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- PDB-5y8b: Periplasmic heme-binding protein RhuT from Roseiflexus sp. RS-1 i... -

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Basic information

Entry
Database: PDB / ID: 5y8b
TitlePeriplasmic heme-binding protein RhuT from Roseiflexus sp. RS-1 in apo form
ComponentsPeriplasmic binding protein
KeywordsTRANSPORT PROTEIN / metal transport
Function / homologyABC 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 / Periplasmic binding protein
Function and homology information
Biological speciesRoseiflexus sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
Model detailsPeriplasmic heme-binding protein RhuT in ABC heme transporter system
AuthorsRahman, M.M. / Naoe, Y. / Nakamura, N. / Doi, A. / Shiro, Y. / Sugimoto, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP23121531 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP25121739 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP15H01655 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
DepositionAug 20, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 11, 2017ID: 5GJ2
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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)28,2953
Polymers28,2461
Non-polymers492
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-9 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.039, 71.039, 78.206
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Periplasmic binding protein


Mass: 28246.318 Da / Num. of mol.: 1 / Fragment: heme binding protein, UNp residues 96-360
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseiflexus sp. (strain 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.02 Å3/Da / Density % sol: 39.01 % / Mosaicity: 0.587 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 9% PEG 400, 0.2 M MgCl2, 50 mM glycine

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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: Jun 19, 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: 2.4→50.01 Å / Num. obs: 9202 / % possible obs: 99.3 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.028 / Rrim(I) all: 0.102 / Χ2: 0.956 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4470.5014500.8970.1930.540.9494.5
2.44-2.498.90.4854250.8660.1690.5150.91699.1
2.49-2.5310.10.4254570.9330.1380.4470.92298.3
2.53-2.5911.60.3864340.9570.1170.4040.901100
2.59-2.6412.60.3634710.9660.1050.3780.95398.9
2.64-2.713.20.3464500.9750.0980.360.96898.9
2.7-2.7713.50.2884400.9840.080.2990.902100
2.77-2.8513.70.2594710.9850.0720.2690.92599.4
2.85-2.9313.60.2294410.9880.0640.2380.91799.3
2.93-3.0213.70.1864480.9910.0510.1930.94999.3
3.02-3.1313.70.174560.9930.0470.1760.99999.6
3.13-3.2613.60.1354640.9950.0370.140.94499.6
3.26-3.4113.60.1144660.9970.0320.1190.99699.8
3.41-3.5813.50.0874470.9980.0240.091.03599.8
3.58-3.8113.60.0744650.9980.0210.0771.0799.8
3.81-4.113.30.064670.9990.0170.0630.98599.8
4.1-4.5213.50.054710.9990.0140.0521.0199.6
4.52-5.1713.20.0494720.9990.0140.0510.995100
5.17-6.51130.0524860.9990.0150.0540.944100
6.51-50120.0325210.9990.0090.0340.79199.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GJ3

5gj3


Resolution: 2.4→50.01 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.494 / SU ML: 0.199 / SU R Cruickshank DPI: 0.7782 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.778 / ESU R Free: 0.291
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2463 447 4.9 %RANDOM
Rwork0.1797 ---
obs0.1831 8719 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.44 Å2 / Biso mean: 36.042 Å2 / Biso min: 5.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å2-0 Å2
2---0.09 Å20 Å2
3---0.3 Å2
Refinement stepCycle: final / Resolution: 2.4→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 2 77 2018
Biso mean--44.77 38.75 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191969
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.9972683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3645262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.90724.10378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79515314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5881517
X-RAY DIFFRACTIONr_chiral_restr0.0840.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211486
LS refinement shellResolution: 2.404→2.466 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 35 -
Rwork0.229 591 -
all-626 -
obs--92.06 %

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