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- PDB-7v5l: Crystal structure of human bleomycin hydrolase -

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Basic information

Entry
Database: PDB / ID: 7v5l
TitleCrystal structure of human bleomycin hydrolase
ComponentsBleomycin hydrolase
KeywordsHYDROLASE / cysteine protease
Function / homology
Function and homology information


bleomycin hydrolase / cysteine-type aminopeptidase activity / homocysteine catabolic process / aminopeptidase activity / cysteine-type peptidase 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 / aminopeptidase activity / cysteine-type peptidase 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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 17, 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
B: Bleomycin hydrolase
C: Bleomycin hydrolase
D: Bleomycin hydrolase


Theoretical massNumber of molelcules
Total (without water)219,1984
Polymers219,1984
Non-polymers00
Water26,5001471
1
A: Bleomycin hydrolase
B: Bleomycin hydrolase

A: Bleomycin hydrolase
B: Bleomycin hydrolase

A: Bleomycin hydrolase
B: Bleomycin hydrolase


Theoretical massNumber of molelcules
Total (without water)328,7976
Polymers328,7976
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area33870 Å2
ΔGint-147 kcal/mol
Surface area96730 Å2
MethodPISA
2
C: Bleomycin hydrolase
D: Bleomycin hydrolase

C: Bleomycin hydrolase
D: Bleomycin hydrolase

C: Bleomycin hydrolase
D: Bleomycin hydrolase


Theoretical massNumber of molelcules
Total (without water)328,7976
Polymers328,7976
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area33730 Å2
ΔGint-137 kcal/mol
Surface area96360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.944, 181.944, 166.307
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 54799.453 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1471 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M sodium chloride, 10% (w/v) PEG 8000, 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: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→30 Å / Num. obs: 209843 / % possible obs: 99.7 % / Redundancy: 4.7 % / CC1/2: 0.99 / Net I/σ(I): 22.9
Reflection shellResolution: 1.74→1.8 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 21057 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CB5

1cb5


Resolution: 1.74→29.47 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.106 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 10468 5 %RANDOM
Rwork0.1654 ---
obs0.1671 198839 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.49 Å2 / Biso mean: 20.264 Å2 / Biso min: 10.71 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.74→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14680 0 0 1479 16159
Biso mean---28.52 -
Num. residues----1808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01315056
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714073
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.64220357
X-RAY DIFFRACTIONr_angle_other_deg1.4111.58132469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22851806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5523.06830
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.937152675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4481581
X-RAY DIFFRACTIONr_chiral_restr0.0790.21869
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217047
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023555
LS refinement shellResolution: 1.74→1.785 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 744 -
Rwork0.223 14212 -
all-14956 -
obs--96.3 %

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