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- PDB-4r42: Crystal structure of KatB, a manganese catalase from Anabaena PCC7120 -

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Basic information

Entry
Database: PDB / ID: 4r42
TitleCrystal structure of KatB, a manganese catalase from Anabaena PCC7120
ComponentsAlr3090 protein
KeywordsOXIDOREDUCTASE / Manganese / Catalase / 4 helix bundle
Function / homology
Function and homology information


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
: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Alr3090 protein
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å
AuthorsBihani, S.C.
CitationJournal: Free Radic. Biol. Med. / Year: 2016
Title: KatB, a cyanobacterial Mn-catalase with unique active site configuration: Implications for enzyme function.
Authors: Bihani, S.C. / Chakravarty, D. / Ballal, A.
History
DepositionAug 19, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Experimental preparation
Revision 1.2Apr 20, 2016Group: Experimental preparation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.5Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alr3090 protein
B: Alr3090 protein
C: Alr3090 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,83719
Polymers79,4243
Non-polymers1,41316
Water6,954386
1
A: Alr3090 protein
B: Alr3090 protein
C: Alr3090 protein
hetero molecules

A: Alr3090 protein
B: Alr3090 protein
C: Alr3090 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,67438
Polymers158,8476
Non-polymers2,82632
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area42290 Å2
ΔGint-344 kcal/mol
Surface area39740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.404, 101.404, 136.198
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

21A-459-

HOH

31A-471-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Alr3090 protein


Mass: 26474.574 Da / Num. of mol.: 3 / Mutation: F2V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Strain: PCC7120 / Gene: alr3090 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: Q8YSJ5

