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- PDB-5gj3: Periplasmic heme-binding protein RhuT from Roseiflexus sp. RS-1 i... -

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Basic information

Entry
Database: PDB / ID: 5gj3
TitlePeriplasmic heme-binding protein RhuT from Roseiflexus sp. RS-1 in two-heme bound form (holo-2)
ComponentsPeriplasmic binding protein
KeywordsTRANSPORT PROTEIN / metal transport
Function / homology
Function and homology information


ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Periplasmic binding protein
Similarity search - Component
Biological speciesRoseiflexus sp. RS-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
Model detailsPeriplasmic heme-binding protein RhuT in ABC heme transporter system
AuthorsRahman, M.M. / Naoe, Y. / Nakamura, N. / Shiro, Y. / Sugimoto, H.
Funding support Japan, 4items
OrganizationGrant numberCountry
JSPSJP24770110 Japan
JSPSJP15H01655 Japan
JSPSJP25121739 Japan
JSPSJP23121531 Japan
CitationJournal: Proteins / Year: 2017
Title: Structural basis for binding and transfer of heme in bacterial heme-acquisition systems.
Authors: Naoe, Y. / Nakamura, N. / Rahman, M.M. / Tosha, T. / Nagatoishi, S. / Tsumoto, K. / Shiro, Y. / Sugimoto, H.
History
DepositionJun 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Nov 15, 2017Group: Database references / Polymer sequence / Category: citation / entity_poly
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity_poly.pdbx_target_identifier
Revision 2.1Nov 8, 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 / pdbx_struct_conn_angle / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7417
Polymers28,2461
Non-polymers1,4956
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-47 kcal/mol
Surface area12630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.326, 86.338, 118.806
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-405-

ZN

21A-406-

ZN

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Components

#1: Protein Periplasmic binding protein / periplasmic heme-binding protein RhuT


Mass: 28246.318 Da / Num. of mol.: 1 / Fragment: heme binding domain, UNP residues 96-360
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseiflexus sp. RS-1 (bacteria) / Strain: RS-1 / Gene: RoseRS_3565 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: A5UZ69
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3.06 Å3/Da / Density % sol: 59.75 % / Mosaicity: 0.796 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 5% PEG 8000, 0.1 M zinc acetate, and 50 mM MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jul 15, 2015 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 23911 / % possible obs: 99.8 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.114 / Net I/av σ(I): 14.679 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.037.10.544197.8
2.03-2.077.30.493199.4
2.07-2.117.60.442199.6
2.11-2.157.90.4071100
2.15-2.280.3491100
2.2-2.2580.3471100
2.25-2.318.10.3011100
2.31-2.378.10.2551100
2.37-2.448.10.241100
2.44-2.528.10.2251100
2.52-2.618.10.1951100
2.61-2.718.10.171100
2.71-2.848.10.1591100
2.84-2.998.20.1361100
2.99-3.178.10.1261100
3.17-3.428.10.1141100
3.42-3.768.10.0961100
3.76-4.318.10.0811100
4.31-5.4380.0671100
5.43-507.60.05199.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MD9

3md9


Resolution: 2→43.21 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.172 / SU ML: 0.091 / SU R Cruickshank DPI: 0.1635 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.15
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 1157 5.1 %RANDOM
Rwork0.1873 ---
obs0.1892 21312 94.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 71.6 Å2 / Biso mean: 26.41 Å2 / Biso min: 11.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å2-0 Å2
2---0.23 Å2-0 Å2
3----0.17 Å2
Refinement stepCycle: final / Resolution: 2→43.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1987 0 90 126 2203
Biso mean--25.57 34.43 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192126
X-RAY DIFFRACTIONr_angle_refined_deg1.8312.0612928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6515271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28223.92479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60915324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0681518
X-RAY DIFFRACTIONr_chiral_restr0.1450.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0221635
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 60 -
Rwork0.175 1141 -
all-1201 -
obs--69.5 %

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