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- PDB-5y89: Periplasmic heme-binding protein BhuT in complex with one heme (h... -

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Basic information

Entry
Database: PDB / ID: 5y89
TitlePeriplasmic heme-binding protein BhuT in complex with one heme (holo-1)
ComponentsPutative hemin transport system, substrate-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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Hemin transport system, substrate-binding protein
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
Model detailsPeriplasmic heme-binding protein BhuT in ABC heme transporter system
AuthorsNaoe, Y. / Nakamura, N. / Rahman, M.M. / Shiro, Y. / Sugimoto, H.
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: 5GJ0
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 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative hemin transport system, substrate-binding protein
B: Putative hemin transport system, substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6719
Polymers56,0322
Non-polymers1,6397
Water3,171176
1
A: Putative hemin transport system, substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7884
Polymers28,0161
Non-polymers7723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative hemin transport system, substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8845
Polymers28,0161
Non-polymers8684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)199.166, 199.166, 117.736
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-532-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 39 - 305 / Label seq-ID: 5 - 271

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Putative hemin transport system, substrate-binding protein


Mass: 28016.029 Da / Num. of mol.: 2 / Fragment: heme binding protein, UNP residues 40-305
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610) (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: hmuT, BCAM2628 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: B4EKB3
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 6.02 Å3/Da / Density % sol: 79.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: 2.0M Ammonium Sulfate, 0.1M Sodium Acetate

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B111
SYNCHROTRONSPring-8 BL26B121.7375
Detector
TypeIDDetectorDateDetails
RAYONIX MX-2251CCDJul 12, 2012mirrors
RAYONIX MX-2252CCDJul 12, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.73751
ReflectionResolution: 2.4→50 Å / Num. obs: 53708 / % possible obs: 99.6 % / Redundancy: 22.1 % / Rmerge(I) obs: 0.101 / Χ2: 0.954 / Net I/σ(I): 7.3 / Num. measured all: 1184361
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.4-2.49210.8652860.974199.4
2.49-2.5921.70.66952300.966199.1
2.59-2.722.20.48952680.965199.3
2.7-2.8522.50.35553100.959199.5
2.85-3.0222.60.25453080.95199.4
3.02-3.2622.60.14953410.95199.7
3.26-3.5822.50.10253530.982199.6
3.58-4.122.40.07753940.932199.8
4.1-5.1722.10.0554720.861199.9
5.17-5021.10.0357461199.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
SHELXCDphasing
BUCCANEERmodel building
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.046 / SU ML: 0.11 / SU R Cruickshank DPI: 0.1744 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.156
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 2706 5 %RANDOM
Rwork0.2003 ---
obs0.2014 50964 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 149.51 Å2 / Biso mean: 52.459 Å2 / Biso min: 22.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0.2 Å2-0 Å2
2---0.41 Å2-0 Å2
3---1.32 Å2
Refinement stepCycle: final / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3902 0 195 176 4273
Biso mean--41.3 41.81 -
Num. residues----534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0194197
X-RAY DIFFRACTIONr_bond_other_d0.0090.024072
X-RAY DIFFRACTIONr_angle_refined_deg1.8062.0375775
X-RAY DIFFRACTIONr_angle_other_deg1.59739251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5085534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.93421.484155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09815593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1841547
X-RAY DIFFRACTIONr_chiral_restr0.1380.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0234864
X-RAY DIFFRACTIONr_gen_planes_other0.0210.023987
Refine LS restraints NCS

Ens-ID: 1 / Number: 29970 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.402→2.464 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 198 -
Rwork0.23 3671 -
all-3869 -
obs--98.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9894-0.58780.33511.20170.29511.23180.12550.33390.6488-0.3655-0.2748-0.2444-0.33070.02730.14940.21210.15510.07180.25990.17880.203665.2524111.05443.6918
20.5655-0.1864-0.33330.52120.39661.25540.0676-0.11120.01610.06550.0981-0.07310.18430.1983-0.16570.11140.0636-0.04790.1251-0.03330.029721.9494113.369919.9835
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1((chain 'A' and resid 39 through 305) or (chain 'A' and resid 401 through 403))A39 - 403
2X-RAY DIFFRACTION2((chain 'B' and resid 39 through 305) or (chain 'B' and resid 401 through 403))B39 - 403

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