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- PDB-8hmo: Crystal Structure of metal-dependent hydrolase complexed with man... -

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Basic information

Entry
Database: PDB / ID: 8hmo
TitleCrystal Structure of metal-dependent hydrolase complexed with manganese from Bacillus smithii
ComponentsMetal-dependent hydrolase
KeywordsHYDROLASE / Metal-dependent hydrolase / manganese
Function / homologyarylformamidase / Kynurenine formamidase/cyclase-like / Kynurenine formamidase superfamily / Putative cyclase / arylformamidase activity / L-tryptophan catabolic process to kynurenine / : / Metal-dependent hydrolase
Function and homology information
Biological speciesBacillus smithii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsYoneda, K. / Sakuraba, H. / Ohshima, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Crystal Structure of metal-dependent hydrolase complexed with manganese from Bacillus smithii
Authors: Yoneda, K. / Sakuraba, H. / Ohshima, T.
History
DepositionDec 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metal-dependent hydrolase
B: Metal-dependent hydrolase
C: Metal-dependent hydrolase
D: Metal-dependent hydrolase
E: Metal-dependent hydrolase
F: Metal-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,82418
Polymers144,1646
Non-polymers65912
Water5,927329
1
A: Metal-dependent hydrolase
B: Metal-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2756
Polymers48,0552
Non-polymers2204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-53 kcal/mol
Surface area17040 Å2
MethodPISA
2
C: Metal-dependent hydrolase
D: Metal-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2756
Polymers48,0552
Non-polymers2204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-54 kcal/mol
Surface area16580 Å2
MethodPISA
3
E: Metal-dependent hydrolase
F: Metal-dependent hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2756
Polymers48,0552
Non-polymers2204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-50 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.210, 70.198, 104.839
Angle α, β, γ (deg.)90.00, 105.77, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
Metal-dependent hydrolase


Mass: 24027.395 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus smithii (bacteria) / Gene: BSM4216_2453 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIPL / References: UniProt: A0A0H4P0S7, arylformamidase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 35% 2-ethoxyethanol, 0.1 M Na/K phosphate buffer pH 6.2, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryo (40% 2-ethoxyethanol) / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.53→44.91 Å / Num. obs: 41332 / % possible obs: 97.3 % / Redundancy: 3.3 % / CC1/2: 0.952 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.066 / Rrim(I) all: 0.121 / Χ2: 1.1 / Net I/σ(I): 8.2
Reflection shellResolution: 2.53→2.63 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4429 / CC1/2: 0.745 / Rpim(I) all: 0.343 / Rrim(I) all: 0.649 / Χ2: 0.84 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.53→43.45 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.889 / SU B: 17.12 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2987 2065 5 %RANDOM
Rwork0.2503 ---
obs0.2528 39259 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.175 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å20.09 Å2
2--0.02 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.53→43.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9573 0 12 329 9914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0139775
X-RAY DIFFRACTIONr_bond_other_d0.0030.0179395
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.64213248
X-RAY DIFFRACTIONr_angle_other_deg1.2491.58321775
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.83651218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32824.449472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.504151778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6191536
X-RAY DIFFRACTIONr_chiral_restr0.0760.21375
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210882
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021926
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_it3.1625.8684892
X-RAY DIFFRACTIONr_mcbond_other3.1575.8674891
X-RAY DIFFRACTIONr_mcangle_it5.1338.796104
X-RAY DIFFRACTIONr_mcangle_other5.1348.7916105
X-RAY DIFFRACTIONr_scbond_it3.1686.3264882
X-RAY DIFFRACTIONr_scbond_other3.1686.3284883
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2869.3167145
X-RAY DIFFRACTIONr_long_range_B_refined10.84671.20510614
X-RAY DIFFRACTIONr_long_range_B_other10.82971.17910605
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.53→2.596 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 162 -
Rwork0.327 2967 -
obs--99.87 %

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