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Non-polymers , 7 types, 402 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 400, 100mM imidazole , 200mM calcium acetate, pH 8.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 15, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.902→82.136 Å / Num. all: 56382 / Num. obs: 56257 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.16 Å2
Reflection shellResolution: 1.902→2.02 Å / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_1701refinement
PDB_EXTRACT3.14data extraction
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.902→45.349 Å / SU ML: 0.14 / σ(F): 1.36 / Phase error: 13.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1599 2844 5.06 %RANDOM
Rwork0.1344 ---
all0.1358 56382 --
obs0.1358 56257 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 192.78 Å2 / Biso mean: 32.8541 Å2 / Biso min: 8.69 Å2
Refinement stepCycle: LAST / Resolution: 1.902→45.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5179 0 70 386 5635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065416
X-RAY DIFFRACTIONf_angle_d1.0287332
X-RAY DIFFRACTIONf_chiral_restr0.038795
X-RAY DIFFRACTIONf_plane_restr0.005958
X-RAY DIFFRACTIONf_dihedral_angle_d14.4031995
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9018-1.93460.20821360.192226062742100
1.9346-1.96980.20541390.177826232762100
1.9698-2.00770.19851670.170326042771100
2.0077-2.04870.19741440.154126412785100
2.0487-2.09320.17831370.142726342771100
2.0932-2.14190.16561350.140226462781100
2.1419-2.19550.15621480.137326282776100
2.1955-2.25480.19731410.132626462787100
2.2548-2.32120.15391360.133426482784100
2.3212-2.39610.14321390.123926322771100
2.3961-2.48170.20311320.127426642796100
2.4817-2.58110.16611320.127726692801100
2.5811-2.69850.1461520.121626572809100
2.6985-2.84080.16771370.121226652802100
2.8408-3.01870.16681370.129126702807100
3.0187-3.25170.16521530.133526812834100
3.2517-3.57890.17441290.132327102839100
3.5789-4.09640.12821520.118127112863100
4.0964-5.15990.12791610.115827472908100
5.1599-45.36210.15671370.16132921305899
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)
16.35-5.32142.51314.5005-2.10961.0710.0645-0.50240.54220.1857-0.0025-0.2911-0.6801-1.15190.24690.7674-0.0527-0.27960.6107-0.07630.9892-1.201339.54141.5427
21.139-1.5441-0.90132.13161.31650.9145-0.24510.94950.5567-0.7056-0.357-0.92190.58140.7450.48761.08590.211-0.02551.29490.05441.09892.317539.8471-12.7673
37.5823-0.3831.74764.9393-5.07635.5145-0.03870.5460.3993-0.1214-0.18550.0003-0.00420.07930.03140.17350.0209-0.00060.19890.00830.19185.803924.8536-23.1173
41.75611.15751.19242.4431.97472.86540.0299-0.07210.19560.0422-0.05240.0675-0.0935-0.05310.04810.09440.00650.01590.11190.00330.151612.517431.61490.7997
57.22223.8034.73069.13412.01313.25930.03080.1560.4398-0.0109-0.24220.3569-0.2977-0.00560.30470.14310.0199-0.00530.16480.05350.20382.948130.2987-15.2555
69.4035-3.21891.04558.3849-5.8018.2349-0.120.3724-0.1415-0.43220.03770.65660.0914-0.69410.23180.1665-0.0071-0.05870.22550.00580.2302-3.271719.4506-24.8084
71.19540.46610.59360.67890.35181.17360.03450.03430.0419-0.0093-0.0048-0.0189-0.0025-0.0113-0.03210.11330.01560.00640.1130.01620.137913.179922.6162-5.5177
83.80131.74613.58451.56692.5293.7514-0.10880.18730.1955-0.07410.03670.03150.00240.19790.14230.1392-0.01280.01550.12190.04180.150919.803934.4958-10.1591
91.1431-0.8564-1.49353.14011.48115.2745-0.1144-0.11970.02110.26210.0719-0.34240.22090.42880.04570.1354-0.0217-0.04430.20030.0030.242239.862920.39719.0725
104.5999-3.68060.11567.7752-3.07083.4860.05030.068-0.37720.18360.0281-0.6665-0.16990.7167-0.02760.1649-0.01190.01620.2766-0.03350.294848.026618.8646-0.3377
117.54481.89660.59813.71681.79580.8831-0.41130.7016-0.13340.02880.9252-1.50490.02271.3895-0.19620.52340.09910.02030.7156-0.03281.35513.527240.3058-0.1507
124.6652-1.31840.89572.7710.67630.72970.012-2.3627-1.63512.4902-0.2066-0.0320.41260.43690.00791.3466-0.03340.00731.27310.38951.11791.448239.130314.4279
135.07172.67531.09473.13942.48792.57750.1366-0.61170.22840.497-0.11210.1759-0.138-0.4602-0.09360.24420.04340.01020.236-0.0170.15145.505722.879124.42
143.8447-1.66434.90371.3412-2.23278.9207-0.10450.09430.11050.0565-0.0407-0.0529-0.14270.04140.09310.09040.00670.00790.0905-0.00680.1318-1.68923.69572.2657
157.1866-1.95636.60572.1297-2.51257.3249-0.20960.30780.483-0.0024-0.08790.0005-0.12110.28510.28570.13170.01960.01440.15550.01560.2009-6.827731.6661-0.2022
