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- PDB-5y8a: Periplasmic heme-binding protein BhuT in complex with two hemes (... -

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Basic information

Entry
Database: PDB / ID: 5y8a
TitlePeriplasmic heme-binding protein BhuT in complex with two hemes (holo-2 form)
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
PROTOPORPHYRIN IX CONTAINING FE / Hemin transport system, substrate-binding protein
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
Model detailsPeriplasmic heme-binding protein BhuT in ABC heme transporter system
AuthorsNakamura, N. / Naoe, Y. / Rahman, M.M. / 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: 5GJ1
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_asym_id / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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_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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)58,5387
Polymers56,0322
Non-polymers2,5065
Water4,810267
1
A: Putative hemin transport system, substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2493
Polymers28,0161
Non-polymers1,2332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-28 kcal/mol
Surface area12090 Å2
MethodPISA
2
B: Putative hemin transport system, substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2894
Polymers28,0161
Non-polymers1,2733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-30 kcal/mol
Surface area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.088, 45.553, 113.002
Angle α, β, γ (deg.)90.000, 100.350, 90.000
Int Tables number3
Space group name H-MP121

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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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.08 Å3/Da / Density % sol: 40.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 2% PEG 3350, 0.2 M calcium acetate, and 0.1 M MES pH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 11, 2012 / 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: 31283 / % possible obs: 99.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 24.25 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.044 / Rrim(I) all: 0.092 / Χ2: 0.894 / Net I/σ(I): 8.4 / Num. measured all: 129249
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.90.43814840.8220.2430.5030.85798.7
2.03-2.073.90.37115510.8710.2060.4260.86198.2
2.07-2.113.90.32415320.8840.180.3710.998.2
2.11-2.153.90.27515440.9170.1530.3160.86498.8
2.15-2.240.22915170.9430.1270.2620.89398.7
2.2-2.2540.22215720.9420.1230.2550.88599.5
2.25-2.3140.19315650.9530.1070.2210.89399.3
2.31-2.374.10.16715370.9660.0920.1910.8799.9
2.37-2.444.10.15115630.9720.0830.1730.87499.9
2.44-2.524.20.12715490.980.070.1450.853100
2.52-2.614.20.10915700.9840.060.1250.855100
2.61-2.714.20.09315830.9870.0510.1060.853100
2.71-2.844.30.08215610.9890.0450.0940.849100
2.84-2.994.30.07415620.990.040.0850.825100
2.99-3.174.30.06815710.9930.0370.0780.97100
3.17-3.424.30.06915920.9920.0380.0781.354100
3.42-3.764.30.08115820.9880.0450.0930.866100
3.76-4.314.30.07115930.9910.0390.0810.856100
4.31-5.434.30.03515920.9970.0190.040.934100
5.43-504.10.02616630.9980.0150.030.74499.8

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Processing

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

5gj3


Resolution: 2.001→23.724 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1580 5.06 %RANDOM
Rwork0.2009 29659 --
obs0.2039 31239 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.15 Å2 / Biso mean: 31.9883 Å2 / Biso min: 8.22 Å2
Refinement stepCycle: final / Resolution: 2.001→23.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3910 0 173 267 4350
Biso mean--45.49 33.21 -
Num. residues----536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094447
X-RAY DIFFRACTIONf_angle_d1.2456140
X-RAY DIFFRACTIONf_chiral_restr0.054683
X-RAY DIFFRACTIONf_plane_restr0.006804
X-RAY DIFFRACTIONf_dihedral_angle_d13.722618
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0014-2.06590.30931300.22742554268496
2.0659-2.13970.29121340.21992663279798
2.1397-2.22530.31531490.21312660280999
2.2253-2.32650.2451340.20942697283199
2.3265-2.44910.31071580.206526682826100
2.4491-2.60230.25091440.205426972841100
2.6023-2.8030.27621390.213327212860100
2.803-3.08450.26711290.217127522881100
3.0845-3.52960.27281410.208627222863100
3.5296-4.44210.22351550.170427152870100
4.4421-23.72590.23991670.191728102977100
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)
11.9061-1.6462-0.54862.67340.2610.4251-0.2431-0.2169-0.04530.67650.33870.0961-0.055-0.00650.24110.2720.0796-0.00930.13050.02010.1384-1.345828.918644.6259
21.3415-0.232-0.28781.9210.3320.6035-0.3987-0.83171.03750.66440.1762-0.0958-0.5380.3130.70170.1145-0.0347-0.0246-0.291-0.00340.2767-8.646947.652938.0444
32.96990.4696-2.28811.813-0.61092.3572-0.37110.6145-0.301-0.29250.15610.10710.4616-0.3211-0.15120.1621-0.0537-0.01630.2513-0.06020.0854-6.125936.158816.3753
42.3774-0.2833-0.84412.19140.8131.2477-0.0523-0.13060.13530.11240.06350.0359-0.10920.03080.00310.1470.0233-0.00870.1089-0.0260.155316.971116.500141.0012
51.0492-0.5659-0.46610.9742-0.33880.73190.1082-0.3167-0.69210.31970.0021-0.18960.08930.3601-0.28280.05380.07580.0222-0.0049-0.05050.278420.9031-2.68831.5006
63.030.88531.24551.5760.99981.718-0.37430.78170.2912-0.49750.142-0.0143-0.63180.2571-0.17830.2652-0.0679-0.01630.31760.04560.077811.64949.38413.2343
70.05810.09170.00110.70840.13250.05370.10970.19980.2025-0.84670.0681-0.07871.1370.3852-0.01380.65950.02710.01660.5109-0.06950.2944-4.479825.297627.7669
83.0331-1.2686-1.34281.33460.58330.5918-0.7529-0.0475-0.9569-0.39760.03161.0128-0.438-0.8514-0.09630.47020.0072-0.01790.45580.02330.368213.745919.898624.5215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 38 through 133)A38 - 133
2X-RAY DIFFRACTION2(chain 'A' and resid 134 through 180)A134 - 180
3X-RAY DIFFRACTION3(chain 'A' and resid 181 through 305)A181 - 305
4X-RAY DIFFRACTION4(chain 'B' and resid 38 through 133)B38 - 133
5X-RAY DIFFRACTION5(chain 'B' and resid 134 through 180)B134 - 180
6X-RAY DIFFRACTION6(chain 'B' and resid 181 through 305)B181 - 305
7X-RAY DIFFRACTION7(chain 'A' and resid 401 through 402)A401 - 402
8X-RAY DIFFRACTION8(chain 'B' and resid 401 through 402)B401 - 402

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