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- PDB-3o72: Crystal structure of EfeB in complex with heme -

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Basic information

Entry
Database: PDB / ID: 3o72
TitleCrystal structure of EfeB in complex with heme
ComponentsRedox component of a tripartite ferrous iron transporter
KeywordsHEME-BINDING PROTEIN / EfeB in complex with heme / Heme deferrochelatase / Heme binding
Function / homology
Function and homology information


protoporphyrin ferrochelatase / iron import into cell / ferrochelatase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / periplasmic space / hydrolase activity / heme binding / metal ion binding
Similarity search - Function
Deferrochelatase / : / : / Dyp-type peroxidase, C-terminal / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel / Epoxide hydrolase-like / alpha/beta hydrolase fold ...Deferrochelatase / : / : / Dyp-type peroxidase, C-terminal / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Putative hydrolase / Deferrochelatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsLiu, X. / Du, Q. / Wang, Z. / Zhu, D. / Huang, Y. / Li, N. / Xu, S. / Gu, L.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal structure and biochemical features of EfeB/YcdB from Escherichia coli O157: ASP235 plays divergent roles in different enzyme-catalyzed processes
Authors: Liu, X. / Du, Q. / Wang, Z. / Zhu, D. / Huang, Y. / Li, N. / Wei, T. / Xu, S. / Gu, L.
History
DepositionJul 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Redox component of a tripartite ferrous iron transporter
B: Redox component of a tripartite ferrous iron transporter
C: Redox component of a tripartite ferrous iron transporter
D: Redox component of a tripartite ferrous iron transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,24212
Polymers177,6484
Non-polymers2,5948
Water20,8611158
1
A: Redox component of a tripartite ferrous iron transporter
B: Redox component of a tripartite ferrous iron transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1216
Polymers88,8242
Non-polymers1,2974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-21 kcal/mol
Surface area30210 Å2
MethodPISA
2
C: Redox component of a tripartite ferrous iron transporter
D: Redox component of a tripartite ferrous iron transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1216
Polymers88,8242
Non-polymers1,2974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-17 kcal/mol
Surface area30280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.640, 155.568, 97.374
Angle α, β, γ (deg.)90.00, 94.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Redox component of a tripartite ferrous iron transporter / EfeB


Mass: 44411.957 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 strain TW1435 / Gene: efeB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C6UPP3, UniProt: Q8XAS4*PLUS
#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-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1158 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 20% PEG 3350, 0.2M ammonium chloride, pH 8.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 104514 / Num. obs: 104514 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 20.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.95-2.025.20.4483.699930.44892.4
4.2-507.50.05837.9109870.05899.9

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Processing

Software
NameVersionClassification
MAR345Dtbdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→50 Å / SU ML: 0.23 / σ(F): 0.05 / σ(I): 0.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 1929 1.91 %RANDOM
Rwork0.1703 ---
all0.171 100818 --
obs0.171 100818 92.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.271 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.7286 Å20 Å2-2.516 Å2
2--2.876 Å20 Å2
3----1.1474 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11732 0 180 1158 13070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812228
X-RAY DIFFRACTIONf_angle_d1.10616623
X-RAY DIFFRACTIONf_dihedral_angle_d18.4244493
X-RAY DIFFRACTIONf_chiral_restr0.0761772
X-RAY DIFFRACTIONf_plane_restr0.0052183
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9502-1.9990.26521140.2053613681
1.999-2.0530.22291330.19647385
2.053-2.11340.24171290.1834664686
2.1134-2.18160.25131330.1903665188
2.1816-2.25960.23741310.1803669188
2.2596-2.35010.2211420.1821683590
2.3501-2.4570.24411290.1865699092
2.457-2.58650.25711370.1861719994
2.5865-2.74850.21761400.1817730996
2.7485-2.96070.22751390.1792747998
2.9607-3.25860.20971510.1737752899
3.2586-3.72980.19451510.15487599100
3.7298-4.69820.14881480.14087655100
4.6982-500.17931520.16157698100

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