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- PDB-5giz: Periplasmic heme-binding protein BhuT in apo form -

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Basic information

Entry
Database: PDB / ID: 5giz
TitlePeriplasmic heme-binding protein BhuT in apo 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
Hemin transport system, substrate-binding protein
Similarity search - Component
Biological speciesBurkholderia cenocepacia J2315 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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, 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 1.2Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)56,3917
Polymers56,0322
Non-polymers3595
Water12,232679
1
A: Putative hemin transport system, substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2444
Polymers28,0161
Non-polymers2283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12390 Å2
MethodPISA
2
B: Putative hemin transport system, substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1483
Polymers28,0161
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-12 kcal/mol
Surface area12450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.983, 46.443, 222.292
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein Putative hemin transport system, substrate-binding protein / periplasmic heme-binding protein BhuT


Mass: 28016.029 Da / Num. of mol.: 2 / Fragment: heme binding domain, UNP residues 40-305
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia J2315 (bacteria)
Strain: J2315 / Gene: hmuT / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: B4EKB3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 679 / 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: 2.12 Å3/Da / Density % sol: 41.93 % / Mosaicity: 0.262 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5 / Details: 28% PEG 3350, 0.1 M TrisHCl, 0.2 M NaSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 26, 2013 / 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: 1.5→50 Å / Num. obs: 77435 / % possible obs: 99.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.062 / Χ2: 1.034 / Net I/av σ(I): 25.891 / Net I/σ(I): 10.2 / Num. measured all: 432781
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.5-1.555.30.613198.6
1.55-1.625.90.467199.8
1.62-1.695.90.346199.9
1.69-1.785.80.259199.7
1.78-1.895.70.17199.8
1.89-2.045.60.107199.7
2.04-2.245.50.08199.7
2.24-2.565.30.084199.9
2.56-3.235.30.0511100
3.23-505.60.026199.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.2data extraction
Cootmodel building
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GJ1

5gj1
PDB Unreleased entry


Resolution: 1.5→35.45 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.744 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.082
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.212 3914 5.1 %RANDOM
Rwork0.1737 ---
obs0.1757 73463 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.14 Å2 / Biso mean: 19.884 Å2 / Biso min: 8.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å2-0 Å20 Å2
2--0.09 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: final / Resolution: 1.5→35.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3929 0 17 679 4625
Biso mean--28.75 27.88 -
Num. residues----539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194150
X-RAY DIFFRACTIONr_bond_other_d0.0010.024126
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9815686
X-RAY DIFFRACTIONr_angle_other_deg0.83439418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4535575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10321.333165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87315628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3191552
X-RAY DIFFRACTIONr_chiral_restr0.0960.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214829
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02959
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 264 -
Rwork0.263 5274 -
all-5538 -
obs--98.07 %
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)
11.65360.97941.02560.58130.60940.63940.00580.1727-0.14830.01290.1009-0.09610.01830.1058-0.10680.12680.018-0.0420.0378-0.01520.0715-10.182418.757610.4572
20.60380.20080.12960.98480.1120.03880.0258-0.02330.01470.0376-0.02870.0228-0.0107-0.01140.00290.08470.0031-0.0280.0291-0.00050.0562-17.285422.552915.448
30.858-0.40330.2690.5461-0.28010.17920.20040.0455-0.1821-0.112-0.07980.11250.12440.0368-0.12060.16410.0115-0.10790.0115-0.02150.1008-11.167811.013216.8441
40.2717-0.5345-0.66021.08441.493.27070.026-0.05990.0683-0.00120.1357-0.15890.17870.1822-0.16170.05260.0121-0.02580.0457-0.02050.08247.568516.908333.6574
51.3045-0.153-0.24410.49260.44750.84560.0162-0.0832-0.0169-0.0191-0.05520.06630.1127-0.08090.03890.059-0.0208-0.02210.0428-0.00070.0771-11.359616.446843.1877
60.0420.00210.13150.25220.19490.71180.029-0.0347-0.02-0.04060.017-0.0069-0.0212-0.0928-0.0460.0733-0.0033-0.01350.0670.00250.0534-5.6326.183441.6179
70.9953-0.1092-0.3180.43680.27010.24840.07060.11510.0098-0.0326-0.0013-0.0553-0.0303-0.0523-0.06930.0860.00720.00660.06460.03520.08312.266135.364610.6457
821.3014-10.1059-1.74624.80430.83460.14840.00490.4894-1.91180.0586-0.19450.91780.0177-0.02720.18950.65330.0526-0.07580.1197-0.02970.26635.838729.84413.9973
91.8544-0.451-0.07060.38320.32520.61040.00920.0202-0.20740.06010.03190.0724-0.03240.0356-0.04120.08040.01580.00250.008-0.00680.084813.505830.502914.5726
101.7782-0.40050.12470.5894-0.0660.57290.05370.07930.0960.0616-0.0038-0.08160.0047-0.0015-0.04980.08070.00730.00490.007-0.00710.062123.223636.168812.7912
111.0248-0.4394-0.27020.2527-0.00180.4650.10830.10150.1381-0.0888-0.0686-0.0544-0.031-0.0682-0.03970.09480.03260.00140.06370.02460.05498.656844.176810.9789
120.2752-0.09430.29860.4276-0.38340.9945-0.0679-0.01240.11920.0399-0.0851-0.04620.00170.05120.1530.04790.0016-0.01920.0321-0.00350.08777.055241.848238.1867
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 61
2X-RAY DIFFRACTION2A62 - 100
3X-RAY DIFFRACTION3A101 - 159
4X-RAY DIFFRACTION4A160 - 185
5X-RAY DIFFRACTION5A186 - 231
6X-RAY DIFFRACTION6A232 - 305
7X-RAY DIFFRACTION7B38 - 56
8X-RAY DIFFRACTION8B57 - 63
9X-RAY DIFFRACTION9B64 - 79
10X-RAY DIFFRACTION10B80 - 117
11X-RAY DIFFRACTION11B118 - 161
12X-RAY DIFFRACTION12B162 - 305

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