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- PDB-6kk8: XN joint refinement of manganese catalase from Thermus Thermophil... -

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Basic information

Entry
Database: PDB / ID: 6kk8
TitleXN joint refinement of manganese catalase from Thermus Thermophilus HB27
ComponentsPseudocatalase
KeywordsOXIDOREDUCTASE / Manganese catalase
Function / homology
Function and homology information


catalase / catalase activity / metal ion binding
Similarity search - Function
Manganese catalase / Manganese catalase, ferritin-like di-iron-binding domain / Manganese containing catalase / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DEUTERATED WATER / MANGANESE (III) ION / OXYGEN ATOM / Pseudocatalase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsYamada, T. / Yano, N. / Kusaka, K.
CitationJournal: J.Appl.Crystallogr. / Year: 2019
Title: Single-crystal time-of-flight neutron Laue methods: application to manganese catalase from Thermus thermophilus HB27
Authors: Yamada, T. / Yano, N. / Hosoya, T. / Kusaka, K.
History
DepositionJul 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pseudocatalase
B: Pseudocatalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,22615
Polymers66,6902
Non-polymers53613
Water4,954275
1
A: Pseudocatalase
B: Pseudocatalase
hetero molecules

A: Pseudocatalase
B: Pseudocatalase
hetero molecules

A: Pseudocatalase
B: Pseudocatalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,67945
Polymers200,0716
Non-polymers1,60839
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area48370 Å2
ΔGint-408 kcal/mol
Surface area43300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.396, 133.396, 133.396
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pseudocatalase


Mass: 33345.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C1872 / Plasmid: pMKE1
Details (production host): a gene inserted at NdeI, HindIII restriction sites
Production host: Thermus thermophilus HB27 (bacteria) / Strain (production host): HB27 / References: UniProt: Q72GH6, catalase

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Non-polymers , 5 types, 288 molecules

#2: Chemical
ChemComp-MN3 / MANGANESE (III) ION / Manganese


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: O
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: D2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.65 % / Description: final pD 8.2
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 1.95 M Ammonium Sulfate d-8, 14.5v/v% ethylenglycol, 50 mM AMPSO buffer pD 9.6. Drop: 32 mg/mL of manganese catalase was mixed with equal volume of Reservoir.

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22931N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-17A10.98
SPALLATION SOURCEJPARC MLF BL-03J-PARC MLF BEAMLINE BL-0323-6
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 6M1PIXELMar 20, 2017Focusing mirrors with rhodium coated silicon single crystal
2Dec 1, 2016Ni-Ti supermirror neutron guide Detector: iBIXDetector type: WSF PSD (Wavelength Shift Fiber Position Sensitive Detector)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooledSINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
231
361
Reflection

Biso Wilson estimate: 16.08 Å2 / Entry-ID: 6KK8

Resolution (Å)Num. obs% possible obs (%)Observed criterion σ(I)Redundancy (%)Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)
1.37-44.5164892100-39.80.0920.03125.7
2.349-14.43250998.2-35.20.3220.15124.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allDiffraction-ID% possible all
1.37-1.398.40.9561.881880.3651100
2.35-2.434.40.7421.4145240.381297

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
Coot0.8.9.1model building
Refinement

% reflection Rfree: 4.99 % / SU ML: 0.14 / R Free selection details: Random selection / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 13.28 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 2V8U

