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- PDB-6a2j: Crystal structure of heme A synthase from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 6a2j
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 / MIRAS / Resolution: 2.2 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
DepositionJun 12, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heme A synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,92227
Polymers34,4661
Non-polymers8,45626
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-32 kcal/mol
Surface area16330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.465, 90.465, 147.309
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 58 molecules

#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.: 3 / 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.: 21 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.37 Å3/Da / Density % sol: 63.46 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7
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

Diffraction
IDMean temperature (K)Ambient temp detailsCrystal-ID
115cooled by He cryo-stream coolers1
240cooled by He cryo-stream coolers1
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONSPring-8 BL44XU21
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELDec 5, 2017
RAYONIX MX300HE2CCDJul 21, 2017
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rotated-inclined double-crystal monochromator , Si (111)SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.2→29.031 Å / Num. obs: 22834 / % possible obs: 99.9 % / Redundancy: 5.242 % / Biso Wilson estimate: 52.75 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.14 / Χ2: 0.975 / Net I/σ(I): 8.02
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.325.0921.231.233850.4941.37299.7
2.32-2.465.3440.8361.8531220.6680.928100
2.46-2.635.2130.5462.8629610.8410.607100
2.63-2.845.1170.3764.2127600.9050.42100
2.84-3.115.3470.2536.3225400.9560.281100
3.11-3.485.2210.159.923050.9860.16799.9
3.48-4.025.3320.0915.7420140.9940.199.9
4.02-4.925.3150.06321.116960.9960.07100
4.92-6.965.3130.06220.6313310.9980.069100
6.96-29.0315.2440.04826.887200.9970.05399.6

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Phasing

PhasingMethod: MIRAS
Phasing MIRResolution: 4.2→20 Å / FOM: 0.63 / Reflection: 3300
Phasing MIR shell
Resolution (Å)FOMReflection
12.67-200.7188
8.83-12.670.7282
7.16-8.830.7352
6.17-7.160.7408
5.5-6.170.67449
5.01-5.50.61490
4.63-5.010.57531
4.33-4.630.55600

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
SOLVE2.13phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MIRAS / Resolution: 2.2→29.031 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 26.88
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 1150 5.04 %0
Rwork0.2064 ---
obs0.2076 22824 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 152.29 Å2 / Biso mean: 58.5128 Å2 / Biso min: 32.2 Å2
Refinement stepCycle: final / Resolution: 2.2→29.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 411 32 2874
Biso mean--78.41 49.9 -
Num. residues----309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172893
X-RAY DIFFRACTIONf_angle_d2.013837
X-RAY DIFFRACTIONf_chiral_restr0.124415
X-RAY DIFFRACTIONf_plane_restr0.007445
X-RAY DIFFRACTIONf_dihedral_angle_d14.7081188
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.30010.39411460.327827002846
2.3001-2.42130.31081390.278527132852
2.4213-2.57290.29381570.239727132870
2.5729-2.77150.22991360.220227022838
2.7715-3.05010.25661170.208727252842
3.0501-3.49080.25011540.197427162870
3.4908-4.39560.20681470.187826922839
4.3956-29.03340.19831540.196527132867

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