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- PDB-5e3x: Crystal structure of thermostable Carboxypeptidase (FisCP) from F... -

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Basic information

Entry
Database: PDB / ID: 5e3x
TitleCrystal structure of thermostable Carboxypeptidase (FisCP) from Fervidobacterium Islandicum AW-1
ComponentsThermostable carboxypeptidase 1
KeywordsHYDROLASE / Carboxypeptidase / Fervidobacterium / FisCP
Function / homology
Function and homology information


carboxypeptidase Taq / metallocarboxypeptidase activity / proteolysis / metal 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
: / Metal-dependent carboxypeptidase
Similarity search - Component
Biological speciesFervidobacterium islandicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.197 Å
AuthorsDhanasingh, I. / Lee, Y.-J. / Lee, D.W. / Lee, S.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Biochemical and structural characterization of a keratin-degrading M32 carboxypeptidase from Fervidobacterium islandicum AW-1
Authors: Lee, Y.-J. / Dhanasingh, I. / Ahn, J.-S. / Jin, H.-S. / Choi, J.M. / Lee, S.H. / Lee, D.-W.
History
DepositionOct 5, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thermostable carboxypeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3752
Polymers57,3161
Non-polymers591
Water5,747319
1
A: Thermostable carboxypeptidase 1
hetero molecules

A: Thermostable carboxypeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7504
Polymers114,6322
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3180 Å2
ΔGint-33 kcal/mol
Surface area40180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.105, 56.757, 89.183
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Thermostable carboxypeptidase 1


Mass: 57316.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fervidobacterium islandicum (bacteria) / Strain: AW-1 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A140UHP3*PLUS
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE OF THE PROTEIN HAS BEEN DEPOSITED TO NCBI WITH ACCESSION NUMBER WP_033190981.1.

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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: 2.38 Å3/Da / Density % sol: 48.3 % / Description: Hexagonal planar
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10%PEG1000 10%PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 26, 2015
RadiationMonochromator: DCM Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.197→50 Å / Num. obs: 28236 / % possible obs: 99.7 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.62
Reflection shellResolution: 2.197→2.275 Å / % possible all: 98.94

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
Cootmodel building
HKL-2000data processing
MOLREPphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WGZ

1wgz
PDB Unreleased entry


Resolution: 2.197→33.324 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1419 5.04 %RANDOM
Rwork0.1772 ---
obs0.1804 28138 98.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.197→33.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4052 0 1 319 4372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074157
X-RAY DIFFRACTIONf_angle_d1.0375619
X-RAY DIFFRACTIONf_dihedral_angle_d14.81566
X-RAY DIFFRACTIONf_chiral_restr0.074589
X-RAY DIFFRACTIONf_plane_restr0.004716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1968-2.27530.3181340.23152447X-RAY DIFFRACTION92
2.2753-2.36640.28571320.22032678X-RAY DIFFRACTION100
2.3664-2.47410.28881410.20372636X-RAY DIFFRACTION100
2.4741-2.60450.30061420.20442655X-RAY DIFFRACTION100
2.6045-2.76760.26991220.19342679X-RAY DIFFRACTION100
2.7676-2.98110.29491720.1962669X-RAY DIFFRACTION100
2.9811-3.28090.24751430.18572692X-RAY DIFFRACTION100
3.2809-3.75510.20841380.15962716X-RAY DIFFRACTION100
3.7551-4.72890.20151490.14382740X-RAY DIFFRACTION100
4.7289-33.32760.20641460.16882807X-RAY DIFFRACTION98

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