Function and homology information


acetylputrescine deacetylase / acetylputrescine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / 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
IODIDE ION / : / Acetylpolyamine amidohydrolase
Similarity search - Component
Biological speciesBurkholderia pseudomallei 1710b (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: J Struct Funct Genomics / Year: 2011
Title: SAD phasing using iodide ions in a high-throughput structural genomics environment.
Authors: Abendroth, J. / Gardberg, A.S. / Robinson, J.I. / Christensen, J.S. / Staker, B.L. / Myler, P.J. / Stewart, L.J. / Edwards, T.E.
History
DepositionMar 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylpolyamine aminohydrolase
B: Acetylpolyamine aminohydrolase
C: Acetylpolyamine aminohydrolase
D: Acetylpolyamine aminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,33853
Polymers158,9024
Non-polymers5,43649
Water9,296516
1
A: Acetylpolyamine aminohydrolase
B: Acetylpolyamine aminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,23327
Polymers79,4512
Non-polymers2,78125
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-163 kcal/mol
Surface area22760 Å2
MethodPISA
2
C: Acetylpolyamine aminohydrolase
D: Acetylpolyamine aminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,10626
Polymers79,4512
Non-polymers2,65524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-161 kcal/mol
Surface area22480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.700, 162.120, 173.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 340
2116B1 - 340
3116C1 - 340
4116D1 - 340

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Acetylpolyamine aminohydrolase


Mass: 39725.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei 1710b (bacteria)
Strain: 1710B / Gene: aphA, BURPS1710b_1309 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3JUN4

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Non-polymers , 5 types, 565 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: I
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: EBS Wizard screen B1: 1.26M ammonium sulphate, 100mM cacodylate pH 6.5; protein at 7.9mg/ml; 1h soak in 1.4M ammonium sulphate, 100mM cacodylate pH 6.5, 200mM NaI, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 14, 2010 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 66538 / Num. obs: 65263 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.8 % / Biso Wilson estimate: 32.72 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 20.1
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4850 / % possible all: 84

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.915 / SU B: 11.943 / SU ML: 0.149 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.309 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3315 5.1 %RANDOM
Rwork0.179 ---
obs0.182 65263 98.1 %-
all-66538 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.25 Å2
Baniso -1Baniso -2Baniso -3
1-3.67 Å20 Å20 Å2
2---1.96 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10236 0 73 516 10825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02110600
X-RAY DIFFRACTIONr_bond_other_d0.0010.026924
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.92814472
X-RAY DIFFRACTIONr_angle_other_deg0.969316619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27951363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4422.375518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.026151378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3931593
X-RAY DIFFRACTIONr_chiral_restr0.0880.21519
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112402
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022435
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6731.56756
X-RAY DIFFRACTIONr_mcbond_other0.171.52755
X-RAY DIFFRACTIONr_mcangle_it1.2210656
X-RAY DIFFRACTIONr_scbond_it2.08633844
X-RAY DIFFRACTIONr_scangle_it3.2454.53811
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 4074 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.335
Bloose positional0.355
Cloose positional0.35
Dloose positional0.365
Aloose thermal3.0310
Bloose thermal2.0110
Cloose thermal2.810
Dloose thermal1.9310
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 206 -
Rwork0.228 3867 -
obs--84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2028-0.02620.00270.9279-0.04630.57870.00550.0371-0.03070.065-0.00340.06210.03820.0355-0.00220.007900.00360.0895-0.0010.088430.2919-1.552647.3872
20.2223-0.10930.36231.5358-0.59851.45690.0464-0.0316-0.0039-0.40430.0063-0.03090.46850.008-0.05270.39640.044-0.00020.1405-0.00920.061233.9256-9.98571.3617
30.41710.5494-0.08841.58810.12350.1246-0.07610.0258-0.0023-0.32190.054-0.01210.0070.0190.02210.18680.0176-0.02240.0759-0.00840.079833.5964-39.930231.9704
40.468-0.14180.14221.82510.63421.88880.00780.1025-0.0111-0.2950.0036-0.1389-0.28310.1442-0.01140.0685-0.00530.0150.13170.01280.095741.362426.677617.8248
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2C-10 - 9999
3X-RAY DIFFRACTION3B-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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