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- PDB-4qoo: Structure of Bacillus pumilus catalase with resorcinol bound. -

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Basic information

Entry
Database: PDB / ID: 4qoo
TitleStructure of Bacillus pumilus catalase with resorcinol bound.
ComponentsCatalase
KeywordsOXIDOREDUCTASE / catalase fold / catalase / peroxidase
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding
Similarity search - Function
: / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. ...: / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / RESORCINOL / Catalase
Similarity search - Component
Biological speciesBacillus pumilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLoewen, P.C.
CitationJournal: Proteins / Year: 2015
Title: Unprecedented access of phenolic substrates to the heme active site of a catalase: Substrate binding and peroxidase-like reactivity of Bacillus pumilus catalase monitored by X-ray ...Title: Unprecedented access of phenolic substrates to the heme active site of a catalase: Substrate binding and peroxidase-like reactivity of Bacillus pumilus catalase monitored by X-ray crystallography and EPR spectroscopy.
Authors: Loewen, P.C. / Villanueva, J. / Switala, J. / Donald, L.J. / Ivancich, A.
History
DepositionJun 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Sep 20, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _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.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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Catalase
B: Catalase
C: Catalase
D: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,76724
Polymers227,1364
Non-polymers5,63120
Water28,9501607
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54650 Å2
ΔGint-347 kcal/mol
Surface area56970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.907, 108.597, 103.524
Angle α, β, γ (deg.)90.000, 92.010, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 6 - 485 / Label seq-ID: 6 - 485

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Catalase


Mass: 56783.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pumilus (bacteria) / Gene: BW16_04845, katX2 / Plasmid: pBluescript / Production host: Escherichia coli (E. coli) / Strain (production host): UM255 / References: UniProt: W8QL66, catalase

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Non-polymers , 5 types, 1627 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-RCO / RESORCINOL / 1,3-BENZENEDIOL / 1,3-DIHYDROXYBENZENE


Mass: 110.111 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1607 / 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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate pH 4.6, 50 mM NaCl, 10 mM CoCl2 and 12-20% 2-methyl-2,4-pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 18, 2014
RadiationMonochromator: Double crystal SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→103.46 Å / Num. all: 197688 / Num. obs: 197688 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rsym value: 0.063 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.75-1.842.50.4231.774848295190.42399.3
1.84-1.962.50.2792.670814278720.27999
1.96-2.092.50.1923.866247260890.19298.7
2.09-2.262.50.1275.760870240400.12797.8
2.26-2.472.50.0977.455762220110.09797.2
2.47-2.772.50.0729.549901196930.07296.1
2.77-3.22.50.05312.443233171220.05394.5
3.2-3.912.60.0415.436455142490.0493.4
3.91-5.532.60.03219.228947109990.03292.7
5.53-46.7422.70.03171637560940.0392.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.21data scaling
REFMAC5.8.0069refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QWL

1qwl


Resolution: 1.75→103.46 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.1987 / WRfactor Rwork: 0.1684 / FOM work R set: 0.8167 / SU B: 5.975 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1263 / SU Rfree: 0.1165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2095 9664 4.9 %RANDOM
Rwork0.1786 ---
obs0.1802 196837 96.38 %-
all-197688 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.07 Å2 / Biso mean: 25.833 Å2 / Biso min: 9.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å2-0.18 Å2
2--2.36 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→103.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15680 0 384 1607 17671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01916745
X-RAY DIFFRACTIONr_bond_other_d0.0090.0215101
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.97822852
X-RAY DIFFRACTIONr_angle_other_deg1.424334783
X-RAY DIFFRACTIONr_chiral_restr0.1230.22262
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02119416
X-RAY DIFFRACTIONr_gen_planes_other0.0080.024179
X-RAY DIFFRACTIONr_mcbond_it1.6711.7177761
X-RAY DIFFRACTIONr_mcbond_other1.6711.7167760
X-RAY DIFFRACTIONr_mcangle_it2.3042.5669715
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A286490.06
12B286490.06
21A284740.07
22C284740.07
31A287020.06
32D287020.06
41B284690.07
42C284690.07
51B287000.06
52D287000.06
61C285120.07
62D285120.07
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 767 -
Rwork0.245 14204 -
all-14971 -
obs--99.26 %
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)
10.27970.0966-0.06340.1259-0.08210.09670.0320.12310.09970.07020.0470.05-0.0413-0.034-0.0790.04550.03940.0260.11880.07270.089140.7062-1.430520.104
20.22450.06330.01460.084-0.08510.13830.02310.0571-0.05890.01260.03590.00660.0089-0.0472-0.0590.0178-0.0049-0.02760.09720.00610.061239.4521-38.275231.6708
30.12430.013-0.03050.0614-0.09870.170.02110.0123-0.03050.0302-0.0208-0.0069-0.03460.0332-0.00030.04190.0025-0.03480.0621-0.00450.061272.2532-30.176443.5998
40.19210.0345-0.02460.1084-0.14190.19510.00160.15090.01220.0189-0.0078-0.0109-0.01810.03180.00620.0104-0.0019-0.01220.1630.01870.01973.5601-11.07189.9857
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 504
2X-RAY DIFFRACTION2B6 - 504
3X-RAY DIFFRACTION3C6 - 503
4X-RAY DIFFRACTION4D6 - 504

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