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- PDB-3hq2: BsuCP Crystal Structure -

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Basic information

Entry
Database: PDB / ID: 3hq2
TitleBsuCP Crystal Structure
ComponentsBacillus subtilis M32 carboxypeptidase
KeywordsHYDROLASE / Metal-binding / Metalloprotease / Protease / Zinc
Function / homology
Function and homology information


carboxypeptidase Taq / metallocarboxypeptidase activity / proteolysis / zinc ion binding
Similarity search - Function
Peptidase M32, carboxypeptidase Taq / Carboxypeptidase Taq (M32) metallopeptidase / Peptidase family M32 domain profile. / Neurolysin; domain 3 - #30 / Neurolysin; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FLUORIDE ION / PHOSPHATE ION / Carboxypeptidase 1
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLee, M.M. / Isaza, C.E. / White, J.D. / Chen, R.P.-Y. / Liang, G.F.-C. / He, H.T.-F. / Chan, S.I. / Chan, M.K.
CitationJournal: Proteins / Year: 2009
Title: Insight into the substrate length restriction of M32 carboxypeptidases: Characterization of two distinct subfamilies.
Authors: Lee, M.M. / Isaza, C.E. / White, J.D. / Chen, R.P. / Liang, G.F. / He, H.T. / Chan, S.I. / Chan, M.K.
History
DepositionJun 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacillus subtilis M32 carboxypeptidase
B: Bacillus subtilis M32 carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,40819
Polymers116,4932
Non-polymers91517
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Bacillus subtilis M32 carboxypeptidase
B: Bacillus subtilis M32 carboxypeptidase
hetero molecules

A: Bacillus subtilis M32 carboxypeptidase
B: Bacillus subtilis M32 carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,81538
Polymers232,9854
Non-polymers1,83034
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-11
Buried area11380 Å2
ΔGint-706 kcal/mol
Surface area74210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.957, 149.002, 217.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-506-

ZN

21A-507-

CL

31A-510-

CL

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bacillus subtilis M32 carboxypeptidase


Mass: 58246.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU22080, ypwA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3
References: UniProt: P50848, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 5 types, 245 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M NH4F, 32% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.2834 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2834 Å / Relative weight: 1
ReflectionResolution: 2.9→43.37 Å / Num. obs: 31847 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.4 / Redundancy: 4.88 % / Biso Wilson estimate: 46.1 Å2 / Rmerge(I) obs: 0.1876
Reflection shellResolution: 2.9→3.08 Å / Rmerge(I) obs: 0.302 / Num. unique all: 4424 / % possible all: 92.5

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Processing

Software
NameClassification
Blu-Icedata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→43.37 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 31393 -random
Rwork0.1879 ---
obs0.1879 31624 96.6 %-
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.43 Å20 Å20 Å2
2--0.58 Å20 Å2
3---4.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.9→43.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8158 0 25 228 8411
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_mcbond_it0.012
X-RAY DIFFRACTIONc_dihedral_angle_d19.5
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2.9→3.08 Å
RfactorNum. reflection% reflection
Rfree0.351 442 -
Rwork0.302 --
obs-4866 92.5 %

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