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- PDB-4b7g: Structure of a bacterial catalase -

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Basic information

Entry
Database: PDB / ID: 4b7g
TitleStructure of a bacterial catalase
ComponentsCATALASE
KeywordsOXIDOREDUCTASE / CATALASE INHIBITION
Function / homology
Function and homology information


Hemocyanin, N-terminal domain - #60 / Cytochrome C Oxidase; Chain J - #20 / Cytochrome C Oxidase; Chain J / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Few Secondary Structures / Irregular / Up-down Bundle / Beta Barrel ...Hemocyanin, N-terminal domain - #60 / Cytochrome C Oxidase; Chain J - #20 / Cytochrome C Oxidase; Chain J / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Few Secondary Structures / Irregular / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / :
Similarity search - Component
Biological speciesCORYNEBACTERIUM GLUTAMICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.2Dec 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 / 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)240,10814
Polymers234,5904
Non-polymers5,51910
Water42,2092343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57110 Å2
ΔGint-297 kcal/mol
Surface area54530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.751, 151.751, 157.682
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11D-2020-

HOH

21D-2021-

HOH

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Components

#1: Protein
CATALASE


Mass: 58647.406 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: PURIFIED PROTEIN PURCHASED FROM SIGMA ALDRICH / Source: (natural) CORYNEBACTERIUM GLUTAMICUM (bacteria) / References: UniProt: Q6M8A6, catalase
#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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2343 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.95 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 161469 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 7
Reflection shellResolution: 1.9→1.92 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.66

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Processing

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

8cat


Resolution: 1.9→48.802 Å / SU ML: 0.17 / σ(F): 0.09 / Phase error: 16.78 / Stereochemistry target values: ML
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FINAL REFINEMENT WAS CARRIED OUT USING PHENIX
RfactorNum. reflection% reflection
Rfree0.1743 8066 5.02 %
Rwork0.133 --
obs0.135 160649 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→48.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16542 0 366 2343 19251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817686
X-RAY DIFFRACTIONf_angle_d1.18324184
X-RAY DIFFRACTIONf_dihedral_angle_d17.9736584
X-RAY DIFFRACTIONf_chiral_restr0.0812393
X-RAY DIFFRACTIONf_plane_restr0.0053228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.92170.28582500.2084817X-RAY DIFFRACTION95
1.9217-1.94430.25112850.20094923X-RAY DIFFRACTION97
1.9443-1.96810.23452510.18345063X-RAY DIFFRACTION99
1.9681-1.9930.22932490.17495066X-RAY DIFFRACTION99
1.993-2.01920.22062710.16195064X-RAY DIFFRACTION100
2.0192-2.04680.20492680.15925115X-RAY DIFFRACTION100
2.0468-2.07610.20762930.15625017X-RAY DIFFRACTION99
2.0761-2.10710.20962890.14615072X-RAY DIFFRACTION100
2.1071-2.140.21092640.14155089X-RAY DIFFRACTION100
2.14-2.17510.19642330.14555091X-RAY DIFFRACTION100
2.1751-2.21260.20012810.13795111X-RAY DIFFRACTION100
2.2126-2.25280.18292680.13665128X-RAY DIFFRACTION100
2.2528-2.29620.19052710.13975088X-RAY DIFFRACTION100
2.2962-2.3430.19062810.13455078X-RAY DIFFRACTION100
2.343-2.3940.18532720.13645090X-RAY DIFFRACTION100
2.394-2.44970.18652590.13165134X-RAY DIFFRACTION100
2.4497-2.51090.19492690.13525094X-RAY DIFFRACTION100
2.5109-2.57880.17472660.13355116X-RAY DIFFRACTION100
2.5788-2.65470.18922760.12745072X-RAY DIFFRACTION100
2.6547-2.74040.18512680.12955117X-RAY DIFFRACTION100
2.7404-2.83830.17672510.1325140X-RAY DIFFRACTION100
2.8383-2.95190.18262710.12915104X-RAY DIFFRACTION100
2.9519-3.08620.17643130.1335066X-RAY DIFFRACTION100
3.0862-3.24890.16352530.13175117X-RAY DIFFRACTION100
3.2489-3.45240.16062620.12245144X-RAY DIFFRACTION100
3.4524-3.71890.12862490.11925127X-RAY DIFFRACTION100
3.7189-4.0930.13922620.11375123X-RAY DIFFRACTION100
4.093-4.68480.13452530.1045144X-RAY DIFFRACTION100
4.6848-5.90080.13722930.11395125X-RAY DIFFRACTION100
5.9008-48.81840.15852950.14075148X-RAY DIFFRACTION99

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