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- PDB-4b7f: Structure of a liganded bacterial catalase -

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Basic information

Entry
Database: PDB / ID: 4b7f
TitleStructure of a liganded bacterial catalase
ComponentsCatalase
KeywordsOXIDOREDUCTASE / NITRIC OXIDE / CATALASE INHIBITION
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / nucleotide binding / heme binding / metal ion binding
Similarity search - Function
Hemocyanin, N-terminal domain - #60 / Cytochrome C Oxidase; Chain J - #20 / Cytochrome C Oxidase; Chain J / Catalase, mono-functional, haem-containing, clades 1 and 3 / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive ...Hemocyanin, N-terminal domain - #60 / Cytochrome C Oxidase; Chain J - #20 / Cytochrome C Oxidase; Chain J / Catalase, mono-functional, haem-containing, clades 1 and 3 / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily / Few Secondary Structures / Irregular / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / NITRIC OXIDE / Catalase
Similarity search - Component
Biological speciesCORYNEBACTERIUM GLUTAMICUM ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsGumiero, A. / Walsh, M.
CitationJournal: Org.Biomol.Chem. / Year: 2013
Title: A Structural and Dynamic Investigation of the Inhibition of Catalase by Nitric Oxide.
Authors: Candelaresi, M. / Gumiero, A. / Adamczyk, K. / Robb, K. / Bellota-Anton, C. / Sangal, V. / Munnoch, J. / Greetham, G.M. / Towrie, M. / Hoskisson, P.A. / Parker, A.W. / Tucker, N.P. / Walsh, M.A. / Hunt, N.T.
History
DepositionAug 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Apr 24, 2019Group: Data collection / Database references ...Data collection / Database references / Other / Source and taxonomy / Structure summary
Category: diffrn_source / entity ...diffrn_source / entity / entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_entity_src_syn / struct_biol / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description ..._diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _entity.src_method / _pdbx_database_status.recvd_author_approval / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.3Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 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 / pdbx_struct_conn_angle / 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 / _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.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_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 "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" 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 "BA" 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 "CC" 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
B: Catalase
C: Catalase
D: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,87226
Polymers234,5904
Non-polymers6,28222
Water20,0871115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59880 Å2
ΔGint-267.7 kcal/mol
Surface area53890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.510, 151.510, 156.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Catalase


Mass: 58647.406 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CORYNEBACTERIUM GLUTAMICUM ATCC 13032 (bacteria)
Description: PROTEIN PURCHASED FROM SIGMA ALDRICH / Gene: cat, APT58_01635, CS176_0252, FM102_06680 / Production host: CORYNEBACTERIUM GLUTAMICUM (bacteria) / References: UniProt: A0A0U4WRC5, catalase

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Non-polymers , 7 types, 1137 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical
ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#7: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1115 / 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: 2.21 Å3/Da / Density % sol: 44.4 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.76→100.58 Å / Num. obs: 186963 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9
Reflection shellResolution: 1.76→1.81 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.4 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 8CAT

8cat


Resolution: 1.76→100.58 Å / SU ML: 0.19 / σ(F): 1.36 / Phase error: 18.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1942 9386 5.02 %
Rwork0.1579 --
obs0.1597 186915 92.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→100.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16557 0 416 1115 18088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717659
X-RAY DIFFRACTIONf_angle_d1.17624108
X-RAY DIFFRACTIONf_dihedral_angle_d16.9686573
X-RAY DIFFRACTIONf_chiral_restr0.082379
X-RAY DIFFRACTIONf_plane_restr0.0053234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.780.2783330.21985914X-RAY DIFFRACTION94
1.78-1.8010.27393130.20935931X-RAY DIFFRACTION93
1.801-1.82290.26132910.20615896X-RAY DIFFRACTION93
1.8229-1.8460.25193110.19795941X-RAY DIFFRACTION93
1.846-1.87030.25463460.19335881X-RAY DIFFRACTION93
1.8703-1.89590.24863210.18695893X-RAY DIFFRACTION93
1.8959-1.9230.25943140.18595890X-RAY DIFFRACTION93
1.923-1.95170.24363270.18075834X-RAY DIFFRACTION93
1.9517-1.98220.22533190.1815926X-RAY DIFFRACTION93
1.9822-2.01470.23743010.1745903X-RAY DIFFRACTION93
2.0147-2.04940.22652910.17645882X-RAY DIFFRACTION93
2.0494-2.08670.21923000.17045893X-RAY DIFFRACTION93
2.0867-2.12690.2083100.16345898X-RAY DIFFRACTION93
2.1269-2.17030.22163130.16465886X-RAY DIFFRACTION92
2.1703-2.21750.22462760.1635911X-RAY DIFFRACTION93
2.2175-2.26910.20173040.15475913X-RAY DIFFRACTION93
2.2691-2.32580.19553040.15655942X-RAY DIFFRACTION93
2.3258-2.38870.2013180.15545991X-RAY DIFFRACTION94
2.3887-2.4590.20073250.15125952X-RAY DIFFRACTION94
2.459-2.53840.21323110.166007X-RAY DIFFRACTION94
2.5384-2.62910.20863140.15565961X-RAY DIFFRACTION94
2.6291-2.73440.19283210.14565998X-RAY DIFFRACTION94
2.7344-2.85880.18972930.14636015X-RAY DIFFRACTION94
2.8588-3.00950.17793380.15255919X-RAY DIFFRACTION94
3.0095-3.19810.18413110.15855949X-RAY DIFFRACTION93
3.1981-3.44510.18943300.15745964X-RAY DIFFRACTION94
3.4451-3.79180.15663120.15285966X-RAY DIFFRACTION93
3.7918-4.34040.14593410.13195918X-RAY DIFFRACTION93
4.3404-5.46850.14672780.13125912X-RAY DIFFRACTION92
5.4685-100.74430.1513200.14535643X-RAY DIFFRACTION87

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