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- PDB-4qop: Structure of Bacillus pumilus catalase with hydroquinone bound. -

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Basic information

Entry
Database: PDB / ID: 4qop
TitleStructure of Bacillus pumilus catalase with hydroquinone 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 active site / Catalase proximal active site signature. / Catalase immune-responsive domain / Catalase-related immune-responsive ...: / 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 active site / Catalase proximal active site signature. / Catalase immune-responsive domain / Catalase-related immune-responsive / 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 / benzene-1,4-diol / Catalase
Similarity search - Component
Biological speciesBacillus pumilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 1.2Feb 28, 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_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
Water26,9321495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53440 Å2
ΔGint-374 kcal/mol
Surface area58070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.279, 109.455, 104.199
Angle α, β, γ (deg.)90.000, 92.050, 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: pBluscript / Production host: Escherichia coli (E. coli) / Strain (production host): UM255 / References: UniProt: W8QL66, catalase

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Non-polymers , 5 types, 1515 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-HQE / benzene-1,4-diol


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.: 1495 / 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: 2.32 Å3/Da / Density % sol: 46.87 %
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: Dec 13, 2013
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: 1.9→104.132 Å / Num. all: 149181 / Num. obs: 149181 / % possible obs: 91.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rsym value: 0.092 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-22.60.4731.558853225280.47395.3
2-2.122.70.4051.856756212710.40595
2.12-2.272.60.2063.350542193240.20691.8
2.27-2.452.70.241348582180850.24192.4
2.45-2.692.70.1345.645534166470.13492.2
2.69-32.80.092840922148360.09291.1
3-3.472.80.06410.835798128960.06489.4
3.47-4.252.70.05611.429310106840.05687.6
4.25-6.012.90.0415.72376683330.0488.2
6.01-48.4452.90.03613.11316645770.03687.2

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Phasing

PhasingMethod: molecular replacement

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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 / Resolution: 1.9→104.13 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2471 / WRfactor Rwork: 0.2155 / FOM work R set: 0.7319 / SU B: 10.312 / SU ML: 0.153 / SU R Cruickshank DPI: 0.2318 / SU Rfree: 0.1856 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 7647 5.2 %RANDOM
Rwork0.2297 ---
obs0.2314 147764 90.83 %-
all-149181 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.09 Å2 / Biso mean: 28.383 Å2 / Biso min: 11.94 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å20 Å20.4 Å2
2--2.17 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.9→104.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15680 0 384 1495 17559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01916707
X-RAY DIFFRACTIONr_bond_other_d0.0070.0215056
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.97822792
X-RAY DIFFRACTIONr_angle_other_deg1.211334669
X-RAY DIFFRACTIONr_chiral_restr0.1120.22255
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02119364
X-RAY DIFFRACTIONr_gen_planes_other0.0070.024169
X-RAY DIFFRACTIONr_mcbond_it1.7042.1197749
X-RAY DIFFRACTIONr_mcbond_other1.7032.1197748
X-RAY DIFFRACTIONr_mcangle_it2.4493.1689697
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A283610.06
12B283610.06
21A281900.07
22C281900.07
31A284480.06
32D284480.06
41B280850.07
42C280850.07
51B284150.06
52D284150.06
61C283970.06
62D283970.06
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.6 557 -
Rwork0.616 10136 -
all-10693 -
obs--89.21 %
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)
10.19320.0654-0.02230.1432-0.06930.13470.00580.06220.06140.0540.060.0316-0.059-0.0492-0.06580.04130.03490.02190.07740.06280.075340.7585-1.506720.2979
20.17250.03220.0130.0907-0.09630.16610.02180.0311-0.0497-0.00630.04780.01250.0371-0.0584-0.06960.022-0.0203-0.03130.06190.02880.071139.5716-38.602131.7944
30.0868-0.00070.0130.0854-0.11880.1970.02440.0096-0.02320.0356-0.02-0.0188-0.02520.0234-0.00440.0395-0.0029-0.02660.02780.00410.074272.4515-30.403743.8176
40.1286-0.00090.01440.0955-0.14970.23730.00160.11450.00920.0129-0.0164-0.0125-0.01870.03630.01480.0039-0.0027-0.00450.10710.0190.03873.7513-11.146710.0921
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 504
2X-RAY DIFFRACTION2B6 - 504
3X-RAY DIFFRACTION3C6 - 504
4X-RAY DIFFRACTION4D6 - 504

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