2v8u

/ Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection obs (%)Diffraction-IDσ(F)Details
1.37-44.465X-RAY DIFFRACTION0.13320.12220.1228823216481699.9811.33Unobserved atoms with zero occupancy were removed from the structure after the refinement.
2.349-14.384NEUTRON DIFFRACTION0.1910.15160.153616223249498.232-2
Refinement stepCycle: LAST / Resolution: 1.37→44.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4572 0 23 275 4870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710929
X-RAY DIFFRACTIONf_angle_d1.26119221
X-RAY DIFFRACTIONf_dihedral_angle_d18.3882903
X-RAY DIFFRACTIONf_chiral_restr0.23698
X-RAY DIFFRACTIONf_plane_restr0.0062111
NEUTRON DIFFRACTIONf_bond_d0.00710929
NEUTRON DIFFRACTIONf_angle_d1.26119221
NEUTRON DIFFRACTIONf_dihedral_angle_d18.3882903
NEUTRON DIFFRACTIONf_chiral_restr0.23698
NEUTRON DIFFRACTIONf_plane_restr0.0062111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3701-1.38560.31042740.30235185X-RAY DIFFRACTION100
1.3856-1.40190.28932720.26755205X-RAY DIFFRACTION100
1.4019-1.4190.24132690.24065224X-RAY DIFFRACTION100
1.419-1.4370.26782730.22345128X-RAY DIFFRACTION100
1.437-1.45590.21512660.20135167X-RAY DIFFRACTION100
1.4559-1.47580.22052730.18935206X-RAY DIFFRACTION100
1.4758-1.49690.19012740.17575154X-RAY DIFFRACTION100
1.4969-1.51930.19912730.16215211X-RAY DIFFRACTION100
1.5193-1.5430.17092710.15465200X-RAY DIFFRACTION100
1.543-1.56830.16062740.15645201X-RAY DIFFRACTION100
1.5683-1.59540.16972690.15015176X-RAY DIFFRACTION100
1.5954-1.62440.15842750.14245217X-RAY DIFFRACTION100
1.6244-1.65560.15082680.14025171X-RAY DIFFRACTION100
1.6556-1.68940.15172700.13865190X-RAY DIFFRACTION100
1.6894-1.72610.14442760.13045200X-RAY DIFFRACTION100
1.7261-1.76630.15282790.12655223X-RAY DIFFRACTION100
1.7663-1.81050.15392780.12415202X-RAY DIFFRACTION100
1.8105-1.85940.12462740.11415178X-RAY DIFFRACTION100
1.8594-1.91410.12832730.11155218X-RAY DIFFRACTION100
1.9141-1.97590.10872710.10835196X-RAY DIFFRACTION100
1.9759-2.04650.12542740.10755261X-RAY DIFFRACTION100
2.0465-2.12850.10972770.10585195X-RAY DIFFRACTION100
2.1285-2.22540.11992740.10675245X-RAY DIFFRACTION100
2.2254-2.34270.11492810.10725213X-RAY DIFFRACTION100
2.3427-2.48940.12162770.10755238X-RAY DIFFRACTION100
2.4894-2.68160.10982660.10785257X-RAY DIFFRACTION100
2.6816-2.95140.12852810.11575273X-RAY DIFFRACTION100
2.9514-3.37840.12822780.11865274X-RAY DIFFRACTION100
3.3784-4.25590.11422760.10165322X-RAY DIFFRACTION100
4.2559-44.48870.11672960.11545454X-RAY DIFFRACTION100
2.349-2.41780.23051340.19952509NEUTRON DIFFRACTION97
2.4178-2.49540.25961360.20212600NEUTRON DIFFRACTION100
2.4954-2.58410.24191300.18942603NEUTRON DIFFRACTION100
2.5841-2.6870.20971320.17062599NEUTRON DIFFRACTION100
2.687-2.80840.20811400.16672569NEUTRON DIFFRACTION100
2.8084-2.95520.23211350.16192600NEUTRON DIFFRACTION100
2.9552-3.13860.19211390.15622590NEUTRON DIFFRACTION100
3.1386-3.3780.20891360.14672611NEUTRON DIFFRACTION100
3.378-3.71270.17211340.1312607NEUTRON DIFFRACTION99
3.7127-4.23780.13751340.11532576NEUTRON DIFFRACTION99
4.2378-5.29460.15351390.12212575NEUTRON DIFFRACTION97
5.2946-14.38470.16641330.14722433NEUTRON DIFFRACTION89

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