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- PDB-4bfl: Structure of natively expressed catalase HPII -

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Basic information

Entry
Database: PDB / ID: 4bfl
TitleStructure of natively expressed catalase HPII
ComponentsCATALASE HPII
KeywordsOXIDOREDUCTASE / NATIVE EXPRESSION / WILD TYPE
Function / homology
Function and homology information


catalase / hyperosmotic response / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / iron ion binding / heme binding / DNA damage response / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Catalase, four-helical domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Large catalase, C-terminal domain / Catalase, mono-functional, haem-containing, clade 2, helical domain / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. ...Catalase, four-helical domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Large catalase, C-terminal domain / Catalase, mono-functional, haem-containing, clade 2, helical domain / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / 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 / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Up-down Bundle / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Catalase HPII
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsGabrielsen, M. / Schuttelkopf, A.W.
CitationJournal: To be Published
Title: Accidents Happen: Crystallisation of Catalase from a Mixed Protein Solution
Authors: Gabrielsen, M. / Schuttelkopf, A.W. / Akpunarlieva, S.N.
History
DepositionMar 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Atomic model
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATALASE HPII
B: CATALASE HPII
C: CATALASE HPII
D: CATALASE HPII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)339,73811
Polymers337,0864
Non-polymers2,6527
Water35,5621974
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area64450 Å2
ΔGint-274.4 kcal/mol
Surface area79760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.402, 171.669, 123.209
Angle α, β, γ (deg.)90.00, 104.67, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.991765, -0.121859, -0.039405), (-0.120732, 0.786921, 0.605128), (-0.042731, 0.604902, -0.795153)-16.2801, -22.3958, 62.969
2given(0.877782, -0.033487, 0.477888), (-0.033272, -0.999407, -0.008919), (0.477903, -0.008071, -0.878376)-15.6955, -32.9169, 59.3719
3given(-0.887444, 0.153769, -0.434509), (0.155241, -0.787911, -0.5959), (-0.433986, -0.596281, 0.675356)0.7793, -10.5265, -3.5574

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Components

#1: Protein
CATALASE HPII / HYDROXYPEROXIDASE II


Mass: 84271.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Variant: PLYSS / Strain: BL21(DE3) / References: UniProt: P21179, catalase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1974 / 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: 2.19 Å3/Da / Density % sol: 43.97 % / Description: NONE
Crystal growpH: 6.5
Details: 10 % PEG 20000, 20% PEG 500MME, 30 MM SODIUM NITRATE, 30 MM DISODIUM HYDROGENPHOSPHATE, 30 MM AMMONIUM SULFATE, AND 100 MM MES/IMIDAZOLE PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.64→48.95 Å / Num. obs: 290359 / % possible obs: 81.1 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 18.26 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.1
Reflection shellResolution: 1.64→1.73 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.5 / % possible all: 35.4

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CF9

1cf9


Resolution: 1.64→48.95 Å / Cor.coef. Fo:Fc: 0.9381 / Cor.coef. Fo:Fc free: 0.9215 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.113 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.106
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=HEM. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=25521. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=168. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=HEM. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=25521. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=168. NUMBER TREATED BY BAD NON-BONDED CONTACTS=4.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 14725 5.07 %RANDOM
Rwork0.1743 ---
obs0.1757 290359 80.85 %-
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.2108 Å20 Å2-2.9753 Å2
2--7.0711 Å20 Å2
3----1.8603 Å2
Refinement stepCycle: LAST / Resolution: 1.64→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23400 0 184 1974 25558
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00924399HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0133251HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8233SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes648HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3603HARMONIC5
X-RAY DIFFRACTIONt_it24399HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion16.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3086SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact30227SEMIHARMONIC4
LS refinement shellResolution: 1.64→1.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2707 380 4.82 %
Rwork0.2479 7505 -
all0.249 7885 -
obs--80.85 %
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)
10.11620.0584-0.17180.4073-0.19580.8460.01720.01230.00440.2482-0.00250.113-0.1503-0.1622-0.01470.34860.02440.10410.0692-0.00520.0304-24.925-13.62254.114
20.12740.0634-0.17480.5902-0.20430.79430.0397-0.01470.0056-0.0319-0.0802-0.146-0.23860.17640.04050.2617-0.04330.04580.08660.0280.03477.992.64212.782
30.12780.0451-0.17910.5139-0.14110.8672-0.02690.0619-0.0142-0.2182-0.01080.01490.0613-0.13150.03780.26110.00260.03110.0728-0.01180.0004-11.251-19.0240.044
40.13980.0247-0.16550.4768-0.19680.8829-0.0591-0.0593-0.05670.1846-0.0618-0.06180.1720.16240.12090.32390.02510.05430.07230.03680.029-2.792-36.68951.643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 10-753
2X-RAY DIFFRACTION2CHAIN B AND RESSEQ 9-753
3X-RAY DIFFRACTION3CHAIN C AND RESSEQ 11-753
4X-RAY DIFFRACTION4CHAIN D AND RESSEQ 19-753

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