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- PDB-5h6t: Crystal structure of Hydrazidase from Microbacterium sp. strain HM58-2 -

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Basic information

Entry
Database: PDB / ID: 5h6t
TitleCrystal structure of Hydrazidase from Microbacterium sp. strain HM58-2
ComponentsAmidase
KeywordsHYDROLASE / amidase
Function / homologyAmidase / Amidase, conserved site / Amidases signature. / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / amidase activity / Amidase
Function and homology information
Biological speciesMicrobacterium sp. HM58-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAkiyama, T. / Ishii, M. / Takuwa, A. / Oinuma, K. / Sasaki, Y. / Takaya, N. / Yajima, S.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural basis of the substrate recognition of hydrazidase isolated from Microbacterium sp. strain HM58-2, which catalyzes acylhydrazide compounds as its sole carbon source
Authors: Akiyama, T. / Ishii, M. / Takuwa, A. / Oinuma, K.I. / Sasaki, Y. / Takaya, N. / Yajima, S.
History
DepositionNov 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amidase
B: Amidase


Theoretical massNumber of molelcules
Total (without water)103,1302
Polymers103,1302
Non-polymers00
Water12,034668
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-11 kcal/mol
Surface area31740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.162, 128.068, 159.304
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Amidase


Mass: 51565.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbacterium sp. HM58-2 (bacteria) / Strain: HM58-2 / Gene: MHM582_3487 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A170QJP8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / 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: 3.02 Å3/Da / Density % sol: 59.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M imidazole, 0.17 M LiSO4, 2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 163385 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 47.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 8.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H0L

3h0l


Resolution: 1.6→33.97 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.997 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17809 8193 5 %RANDOM
Rwork0.16485 ---
obs0.16551 155116 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.388 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.5 Å20 Å2
3----0.51 Å2
Refinement stepCycle: 1 / Resolution: 1.6→33.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7040 0 0 668 7708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197190
X-RAY DIFFRACTIONr_bond_other_d0.0060.026782
X-RAY DIFFRACTIONr_angle_refined_deg1.391.9719785
X-RAY DIFFRACTIONr_angle_other_deg0.971315624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7955941
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.30822.928321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.285151145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3211579
X-RAY DIFFRACTIONr_chiral_restr0.0830.21122
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218207
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021460
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_it0.781.2923752
X-RAY DIFFRACTIONr_mcbond_other0.7791.2923751
X-RAY DIFFRACTIONr_mcangle_it1.2591.944691
X-RAY DIFFRACTIONr_mcangle_other1.2591.944692
X-RAY DIFFRACTIONr_scbond_it1.5321.5273438
X-RAY DIFFRACTIONr_scbond_other1.5321.5273439
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4012.2135093
X-RAY DIFFRACTIONr_long_range_B_refined3.39516.5417954
X-RAY DIFFRACTIONr_long_range_B_other3.33616.3557886
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.599→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.193 612 -
Rwork0.171 11223 -
obs--98.21 %

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