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- PDB-1ggf: CRYSTAL STRUCTURE OF CATALASE HPII FROM ESCHERICHIA COLI, VARIANT... -

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Basic information

Entry
Database: PDB / ID: 1ggf
TitleCRYSTAL STRUCTURE OF CATALASE HPII FROM ESCHERICHIA COLI, VARIANT HIS128ASN, COMPLEX WITH HYDROGEN PEROXIDE.
ComponentsCATALASE HPII
KeywordsOXIDOREDUCTASE / BETA BARREL / ALPHA HELICAL DOMAIN / FLAVODOXIN LIKE DOMAIN
Function / homology
Function and homology information


catalase / catalase activity / hyperosmotic response / hydrogen peroxide catabolic process / response to oxidative stress / iron ion binding / heme binding / DNA damage response / identical protein binding / cytoplasm / cytosol
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 / HYDROGEN PEROXIDE / Catalase HPII
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.28 Å
AuthorsMelik-Adamyan, W.R. / Bravo, J. / Carpena, X. / Switala, J. / Mate, M.J. / Fita, I. / Loewen, P.C.
Citation
Journal: Proteins / Year: 2001
Title: Substrate flow in catalases deduced from the crystal structures of active site variants of HPII from Escherichia coli.
Authors: Melik-Adamyan, W. / Bravo, J. / Carpena, X. / Switala, J. / Mate, M.J. / Fita, I. / Loewen, P.C.
#1: Journal: Structure / Year: 1995
Title: Crystal Structure of Catalase HPII from Escherichia coli
Authors: Bravo, J. / Verdaguer, N. / Tormo, J. / Betzel, C. / Switala, J. / Loewen, P.C. / Fita, I.
#2: Journal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 1999
Title: Structure of Catalase Hpii from Escherichia Coli at 1.9 A Resolution
Authors: Bravo, J. / Mate, M.J. / Schneider, T. / Switala, J. / Wilson, K. / Loewen, P.C. / Fita, I.
History
DepositionAug 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)339,89821
Polymers336,9904
Non-polymers2,90817
Water36,4802025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60650 Å2
ΔGint-245 kcal/mol
Surface area80170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.372, 133.415, 121.918
Angle α, β, γ (deg.)90.00, 109.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CATALASE HPII


Mass: 84247.406 Da / Num. of mol.: 4 / Mutation: H128N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PH128N / Production host: Escherichia coli (E. coli) / 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-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: H2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2025 / 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: 2.12 Å3/Da / Density % sol: 42.01 %
Crystal growTemperature: 297 K / pH: 9
Details: PEG 3350, LiCl, Tris-HCl. Before data collection the protein crystal was soaked during a few seconds in the solution with 2M hydrogen peroxide., pH 9.0, temperature 297.0K
Crystal grow
*PLUS
pH: 9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
215-17 %PEG33501reservoir
31.6-1.5 M1reservoirLiCl
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 120 K
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.28→19.84 Å / Num. all: 128033 / Num. obs: 125885 / % possible obs: 98.5 % / Biso Wilson estimate: 33.9 Å2
Reflection shellResolution: 2.28→2.34 Å / Num. unique all: 9488 / % possible all: 95.9
Reflection
*PLUS
Num. all: 128033 / Rmerge(I) obs: 0.107
Reflection shell
*PLUS
% possible obs: 95.9 % / Num. unique obs: 9488 / Rmerge(I) obs: 0.365

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementResolution: 2.28→87.95 Å / Stereochemistry target values: CCP4, protin_jp.idl
Details: REFMAC, WEIGHT MATRIX 0.2. X-Plor was also used during refinement.
RfactorNum. reflection% reflection
Rfree0.254 6348 -
Rwork0.174 --
obs0.185 119537 98.3 %
all-121599 -
Refinement stepCycle: LAST / Resolution: 2.28→87.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22976 0 198 2025 25199
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d0.031
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 19.8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_plane_restr0.02
X-RAY DIFFRACTIONp_chiral_restr0.117
LS refinement shell
*PLUS
Highest resolution: 2.28 Å / Lowest resolution: 2.34 Å / Rfactor Rfree: 0.296 / Rfactor obs: 0.198

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