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- PDB-6sj4: Amidohydrolase, AHS with substrate analog -

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Basic information

Entry
Database: PDB / ID: 6sj4
TitleAmidohydrolase, AHS with substrate analog
ComponentsAmidohydrolase
KeywordsHYDROLASE / Amidohydrolase / AHS with substrate analog
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / metal ion binding
Similarity search - Function
Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
3-(3-hydroxyphenyl)carbonyloxybenzoic acid / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Amidohydrolase
Similarity search - Component
Biological speciesStreptomyces sp. Tu 6176 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsNaismith, J.H. / Song, H.
Citation
Journal: 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.
#1: Journal: To Be Published
Title: PaaK-ligase with ANP
Authors: Song, H. / 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)113,7679
Polymers112,8012
Non-polymers9667
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint-24 kcal/mol
Surface area32580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.320, 54.337, 139.844
Angle α, β, γ (deg.)90.000, 111.450, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Amidohydrolase


Mass: 56400.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. Tu 6176 (bacteria) / Gene: natAM, CF54_07360 / Production host: Streptomyces albus (bacteria) / References: UniProt: A0A022MQ12

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Non-polymers , 6 types, 335 molecules

#2: Chemical ChemComp-LFK / 3-(3-hydroxyphenyl)carbonyloxybenzoic acid


Mass: 258.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H10O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 45.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M MgCl2, 0.1 M Bis-Tris pH 6.5 and 25% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.81→65.08 Å / Num. obs: 86621 / % possible obs: 100 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.5
Reflection shellResolution: 1.81→1.84 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.087 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4510 / CC1/2: 0.587 / % possible all: 100

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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: 6JS0

6js0
PDB Unreleased entry


Resolution: 1.81→65.08 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.877 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.12
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2097 4215 4.9 %RANDOM
Rwork0.1823 ---
obs0.1837 82384 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 96.74 Å2 / Biso mean: 35.811 Å2 / Biso min: 18.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å2-2.43 Å2
2---0.53 Å20 Å2
3---1.23 Å2
Refinement stepCycle: final / Resolution: 1.81→65.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7465 0 61 328 7854
Biso mean--53.82 34.94 -
Num. residues----989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137723
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177282
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.64810478
X-RAY DIFFRACTIONr_angle_other_deg1.3661.57816701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91251005
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.83119.616443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.822151237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7961596
X-RAY DIFFRACTIONr_chiral_restr0.0730.2988
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028957
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021775
LS refinement shellResolution: 1.81→1.857 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 290 -
Rwork0.355 6039 -
all-6329 -
obs--99.78 %
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)
10.9603-0.04540.56740.6350.19371.1996-0.02070.30830.1296-0.28360.0114-0.0742-0.08450.1180.00930.1855-0.02780.09560.19470.04350.1135-13.3836-25.920614.8027
20.5327-0.01310.2140.7201-0.07590.7507-0.0299-0.00720.026-0.00720.049-0.0994-0.01350.003-0.01910.0161-0.00480.02990.0248-0.01660.0805-11.6102-27.137249.8006
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 601
2X-RAY DIFFRACTION2B0 - 701

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