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- PDB-7v5s: Crystal structure of human bleomycin hydrolase C73A mutant -

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Basic information

Entry
Database: PDB / ID: 7v5s
TitleCrystal structure of human bleomycin hydrolase C73A mutant
ComponentsBleomycin hydrolase
KeywordsHYDROLASE / cysteine protease
Function / homology
Function and homology information


bleomycin hydrolase / cysteine-type aminopeptidase activity / homocysteine catabolic process / cysteine-type peptidase activity / aminopeptidase activity / carboxypeptidase activity / response to toxic substance / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / response to xenobiotic stimulus ...bleomycin hydrolase / cysteine-type aminopeptidase activity / homocysteine catabolic process / cysteine-type peptidase activity / aminopeptidase activity / carboxypeptidase activity / response to toxic substance / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / response to xenobiotic stimulus / cysteine-type endopeptidase activity / proteolysis / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Peptidase C1B, bleomycin hydrolase / Peptidase C1-like family / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Bleomycin hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsChang, C.Y. / Zheng, Y.Z. / Huang, S.J. / Wang, Y.L. / Toh, S.I. / Lin, E.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)110-2113-M-A49 -026 -MY3 Taiwan
CitationJournal: Chembiochem / Year: 2022
Title: The Structure-Function Relationship of Human Bleomycin Hydrolase: Mutation of a Cysteine Protease into a Serine Protease.
Authors: Zheng, Y.Z. / Cui, J. / Wang, Y.L. / Huang, S.J. / Lin, E.C. / Huang, S.C. / Rudolf, J.D. / Yan, X. / Chang, C.Y.
History
DepositionAug 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bleomycin hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1123
Polymers54,7671
Non-polymers3442
Water34219
1
A: Bleomycin hydrolase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)330,67118
Polymers328,6046
Non-polymers2,06612
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation14_444-y-1/4,-x-1/4,-z-1/41
crystal symmetry operation19_444-x-1/4,-z-1/4,-y-1/41
crystal symmetry operation24_444-z-1/4,-y-1/4,-x-1/41
Buried area38810 Å2
ΔGint-84 kcal/mol
Surface area95780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)318.269, 318.269, 318.269
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein Bleomycin hydrolase / / BH / BLM hydrolase / BMH


Mass: 54767.387 Da / Num. of mol.: 1 / Mutation: C73A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLMH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13867, bleomycin hydrolase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 12.26 Å3/Da / Density % sol: 89.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30% (w/v) PEG 400, 0.1mM CHES, pH 9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9732 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9732 Å / Relative weight: 1
ReflectionResolution: 3.02→30 Å / Num. obs: 53491 / % possible obs: 100 % / Redundancy: 11.3 % / CC1/2: 0.98 / Net I/σ(I): 14.2
Reflection shellResolution: 3.02→3.13 Å / Redundancy: 11.9 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5272 / CC1/2: 0.865 / % possible all: 100

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V5L

7v5l


Resolution: 3.02→29.83 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.095 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1972 2641 4.9 %RANDOM
Rwork0.18 ---
obs0.1808 50745 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.08 Å2 / Biso mean: 63.93 Å2 / Biso min: 39.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 3.02→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3684 0 23 19 3726
Biso mean--109.69 53.37 -
Num. residues----454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133796
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173556
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.6425123
X-RAY DIFFRACTIONr_angle_other_deg1.2871.5818208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8575453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39623.125208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.09715670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1631520
X-RAY DIFFRACTIONr_chiral_restr0.0690.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024275
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02889
LS refinement shellResolution: 3.023→3.101 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 186 -
Rwork0.332 3618 -
all-3804 -
obs--98.83 %

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