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- PDB-2cb5: HUMAN BLEOMYCIN HYDROLASE, C73S/DELE455 MUTANT -

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Basic information

Entry
Database: PDB / ID: 2cb5
TitleHUMAN BLEOMYCIN HYDROLASE, C73S/DELE455 MUTANT
ComponentsPROTEIN (BLEOMYCIN HYDROLASE)
KeywordsHYDROLASE / AMINOPEPTIDASE / CYSTEINE PROTEASE / SELF-COMPARTMENTALIZING / BLEOMYCIN / CYLINASE
Function / homology
Function and homology information


bleomycin hydrolase / cysteine-type aminopeptidase activity / homocysteine catabolic process / aminopeptidase activity / carboxypeptidase activity / cysteine-type peptidase 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 / carboxypeptidase activity / cysteine-type peptidase 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 proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsO'Farrell, P.A. / Gonzalez, F. / Zheng, W. / Johnston, S.A. / Joshua-Tor, L.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structure of human bleomycin hydrolase, a self-compartmentalizing cysteine protease.
Authors: O'Farrell, P.A. / Gonzalez, F. / Zheng, W. / Johnston, S.A. / Joshua-Tor, L.
History
DepositionMar 2, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Nov 3, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 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: PROTEIN (BLEOMYCIN HYDROLASE)
B: PROTEIN (BLEOMYCIN HYDROLASE)


Theoretical massNumber of molelcules
Total (without water)104,6552
Polymers104,6552
Non-polymers00
Water10,160564
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN (BLEOMYCIN HYDROLASE)
x 6


Theoretical massNumber of molelcules
Total (without water)313,9666
Polymers313,9666
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
crystal symmetry operation4_645y+1,x-1,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_765-x+2,-x+y+1,-z1
Buried area33360 Å2
ΔGint-158 kcal/mol
Surface area96280 Å2
MethodPISA, PQS
3
B: PROTEIN (BLEOMYCIN HYDROLASE)
x 6


Theoretical massNumber of molelcules
Total (without water)313,9666
Polymers313,9666
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
crystal symmetry operation10_545y+2/3,x-2/3,-z+1/31
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
crystal symmetry operation12_765-x+8/3,-x+y+4/3,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)179.512, 179.512, 164.148
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (1, -1.9E-5, -1.7E-5), (-1.9E-5, -1, -3.0E-6), (-1.7E-5, 3.0E-6, -1)
Vector: -0.00192, 0.00322, 0.00266)

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Components

#1: Protein PROTEIN (BLEOMYCIN HYDROLASE)


Mass: 52327.672 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Plasmid: PKH260HUBH-C73SDELE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/PLYSS
References: UniProt: Q13867, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growpH: 8 / Details: pH 8.00
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
225 mMTris-HCl1drop
35 %glycerol1drop
4140 mM1dropKCl
51 mMdithiothreitol1drop
616-20 %PEG100001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.115
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115 Å / Relative weight: 1
ReflectionResolution: 1.85→100 Å / Num. obs: 77497 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 14.9 Å2 / Rsym value: 8.2 / Net I/σ(I): 20.3
Reflection shellResolution: 1.85→1.97 Å / % possible all: 86.8
Reflection
*PLUS
% possible obs: 89.9 % / Num. measured all: 317648 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 86.8 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GCB

1gcb


Resolution: 1.85→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high rms absF: 1848617.65 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 383-385 LIE IN A LOOP REGION FOR WHICH THE DENSITY IS DIFFICULT TO INTERPRET. THEY HAVE BEEN MODELED, BUT OCCUPANCY HAS BEEN SET TO ZERO FOR NON-MAINCHAIN ATOMS. OCCUPANCY HAS ALSO ...Details: RESIDUES 383-385 LIE IN A LOOP REGION FOR WHICH THE DENSITY IS DIFFICULT TO INTERPRET. THEY HAVE BEEN MODELED, BUT OCCUPANCY HAS BEEN SET TO ZERO FOR NON-MAINCHAIN ATOMS. OCCUPANCY HAS ALSO BEEN SET TO ZERO FOR SOME SIDE-CHAIN ATOMS ON THE PROTEIN SURFACE.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 3698 4.8 %RANDOM
Rwork0.182 ---
obs0.182 77497 89.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.44 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1--4.09 Å20.42 Å20 Å2
2---4.09 Å20 Å2
3---8.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7348 0 0 564 7912
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.243 592 4.8 %
Rwork0.212 11782 -
obs--86.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95

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