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- PDB-1wxr: Crystal structure of Heme Binding protein, an autotransporter hem... -

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Basic information

Entry
Database: PDB / ID: 1wxr
TitleCrystal structure of Heme Binding protein, an autotransporter hemoglobine protease from pathogenic Escherichia coli
Componentshaemoglobin protease
KeywordsHYDROLASE / hemoglobine protease / autotransporter / beta helix / heme uptake / SPATE
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / periplasmic space / serine-type endopeptidase activity / cell surface / proteolysis / extracellular region
Similarity search - Function
Double Stranded RNA Binding Domain - #280 / : / Pectate Lyase C-like - #20 / Peptidase S6, IgA endopeptidase / Peptidase family S6 domain / Immunoglobulin A1 protease / Peptidase family S6 domain profile. / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain ...Double Stranded RNA Binding Domain - #280 / : / Pectate Lyase C-like - #20 / Peptidase S6, IgA endopeptidase / Peptidase family S6 domain / Immunoglobulin A1 protease / Peptidase family S6 domain profile. / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / Autotransporter, pectate lyase C-like domain superfamily / Thrombin, subunit H - #120 / Pectate Lyase C-like / Pectin lyase fold/virulence factor / 3 Solenoid / Double Stranded RNA Binding Domain / Thrombin, subunit H / Peptidase S1, PA clan / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemoglobin-binding protease hbp autotransporter
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsOtto, B.R. / Sijbrandi, R. / Luirink, J. / Oudega, B. / Heddle, J.G. / Mizutani, K. / Park, S.-Y. / Tame, J.R.H.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of heme binding protein, an autotransporter hemoglobin protease from pathogenic escherichia coli
Authors: Otto, B.R. / Sijbrandi, R. / Luirink, J. / Oudega, B. / Heddle, J.G. / Mizutani, K. / Park, S.-Y. / Tame, J.R.H.
History
DepositionJan 31, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: haemoglobin protease


Theoretical massNumber of molelcules
Total (without water)111,9641
Polymers111,9641
Non-polymers00
Water7,116395
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.028, 115.028, 437.057
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein haemoglobin protease


Mass: 111963.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: HBP / Plasmid: pACYC184 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 alpha / References: UniProt: O88093
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 3.8 Å3/Da / Density % sol: 67.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 6000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL45PX10.9794, 0.97925, 1.02
SYNCHROTRONPhoton Factory BL-5A21
Detector
TypeIDDetectorDate
RIGAKU RAXIS V1IMAGE PLATEApr 12, 2002
ADSC QUANTUM 3152CCDDec 10, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111MADMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.979251
31.021
411
ReflectionResolution: 2.2→30 Å / Num. obs: 81242 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→29.36 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.339 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24262 4073 5 %RANDOM
Rwork0.20315 ---
obs0.20514 77169 92.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.145 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7802 0 0 395 8197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0217946
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.731.92110802
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.49551031
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.19525.608378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.145151230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3321531
X-RAY DIFFRACTIONr_chiral_restr0.1390.21212
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026160
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.23447
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.25286
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2524
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8881.55185
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50328135
X-RAY DIFFRACTIONr_scbond_it2.36633119
X-RAY DIFFRACTIONr_scangle_it3.6834.52667
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 208 -
Rwork0.281 4138 -
obs--70.8 %

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