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- PDB-5t63: The HhoA protease from Synechocystis sp. PCC 6803 -

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Basic information

Entry
Database: PDB / ID: 5t63
TitleThe HhoA protease from Synechocystis sp. PCC 6803
Components
  • ALA-ALA-ALA-ALA
  • Putative serine protease HhoA
KeywordsHYDROLASE / protease / PDZ domain
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / serine-type endopeptidase activity / proteolysis / identical protein binding
Similarity search - Function
: / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / Thrombin, subunit H - #120 / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain ...: / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / Thrombin, subunit H - #120 / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin / Thrombin, subunit H / Roll / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Putative serine protease HhoA
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPersson, K. / Hall, M. / Funk, C.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Energy Agency2012-005889 Sweden
Formas2013-2014-1504 Sweden
Swedish Research Council Sweden
CitationJournal: J. Struct. Biol. / Year: 2017
Title: The HhoA protease from Synechocystis sp. PCC 6803 - Novel insights into structure and activity regulation.
Authors: Hall, M. / Wagner, R. / Lam, X.T. / Funk, C. / Persson, K.
History
DepositionSep 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative serine protease HhoA
C: ALA-ALA-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8293
Polymers38,8052
Non-polymers241
Water70339
1
A: Putative serine protease HhoA
C: ALA-ALA-ALA-ALA
hetero molecules

A: Putative serine protease HhoA
C: ALA-ALA-ALA-ALA
hetero molecules

A: Putative serine protease HhoA
C: ALA-ALA-ALA-ALA
hetero molecules

A: Putative serine protease HhoA
C: ALA-ALA-ALA-ALA
hetero molecules

A: Putative serine protease HhoA
C: ALA-ALA-ALA-ALA
hetero molecules

A: Putative serine protease HhoA
C: ALA-ALA-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,97518
Polymers232,82912
Non-polymers1466
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Unit cell
Length a, b, c (Å)134.228, 134.228, 115.063
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-401-

MG

21A-503-

HOH

31A-529-

HOH

41A-539-

HOH

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Components

#1: Protein Putative serine protease HhoA


Mass: 38502.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Gene: hhoA, sll1679 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P72780
#2: Protein/peptide ALA-ALA-ALA-ALA


Mass: 302.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Peptide found in the active site / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.6 Å3/Da / Density % sol: 29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Na-acetate pH5.0, 0.2 M MgCl2, 30% pentaerythriol propoxylate (17/8)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.5→51.88 Å / Num. obs: 13940 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 66.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.021 / Rrim(I) all: 0.055 / Net I/σ(I): 20.5 / Num. measured all: 93929
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.66.90.7151076615610.7880.2930.7742.8100
9.01-51.885.60.04318303280.9980.0190.04848.199.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3pv3

3pv3


Resolution: 2.5→51.562 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 655 4.7 %RANDOM
Rwork0.2175 13282 --
obs0.2195 13937 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.98 Å2 / Biso mean: 86.0173 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.5→51.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 1 39 2129
Biso mean--69.17 70.09 -
Num. residues----287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012108
X-RAY DIFFRACTIONf_angle_d1.2472868
X-RAY DIFFRACTIONf_chiral_restr0.066354
X-RAY DIFFRACTIONf_plane_restr0.007382
X-RAY DIFFRACTIONf_dihedral_angle_d13.746767
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.6930.3741290.345226222751
2.693-2.9640.33511400.304126242764
2.964-3.39290.33771240.2726392763
3.3929-4.27430.28731250.210226662791
4.2743-51.57310.20041370.177527312868
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.20260.7547-0.59538.24160.84452.56250.51970.60521.01170.4275-0.15130.1191-0.45140.0703-0.2550.53940.0010.13090.41160.22860.6725-6.140319.1901-31.2646
22.64461.3454-0.64458.9335-6.47774.463-0.56940.42070.5053-2.46111.55390.561.4781-1.152-0.65291.0744-0.3438-0.01310.608-0.01390.6607-35.53428.4597-13.4462
32.52911.3051-0.69432.5611-0.12690.5964-0.77270.4847-0.3457-0.7375-0.0556-1.45960.92330.28510.53310.8271-0.68190.8454-0.74280.52730.9412-27.50928.3864-16.0381
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 54 through 279 )A54 - 279
2X-RAY DIFFRACTION2chain 'A' and (resid 280 through 390 )A280 - 390
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 4 )C1 - 4

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