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- PDB-4xed: PKD domain of M14-like peptidase from Thermoplasmatales archaeon ... -

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Basic information

Entry
Database: PDB / ID: 4xed
TitlePKD domain of M14-like peptidase from Thermoplasmatales archaeon SCGC AB-540-F20
ComponentsPeptidase M14, carboxypeptidase A
KeywordsPROTEIN BINDING / single cell genomics / marine sediment / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


metallocarboxypeptidase activity / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Immune inhibitor A-like, MAM domain / Carboxypeptidase T / PKD domain / Zn_pept / PKD domain superfamily / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Immunoglobulin-like fold
Similarity search - Domain/homology
Peptidase M14, carboxypeptidase A
Similarity search - Component
Biological speciesThermoplasmatales archaeon SCGC AB-540-F20 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.23 Å
AuthorsMichalska, K. / Joachimiak, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: To Be Published
Title: PKD domain of M14-like peptidase from Thermoplasmatales archaeon SCGC AB-540-F20
Authors: Michalska, K. / Joachimiak, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionDec 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / pdbx_validate_symm_contact / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase M14, carboxypeptidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2634
Polymers11,0991
Non-polymers1643
Water2,216123
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.186, 48.869, 78.509
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-281-

HOH

21A-283-

HOH

31A-287-

HOH

41A-304-

HOH

51A-305-

HOH

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Components

#1: Protein Peptidase M14, carboxypeptidase A


Mass: 11098.851 Da / Num. of mol.: 1 / Fragment: PKD domain residues 667-762
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasmatales archaeon SCGC AB-540-F20 (archaea)
Gene: MBGDF03_00742 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pGrow7-K / References: UniProt: M7U057
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 38.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2 M Ca acetate, 0.1 M Na acetate/acetic acid pH 4.5, 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2014 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.23→20 Å / Num. obs: 25859 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 12.81
Reflection shellResolution: 1.23→1.25 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.98 / % possible all: 89.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000phasing
HKL-3000data scaling
SBC-Collectdata collection
SHELXphasing
MLPHAREphasing
DMphasing
ARPmodel building
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.23→19.9 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.48 / Stereochemistry target values: ML
Details: HYDROGEN ATOMS HAVE BEEN ADDED IN RIDING POSITIONS, UNMODELED DENSITY NEAR THR89 POSSIBLY CORRESPONDS TO CALCIUM ION BUT DUE TO INCOMPLETE AND INCOSISTENT COORDINATION IT COULD NOT BE MODELED WITH CONFIDENCE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1687 1058 4.09 %random
Rwork0.1382 ---
obs0.1394 25851 98.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.23→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms769 0 9 123 901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012863
X-RAY DIFFRACTIONf_angle_d1.4351187
X-RAY DIFFRACTIONf_dihedral_angle_d12.94307
X-RAY DIFFRACTIONf_chiral_restr0.087124
X-RAY DIFFRACTIONf_plane_restr0.009157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.23-1.28330.1951120.17472803X-RAY DIFFRACTION90
1.2833-1.3510.25871430.17633026X-RAY DIFFRACTION98
1.351-1.43560.20441390.15833107X-RAY DIFFRACTION99
1.4356-1.54640.19491200.14023119X-RAY DIFFRACTION100
1.5464-1.70190.16531330.13023127X-RAY DIFFRACTION100
1.7019-1.9480.14951360.11483152X-RAY DIFFRACTION100
1.948-2.45360.1491350.12083199X-RAY DIFFRACTION100
2.4536-19.90680.15831400.14413260X-RAY DIFFRACTION99

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