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- PDB-1qwm: Structure of Helicobacter pylori catalase with formic acid bound -

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Basic information

Entry
Database: PDB / ID: 1qwm
TitleStructure of Helicobacter pylori catalase with formic acid bound
ComponentsKatA catalase
KeywordsOXIDOREDUCTASE / beta barrel / azide complex / formate complex
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to hydrogen peroxide / heme binding / metal ion binding / cytoplasm
Similarity search - Function
Catalase, clade 3 / 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 / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive domain ...Catalase, clade 3 / 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 / 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
AZIDE ION / FORMIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Catalase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLoewen, P.C. / Carpena, X. / Perez-Luque, R. / Rovira, C. / Haas, R. / Odenbreit, S. / Nicholls, P. / Fita, I.
CitationJournal: Biochemistry / Year: 2004
Title: Structure of Helicobacter pylori Catalase, with and without Formic Acid Bound, at 1.6 A Resolution
Authors: Loewen, P.C. / Carpena, X. / Rovira, C. / Ivancich, A. / Perez-Luque, R. / Haas, R. / Obenbreit, S. / Nicholls, P. / Fita, I.
History
DepositionSep 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: 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_initial_refinement_model / struct_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_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_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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

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Assembly

Deposited unit
A: KatA catalase
B: KatA catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,39241
Polymers117,4602
Non-polymers2,93239
Water16,808933
1
A: KatA catalase
B: KatA catalase
hetero molecules

A: KatA catalase
B: KatA catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,78482
Polymers234,9204
Non-polymers5,86478
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area62380 Å2
ΔGint-266 kcal/mol
Surface area55910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.756, 154.961, 96.163
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: MET / End label comp-ID: MET / Refine code: 6 / Auth seq-ID: 1 - 490 / Label seq-ID: 1 - 490

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein KatA catalase


Mass: 58730.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: katA (hp0875) / Plasmid: pSO100 / Production host: Escherichia coli (E. coli) / Strain (production host): UM255 / References: UniProt: P77872, catalase
#2: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 933 / 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: 2.05 Å3/Da / Density % sol: 40.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG MME 550, 0.1 M sodium citrate, 10 mM ZnSO4, 3 mM NaN3, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 21, 2002
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→29.9 Å / Num. all: 124796 / Num. obs: 118512 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.047
Reflection shellResolution: 1.6→1.69 Å / Num. unique all: 8557 / Rsym value: 0.179 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QWL

1qwl


Resolution: 1.6→29.88 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.902 / SU B: 1.698 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.106 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22695 6282 5 %RANDOM
Rwork0.19387 ---
all0.194 124796 --
obs0.19555 118512 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.149 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2---0.19 Å20 Å2
3----0.75 Å2
Refine analyzeLuzzati sigma a obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.6→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8040 0 197 933 9170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0218503
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.9611480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0675980
X-RAY DIFFRACTIONr_chiral_restr0.1180.21128
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026641
X-RAY DIFFRACTIONr_nbd_refined0.2130.24021
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.2369
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.2126
X-RAY DIFFRACTIONr_mcbond_it0.9241.54976
X-RAY DIFFRACTIONr_mcangle_it1.45327948
X-RAY DIFFRACTIONr_scbond_it2.31933527
X-RAY DIFFRACTIONr_scangle_it3.544.53532
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4017 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.215
loose thermal1.4110
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.265 429
Rwork0.214 8128

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