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- PDB-5d88: The Structure of the U32 Peptidase Mk0906 -

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Basic information

Entry
Database: PDB / ID: 5d88
TitleThe Structure of the U32 Peptidase Mk0906
ComponentsPredicted protease of the collagenase family
KeywordsHYDROLASE / U32 peptidase / TIM barrel
Function / homologyPeptidase U32 / Peptidase family U32 / Thiamin phosphate synthase superfamily / peptidase activity / metal ion binding / ACETATE ION / Predicted protease of the collagenase family
Function and homology information
Biological speciesMethanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.66 Å
AuthorsBaumann, U. / Schacherl, M. / Monatda, A.A.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: The first crystal structure of the peptidase domain of the U32 peptidase family.
Authors: Schacherl, M. / Montada, A.A. / Brunstein, E. / Baumann, U.
History
DepositionAug 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jul 20, 2016Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Predicted protease of the collagenase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5493
Polymers28,4251
Non-polymers1242
Water2,900161
1
A: Predicted protease of the collagenase family
hetero molecules

A: Predicted protease of the collagenase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0986
Polymers56,8492
Non-polymers2494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area3880 Å2
ΔGint-102 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.150, 79.150, 89.158
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-301-

ZN

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Components

#1: Protein Predicted protease of the collagenase family


Mass: 28424.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea) / Gene: MK0906 / Plasmid: pJExpress411 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8TWX5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.5 M NaOAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. obs: 73564 / % possible obs: 99.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 26.7 Å2 / Rsym value: 0.026 / Net I/σ(I): 29.7
Reflection shellResolution: 1.66→1.76 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 3.1 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.10-2131refinement
XDSdata reduction
XDSdata scaling
PHENIX1.8phasing
RefinementMethod to determine structure: SAD / Resolution: 1.66→39.56 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.152 1466 2 %Random
Rwork0.133 ---
obs0.133 73545 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.66→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1950 0 5 161 2116
LS refinement shellResolution: 1.66→1.72 Å
RfactorNum. reflection% reflection
Rfree0.274 147 2 %
Rwork0.215 7163 -
obs--98 %

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