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- PDB-6ied: Crystal structure of heme A synthase from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 6ied
TitleCrystal structure of heme A synthase from Bacillus subtilis
ComponentsHeme A synthase
KeywordsMEMBRANE PROTEIN / oxidoreductase / heam biosynthesis
Function / homology
Function and homology information


heme a synthase / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / heme A biosynthetic process / metal ion binding / plasma membrane
Similarity search - Function
Heme A synthase, type 1 / COX15/CtaA family / Cytochrome oxidase assembly protein
Similarity search - Domain/homology
COPPER (II) ION / PROTOPORPHYRIN IX CONTAINING FE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Heme A synthase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsNiwa, S. / Takeda, K. / Kosugi, M. / Tsutsumi, E. / Miki, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
Japan Society for the Promotion of Science15J02413 Japan
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Crystal structure of heme A synthase fromBacillus subtilis.
Authors: Niwa, S. / Takeda, K. / Kosugi, M. / Tsutsumi, E. / Mogi, T. / Miki, K.
History
DepositionSep 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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: Heme A synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0517
Polymers34,4661
Non-polymers1,5856
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-48 kcal/mol
Surface area15250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.528, 90.528, 147.230
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Heme A synthase / HAS / Cytochrome aa3-controlling protein


Mass: 34466.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: ctaA, BSU14870 / Production host: Escherichia coli (E. coli)
References: UniProt: P12946, Oxidoreductases; Acting on the CH-CH group of donors
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4

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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: 3.37 Å3/Da / Density % sol: 63.49 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 30% PEG 600, 0.1M sodium chloride, 0.1M lithium sulfate, 0.1M sodium HEPES pH 7.4

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Data collection

DiffractionMean temperature: 15 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.75 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.75 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 8987 / % possible obs: 100 % / Redundancy: 19.9 % / Rmerge(I) obs: 0.277 / Rpim(I) all: 0.064 / Rrim(I) all: 0.284 / Χ2: 0.458 / Net I/σ(I): 2 / Num. measured all: 178985
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.1119.71.138960.8240.261.160.421100
3.11-3.2318.70.9719020.8660.230.9990.422100
3.23-3.3820.80.7328980.930.1640.750.431100
3.38-3.5620.50.5768890.9630.1310.5910.433100
3.56-3.7820.30.4559060.9750.1030.4660.45599.8
3.78-4.0718.50.3049050.9870.0720.3120.462100
4.07-4.4819.60.2188960.9930.050.2240.494100
4.48-5.1320.40.1738950.9970.0390.1770.487100
5.13-6.4620.60.2048980.9950.0460.2090.462100
6.46-5020.10.07390210.0170.0750.507100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CNS1.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A2J

6a2j


Resolution: 3→20 Å / Cross valid method: FREE R-VALUE / σ(F): 129
RfactorNum. reflection% reflection
Rfree0.2447 454 5.1 %
Rwork0.233 --
obs-8826 98.4 %
Solvent computationBsol: 72.3398 Å2
Displacement parametersBiso max: 137.33 Å2 / Biso mean: 48.7383 Å2 / Biso min: 17.62 Å2
Baniso -1Baniso -2Baniso -3
1-7.774 Å20 Å20 Å2
2--7.774 Å20 Å2
3----15.548 Å2
Refinement stepCycle: final / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 91 0 2522
Biso mean--52.84 --
Num. residues----309
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it0.7591.5
X-RAY DIFFRACTIONc_mcangle_it0.832
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6hem.param
X-RAY DIFFRACTION7so4.param
X-RAY DIFFRACTION8olc.param

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