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- PDB-5gnd: Structure of Deg protease HhoA from Synechocystis sp. PCC 6803 -

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Basic information

Entry
Database: PDB / ID: 5gnd
TitleStructure of Deg protease HhoA from Synechocystis sp. PCC 6803
Components
  • Putative serine protease HhoA
  • UNK-UNK-UNK-UNK-TRP
KeywordsHYDROLASE / Serine Protease
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 BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDong, W. / Wang, J. / Liu, L.
CitationJournal: Febs Lett. / Year: 2016
Title: Crystal structure of the zinc-bound HhoA protease from Synechocystis sp. PCC 6803
Authors: Dong, W. / Wang, J. / Niu, G. / Zhao, S. / Liu, L.
History
DepositionJul 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Nov 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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

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Assembly

Deposited unit
A: Putative serine protease HhoA
U: UNK-UNK-UNK-UNK-TRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5024
Polymers37,4132
Non-polymers882
Water1,15364
1
A: Putative serine protease HhoA
U: UNK-UNK-UNK-UNK-TRP
hetero molecules

A: Putative serine protease HhoA
U: UNK-UNK-UNK-UNK-TRP
hetero molecules

A: Putative serine protease HhoA
U: UNK-UNK-UNK-UNK-TRP
hetero molecules

A: Putative serine protease HhoA
U: UNK-UNK-UNK-UNK-TRP
hetero molecules

A: Putative serine protease HhoA
U: UNK-UNK-UNK-UNK-TRP
hetero molecules

A: Putative serine protease HhoA
U: UNK-UNK-UNK-UNK-TRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,01024
Polymers224,48012
Non-polymers53012
Water21612
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
Unit cell
Length a, b, c (Å)135.219, 135.219, 113.754
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-501-

ZN

21A-502-

NA

31A-618-

HOH

41A-628-

HOH

51A-658-

HOH

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Components

#1: Protein Putative serine protease HhoA


Mass: 36868.691 Da / Num. of mol.: 1 / Fragment: UNP residues 56-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa / Gene: hhoA / Plasmid: pET-22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P72780
#2: Protein/peptide UNK-UNK-UNK-UNK-TRP


Mass: 544.644 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: This peptide is a co-purified peptide produced by Escherichia coli BL21(DE3).
Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M Na acetate, 25%(w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 13981 / % possible obs: 100 % / Redundancy: 11.1 % / Net I/σ(I): 59.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 2.9 / CC1/2: 0.807 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B6L

5b6l


Resolution: 2.5→37.92 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.72
RfactorNum. reflection% reflection
Rfree0.305 675 4.98 %
Rwork0.247 12882 -
obs0.25 13557 97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.32 Å2 / Biso mean: 37.37 Å2 / Biso min: 10.17 Å2
Refinement stepCycle: final / Resolution: 2.5→37.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 2 64 2127
Biso mean--24.76 35.09 -
Num. residues----285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052104
X-RAY DIFFRACTIONf_angle_d1.1282869
X-RAY DIFFRACTIONf_chiral_restr0.069349
X-RAY DIFFRACTIONf_plane_restr0.004383
X-RAY DIFFRACTIONf_dihedral_angle_d15.486759
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4999-2.69290.36241290.31212216234585
2.6929-2.96380.36531440.315726122756100
2.9638-3.39240.33381300.271726592789100
3.3924-4.27320.30451320.229526612793100
4.2732-37.92230.24971400.205727342874100
Refinement TLS params.Method: refined / Origin x: -18.9689 Å / Origin y: 14.4422 Å / Origin z: 32.6502 Å
111213212223313233
T0.0901 Å2-0.4821 Å20.3513 Å2--0.7035 Å20.5252 Å2---0.0705 Å2
L0.1803 °2-0.0145 °2-0.2369 °2-0.0543 °2-0.1895 °2--0.4555 °2
S0.235 Å °0.0913 Å °0.3615 Å °0.0309 Å °-0.3057 Å °0.348 Å °-0.0212 Å °-0.2937 Å °-0.0098 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA56 - 390
2X-RAY DIFFRACTION1ALLU95 - 99
3X-RAY DIFFRACTION1ALLA501 - 665
4X-RAY DIFFRACTION1ALLU101

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