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- PDB-5t69: The HhoA protease from Synechocystis sp. PCC 6803, active site mutant -

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Basic information

Entry
Database: PDB / ID: 5t69
TitleThe HhoA protease from Synechocystis sp. PCC 6803, active site mutant
ComponentsPutative 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
ACETATE ION / Putative serine protease HhoA
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5703
Polymers38,4871
Non-polymers832
Water77543
1
A: Putative serine protease HhoA
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)231,41918
Polymers230,9196
Non-polymers50012
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_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area11840 Å2
ΔGint-39 kcal/mol
Surface area74190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.276, 134.276, 115.290
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-402-

MG

21A-502-

HOH

31A-533-

HOH

41A-536-

HOH

51A-543-

HOH

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Components

#1: Protein Putative serine protease HhoA


Mass: 38486.520 Da / Num. of mol.: 1 / Mutation: S237A
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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#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.: 43 / 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: 52.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M Na acetate pH 5.0 0.2 M Mgcl2 30% pentaerythriol propoxylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97717 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97717 Å / Relative weight: 1
ReflectionResolution: 2.1→81.88 Å / Num. obs: 23412 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 52.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.021 / Rrim(I) all: 0.072 / Net I/σ(I): 17.9 / Num. measured all: 267159 / Scaling rejects: 169
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
2.1-2.1611.90.7952245918920.8550.2370.833.4100
8.91-81.88100.06834163420.9870.0230.07238.599.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.1.26data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PV3

3pv3


Resolution: 2.1→67.138 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2756 1204 5.14 %RANDOM
Rwork0.2408 22204 --
obs0.2425 23408 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.96 Å2 / Biso mean: 83.5594 Å2 / Biso min: 41.42 Å2
Refinement stepCycle: final / Resolution: 2.1→67.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 5 43 2122
Biso mean--115.5 71.52 -
Num. residues----284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092099
X-RAY DIFFRACTIONf_angle_d0.9332856
X-RAY DIFFRACTIONf_chiral_restr0.061353
X-RAY DIFFRACTIONf_plane_restr0.007380
X-RAY DIFFRACTIONf_dihedral_angle_d9.0961269
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0997-2.18380.36211410.349824282569
2.1838-2.28320.37551140.349824602574
2.2832-2.40360.34421360.355824352571
2.4036-2.55420.40941500.340624322582
2.5542-2.75140.34931450.310424422587
2.7514-3.02830.34171220.302424692591
3.0283-3.46650.29841130.268125072620
3.4665-4.36730.28331470.212124652612
4.3673-67.17230.19741360.18625662702
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)
19.3226-2.32511.17297.4008-0.64621.55-0.27530.2181-0.2886-0.08240.5475-1.17410.23310.2838-0.28110.4990.0710.07110.5403-0.26980.6219.7028-4.310726.92
27.1737-3.9537-4.15883.91314.04974.5711.71851.24720.1109-1.8356-0.824-0.4549-1.8876-0.6521-0.50491.08040.33490.0110.63790.01310.545325.193826.568844.2728
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

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