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- PDB-6jsd: Crystal structure of the domain-swapped dimer H434A variant of th... -

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Basic information

Entry
Database: PDB / ID: 6jsd
TitleCrystal structure of the domain-swapped dimer H434A variant of the C-terminal domain of HtaA from Corynebacterium glutamicum
ComponentsHypothetical membrane protein
KeywordsHEME-BINDING PROTEIN / heme / heme transport
Function / homologyHtaa / Htaa / metal ion binding / ISOPROPYL ALCOHOL / Hypothetical membrane protein
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.042 Å
AuthorsMuraki, N. / Aono, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17K15081 Japan
CitationJournal: Chem.Commun.(Camb.) / Year: 2019
Title: Structural basis for the heme transfer reaction in heme uptake machinery from Corynebacteria.
Authors: Muraki, N. / Kitatsuji, C. / Okamoto, Y. / Uchida, T. / Ishimori, K. / Aono, S.
History
DepositionApr 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Hypothetical membrane protein
B: Hypothetical membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3833
Polymers36,3232
Non-polymers601
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer (gel filtration)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-35 kcal/mol
Surface area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.900, 40.230, 87.020
Angle α, β, γ (deg.)90.00, 113.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hypothetical membrane protein


Mass: 18161.576 Da / Num. of mol.: 2 / Mutation: H434A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria)
Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: Cgl0388 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NTB9
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG3350, Tris-HCl pH8, 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 23, 2017
RadiationMonochromator: Si (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.04→40 Å / Num. obs: 21370 / % possible obs: 98.71 % / Redundancy: 3.7 % / Biso Wilson estimate: 41.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0529 / Rpim(I) all: 0.0321 / Rrim(I) all: 0.062 / Net I/σ(I): 15.06
Reflection shellResolution: 2.04→2.12 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.816 / Num. unique obs: 2022 / CC1/2: 0.602 / Rpim(I) all: 0.498 / Rrim(I) all: 0.959 / % possible all: 93.86

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JSA

6jsa


Resolution: 2.042→39.608 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 1067 5 %Random selection
Rwork0.2035 ---
obs0.2056 21341 98.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.042→39.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 0 4 11 2361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072400
X-RAY DIFFRACTIONf_angle_d0.7523262
X-RAY DIFFRACTIONf_dihedral_angle_d10.9551365
X-RAY DIFFRACTIONf_chiral_restr0.055366
X-RAY DIFFRACTIONf_plane_restr0.004439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0415-2.13440.36741250.32332366X-RAY DIFFRACTION94
2.1344-2.2470.32691350.28242552X-RAY DIFFRACTION100
2.247-2.38770.31721320.27982509X-RAY DIFFRACTION99
2.3877-2.5720.3241350.25562555X-RAY DIFFRACTION100
2.572-2.83080.30811330.23542557X-RAY DIFFRACTION100
2.8308-3.24030.26161340.21972550X-RAY DIFFRACTION100
3.2403-4.08180.22821370.17612585X-RAY DIFFRACTION99
4.0818-39.61560.19381360.16782600X-RAY DIFFRACTION98
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)
12.18291.7142-0.51234.5568-0.2131.2781-0.1136-0.4278-0.1422-0.33980.0906-0.0065-0.0749-0.251-0.02380.3874-0.0105-0.03650.45430.13550.3603-33.0858-16.775523.7113
22.41281.0864-1.28531.5351-0.72575.3425-0.0750.28620.0904-0.1981-0.0847-0.17680.19930.53470.14680.29280.01850.02810.33780.08750.3483-14.912812.21576.9022
32.9410.3238-0.16671.2077-1.38844.3862-0.0037-0.0803-0.2377-0.40620.0034-0.02520.53980.455-0.04340.38840.0371-0.00050.32830.04230.3881-11.16156.79053.2912
43.14410.7419-0.91493.4303-0.43612.7738-0.289-0.2337-0.7459-0.01260.38010.2090.95670.3724-0.03340.61920.13550.09030.42050.03930.5398-13.26892.84324.3628
51.59371.5894-1.14626.1938-4.17914.1007-0.05160.03860.07770.0726-0.00090.14180.03620.12490.00750.4336-0.02320.01390.42440.03420.4302-19.19195.51137.0647
65.1329-1.00710.14792.6474-0.08673.6043-0.0582-0.3537-0.0877-0.10710.19440.2037-0.0961-0.4986-0.15630.35710.0141-0.00320.35940.10110.2849-30.7549-22.729725.5035
75.4270.49963.18463.0923-1.39314.0984-0.8085-0.34480.63980.20940.51020.4597-0.8163-0.42850.25860.4780.1346-0.04630.53270.0240.3577-34.0759-16.535431.8095
82.78512.7013-0.43868.2877-2.18391.3352-0.0613-0.4566-0.1006-0.28240.0844-0.0379-0.1204-0.1957-0.02480.4338-0.0161-0.05260.50980.13140.5299-35.662-8.78520.718
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 364 through 389)
2X-RAY DIFFRACTION2chain 'A' and (resid 390 through 452)
3X-RAY DIFFRACTION3chain 'A' and (resid 453 through 500 )
4X-RAY DIFFRACTION4chain 'A' and (resid 501 through 528)
5X-RAY DIFFRACTION5chain 'B' and (resid 364 through 389)
6X-RAY DIFFRACTION6chain 'B' and (resid 390 through 452 )
7X-RAY DIFFRACTION7chain 'B' and (resid 453 through 500 )
8X-RAY DIFFRACTION8chain 'B' and (resid 501 through 528 )

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