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- PDB-6jbn: Crystal structure of Sphingomonas sp. A1 peroxidase EfeB responsi... -

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Basic information

Entry
Database: PDB / ID: 6jbn
TitleCrystal structure of Sphingomonas sp. A1 peroxidase EfeB responsible for import of iron
ComponentsPeroxidase EfeB
KeywordsOXYGEN BINDING / peroxidase / protoporphyrin IX / iron transport
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesSphingomonas sp. A1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsOkumura, K. / Takase, R. / Mikami, B. / Murata, K. / Hashimoto, W.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science Japan
CitationJournal: To Be Published
Title: Rare metal binding by a cell-surface component of bacterial EfeUOB iron importer
Authors: Okumura, K. / Takase, R. / Mikami, B. / Murata, K. / Hashimoto, W.
History
DepositionJan 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxidase EfeB
B: Peroxidase EfeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,45438
Polymers96,6872
Non-polymers3,76836
Water4,630257
1
A: Peroxidase EfeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,17920
Polymers48,3431
Non-polymers1,83619
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint6 kcal/mol
Surface area19690 Å2
MethodPISA
2
B: Peroxidase EfeB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,27518
Polymers48,3431
Non-polymers1,93217
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint8 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.020, 104.990, 83.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Peroxidase EfeB


Mass: 48343.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. A1 (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 293 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.28 Å3/Da / Density % sol: 45.95 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 15% PEG 400, 100 mM Sodium acetate (pH 4.6), 100 mM Calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 39361 / % possible obs: 98.6 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.0577 / Net I/σ(I): 14.1
Reflection shellResolution: 2.3005→2.358 Å / Rmerge(I) obs: 0.1587 / Num. unique obs: 3588 / CC1/2: 0.202

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O72

3o72


Resolution: 2.3→44.489 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.53
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2975 1967 5 %
Rwork0.234 --
obs0.2371 39361 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→44.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6001 0 251 260 6512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086388
X-RAY DIFFRACTIONf_angle_d0.9718649
X-RAY DIFFRACTIONf_dihedral_angle_d19.0013829
X-RAY DIFFRACTIONf_chiral_restr0.057925
X-RAY DIFFRACTIONf_plane_restr0.0071148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3005-2.3580.35961370.24782619X-RAY DIFFRACTION98
2.358-2.42170.33051370.23722619X-RAY DIFFRACTION99
2.4217-2.4930.35311400.23632649X-RAY DIFFRACTION99
2.493-2.57340.30661390.22952634X-RAY DIFFRACTION99
2.5734-2.66540.33331400.24752634X-RAY DIFFRACTION99
2.6654-2.77210.32851400.25542646X-RAY DIFFRACTION98
2.7721-2.89830.36491390.24932655X-RAY DIFFRACTION99
2.8983-3.0510.39741390.25452648X-RAY DIFFRACTION99
3.051-3.24210.35511390.24122653X-RAY DIFFRACTION99
3.2421-3.49240.29741410.22782669X-RAY DIFFRACTION99
3.4924-3.84360.25221400.21952672X-RAY DIFFRACTION99
3.8436-4.39940.23771410.21252695X-RAY DIFFRACTION99
4.3994-5.54110.26761450.21822751X-RAY DIFFRACTION100
5.5411-44.49680.27241500.25562850X-RAY DIFFRACTION99

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