164.1361-2.62145.59375.4767-3.50057.8266-0.3642-0.08420.23230.44290.069-0.2932-0.52590.01960.43510.18290.0186-0.01660.1689-0.04330.160210.608826.772422.085
171.9701-0.15981.08460.562-0.03511.44970.0243-0.0515-0.01550.06460.01070.0665-0.0062-0.1339-0.03990.10830.0080.01270.09660.01490.11650.714618.62427.6712
182.665-0.20532.71540.8691-0.05675.0629-0.1498-0.40450.23190.09590.00510.0743-0.1781-0.5060.09890.14870.03940.02930.2548-0.01050.189-10.949725.790813.0454
192.7855-1.93870.30663.3156-0.52723.70710.27020.2575-0.4888-0.2478-0.31740.54430.6071-0.45790.0580.2274-0.0712-0.06710.391-0.0490.3133-22.74386.9643-8.9735
208.54511.9681.04896.23312.23019.21640.280.0181-0.25890.1374-0.07671.03770.8068-1.8908-0.2450.4695-0.20790.05360.8932-0.00140.6138-28.9195-1.29360.1854
210.00350.0018-0.00060.00380.00490.01590.11660.11680.12520.01270.15690.01510.0601-0.0077-0.00050.7755-0.01520.10090.93350.09461.0202-10.8219-14.55091.509
220.7097-0.237-0.46662.74111.91212.00730.85541.0380.7999-2.71260.0758-0.43670.29140.5145-0.82841.21930.1-0.03891.1855-0.23471.1807-13.544-11.9583-12.9238
232.0747-2.06870.39753.2111.06762.07040.18111.01690.0046-0.685-0.31320.3140.1858-0.35620.10050.23390.0117-0.03220.324-0.03570.1576-2.4840.1424-23.7145
244.6996-0.3303-3.53111.67460.87925.7018-0.03-0.0535-0.2880.0817-0.07260.07890.1133-0.20170.06130.0768-0.0085-0.0280.11420.02340.1463-7.532.71-1.006
258.7654-1.7687-6.94732.20932.16035.3805-0.40020.095-0.67840.1735-0.11640.37450.627-0.31540.43390.1893-0.04-0.04050.18270.02730.254-11.1631-3.2828-5.9884
268.9262-1.3145-0.2534.35934.27864.52560.09551.3254-0.7856-0.8259-0.2554-0.5641-0.01090.44260.14420.32450.03310.05730.3786-0.07750.30068.8014-2.6062-26.8185
271.0534-0.2425-1.00140.42130.47091.8310.02610.05740.0097-0.00960.00210.0616-0.0018-0.1376-0.01370.1057-0.0019-0.01340.11990.02610.1288-4.23536.5327-5.2127
282.9997-0.4049-1.95351.38621.61676.92640.06320.3824-0.1846-0.1034-0.15070.1936-0.016-0.61720.09460.13910.0179-0.0540.24270.01530.2126-17.34356.1877-10.8491
291.86550.93460.73832.9944-0.76982.8832-0.0666-0.37280.27180.1546-0.09420.0809-0.3231-0.33210.11030.1910.09880.02460.2963-0.04140.239-15.736128.650910.6717
307.45990.4552.337.42641.18868.1501-0.1588-0.47770.47250.37750.12360.4677-0.6074-0.6958-0.00090.28310.1249-0.01480.28220.00230.3289-18.758537.62111.4103
311.40561.774-2.29073.2013-3.06223.76990.1892-0.3948-1.27470.77850.499-0.67821.79020.7325-0.67540.54730.1554-0.01910.29580.00610.6011-9.193744.76114.7169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:5 )A1 - 5
2X-RAY DIFFRACTION2( CHAIN A AND RESID 6:12 )A6 - 12
3X-RAY DIFFRACTION3( CHAIN A AND RESID 13:24 )A13 - 24
4X-RAY DIFFRACTION4( CHAIN A AND RESID 25:69 )A25 - 69
5X-RAY DIFFRACTION5( CHAIN A AND RESID 70:79 )A70 - 79
6X-RAY DIFFRACTION6( CHAIN A AND RESID 80:90 )A80 - 90
7X-RAY DIFFRACTION7( CHAIN A AND RESID 91:141 )A91 - 141
8X-RAY DIFFRACTION8( CHAIN A AND RESID 142:180 )A142 - 180
9X-RAY DIFFRACTION9( CHAIN A AND RESID 181:202 )A181 - 202
10X-RAY DIFFRACTION10( CHAIN A AND RESID 209:225 )A209 - 225
11X-RAY DIFFRACTION11( CHAIN B AND RESID 1:4 )B1 - 4
12X-RAY DIFFRACTION12( CHAIN B AND RESID 5:12 )B5 - 12
13X-RAY DIFFRACTION13( CHAIN B AND RESID 13:24 )B13 - 24
14X-RAY DIFFRACTION14( CHAIN B AND RESID 25:49 )B25 - 49
15X-RAY DIFFRACTION15( CHAIN B AND RESID 50:70 )B50 - 70
16X-RAY DIFFRACTION16( CHAIN B AND RESID 71:87 )B71 - 87
17X-RAY DIFFRACTION17( CHAIN B AND RESID 88:141 )B88 - 141
18X-RAY DIFFRACTION18( CHAIN B AND RESID 142:177 )B142 - 177
19X-RAY DIFFRACTION19( CHAIN B AND RESID 178:201 )B178 - 201
20X-RAY DIFFRACTION20( CHAIN B AND RESID 209:225 )B209 - 225
21X-RAY DIFFRACTION21( CHAIN C AND RESID 1:4 )C1 - 4
22X-RAY DIFFRACTION22( CHAIN C AND RESID 5:12 )C5 - 12
23X-RAY DIFFRACTION23( CHAIN C AND RESID 13:24 )C13 - 24
24X-RAY DIFFRACTION24( CHAIN C AND RESID 25:49 )C25 - 49
25X-RAY DIFFRACTION25( CHAIN C AND RESID 50:83 )C50 - 83
26X-RAY DIFFRACTION26( CHAIN C AND RESID 84:91 )C84 - 91
27X-RAY DIFFRACTION27( CHAIN C AND RESID 92:141 )C92 - 141
28X-RAY DIFFRACTION28( CHAIN C AND RESID 142:178 )C142 - 178
29X-RAY DIFFRACTION29( CHAIN C AND RESID 179:202 )C179 - 202
30X-RAY DIFFRACTION30( CHAIN C AND RESID 208:222 )C208 - 222
31X-RAY DIFFRACTION31( CHAIN C AND RESID 223:225 )C223 - 225

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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