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- PDB-6sj1: Amidohydrolase, AHS -

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Basic information

Entry
Database: PDB / ID: 6sj1
TitleAmidohydrolase, AHS
ComponentsAmidohydrolase
KeywordsHYDROLASE / PaaK like ligase / ligase
Function / homologyhydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase / metal ion binding / Amidohydrolase
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsNaismith, J.H. / Song, H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: The Biosynthesis of the Benzoxazole in Nataxazole Proceeds via an Unstable Ester and has Synthetic Utility.
Authors: Song, H. / Rao, C. / Deng, Z. / Yu, Y. / Naismith, J.H.
History
DepositionAug 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amidohydrolase
B: Amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9324
Polymers112,8012
Non-polymers1312
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-109 kcal/mol
Surface area32850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.610, 54.510, 141.540
Angle α, β, γ (deg.)90.000, 111.870, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 1 - 493 / Label seq-ID: 26 - 518

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Amidohydrolase


Mass: 56400.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: natAM, CF54_07360 / Production host: Streptomyces albus (bacteria) / References: UniProt: A0A022MQ12
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.05 M MgCl2, 0.1 M HEPES pH 7.5 and 30% v/v polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.2818 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2818 Å / Relative weight: 1
ReflectionResolution: 2.06→67.36 Å / Num. obs: 59518 / % possible obs: 99.5 % / Redundancy: 12.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.178 / Net I/σ(I): 11.6
Reflection shellResolution: 2.06→2.1 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.37 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3123 / CC1/2: 0.494 / % possible all: 96.5

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Processing

Software
NameVersionClassification
xia2data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SJ0

6sj0


Resolution: 2.06→67.36 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 11.623 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.17
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 3006 5.1 %RANDOM
Rwork0.1815 ---
obs0.1833 56511 99.45 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 143.39 Å2 / Biso mean: 30.408 Å2 / Biso min: 13.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å2-2.09 Å2
2---0.33 Å20 Å2
3---0.9 Å2
Refinement stepCycle: final / Resolution: 2.06→67.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7471 0 2 236 7709
Biso mean--28.72 28.61 -
Num. residues----989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0137606
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177175
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.64110318
X-RAY DIFFRACTIONr_angle_other_deg1.2721.57516452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7695989
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.44119.68438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.665151223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.841594
X-RAY DIFFRACTIONr_chiral_restr0.060.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028809
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021737
Refine LS restraints NCS

Ens-ID: 1 / Number: 15267 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.06→2.114 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 226 -
Rwork0.336 4068 -
all-4294 -
obs--97.46 %
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)
10.4438-0.07650.58430.21140.01310.8751-0.05710.17890.0376-0.04260.00070.0179-0.04160.23810.05640.1211-0.0398-0.01780.11860.02480.0073-13.506-24.898115.139
20.348-0.01750.18530.1787-0.0070.3111-0.0211-0.00440.00540.01650.0223-0.00180.0048-0.0013-0.00120.11830.0024-0.01120.0368-0.00590.0187-12.3227-26.163950.27
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 494
2X-RAY DIFFRACTION2B0 - 494

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